http://2008.igem.org/wiki/index.php?title=Special:Contributions/Nickvd&feed=atom&limit=50&target=Nickvd&year=&month=2008.igem.org - User contributions [en]2024-03-28T15:04:24ZFrom 2008.igem.orgMediaWiki 1.16.5http://2008.igem.org/Team:KULeuven/EvaluationTeam:KULeuven/Evaluation2008-10-16T16:16:15Z<p>Nickvd: /* Nick */</p>
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UNDER CONSTRUCTION<br />
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<br />
== Our road towards the golden dream ... ==<br />
<br />
At the end of a project people often tend to look only at the results. But the road towards these results is as important, especially if other students will discover the same path next year. Therefore we want to reflect on our obtained results and the path towards them.<br />
<br />
During the summer period we divided our team into two major parts: a lab team and a modelling team. The work in the dry lab resulted in an extensive model of our full system. Building the main model backbone was finished during the first six - seven weeks. During these weeks the model was gradually built and updated several times. A lot of time and effort was put into searching the literature for biologically relevant values of all parameters. There were a few parameters where we couldn't find any values, in those cases we had to make an educted guess. We made sure that even in those cases there are references to papers and sources that allowed us to make these estimates. <br />
Every subsystem was extensively tested and simulated before we connected them to each other. This was very tricky because every part had to be in tune with the others and tinkering with one part often messed up our entire system. Hereafter we further investigated the diffusion of HSL into the medium and the effect of multiple cells on the behaviour of one single cell. This resulted in one of our own written software tools: a multi-cell toolbox. During the entire summer, our modelling team have made a beautiful wiki on which our progress and results could be consulted at any time: we've been working as "open source" as possible.<br />
<br />
While the modelling team was busy building and simulating our Dr. Coli, the lab team was tried to connect the different BioBricks. Unfortunately, our lab team was very often withheld from a fast progress:<br />
* punching the bricks: ...<br />
* adjustments by the modelling team to the DNA sequence of different subsystems: While the modelling team was building the model, they often saw by simulations a malfunctional subsystem. This resulted in many changes of the DNA sequences of the different subsystems. A good example is the memory. Our first memory would probably have switched automatically from state zero to state one, which basically makes it completely useless. This resulted in a totaly new memory system. <br />
Many ribosome binding sites were upregulated or downregulated. All these changes made many ligations useless and a lot of work had to be redone. This was the main reason the lab team couldn't keep up with the modelling team. But we did not have many other choices, but to carry on with the work, because we had a very ambitious project and only 3 months time... As an advice for the team of next year, we recommend to start modelling as soon as possible so that changes to the system don't lead to too much useless work.<br />
* ...<br />
Despite these obstacles, the lab team could finish different parts which resulted in some great biobricks.<br />
<br />
TODO: hier nog iets zeggen over de behaalde resultaten in het labo<br />
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When it comes to the iGEM judging criteria, we believe we have fulfilled many different requirements like submitting the DNA sequence of a new biobrick: GFP with a LVA-tag. Furthermore this biobrick works fine and has an experimentally proven faster degradation rate than GFP without the LVA-tag. Based on these experiments we could even characterize the biobrick by determing its degradation constant. Besides these lab criteria we also made an effort to make a contribution to the world on Ethics and Human Practices in synthetic biology by outlining and detailling an issue about these two subjects related to our project. Our approach is based on the Three Laws of Robotics formulated by Isaac Asimov halfway the twenthieth century. We were also proud to see some of our wiki-tools show up on other team's wikis. Based on all these facts, we started dreaming of a golden medal...<br />
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TODO: nog iets over grand prizes?<br />
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== Personal Evaluation ==<br />
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=== Students ===<br />
<br />
==== Maarten ====<br />
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<blockquote>A once in a life time opportunity broadening my view in different aspects</blockquote><br />
<br />
As a civil engineer, I started this project without a precise view on the work I was expected to do. It was a step in the dark. At the end, I can say that this once in a life time oppurtinity, has broadened my view in many aspects:<br />
* Till now I've only modelled based on the "black box system"-principle. This was the first time in my student carreer that I helped building a white box model based on biological laws.<br />
* This project was a nice introduction into the world of synthetic biology which was unknown to me.<br />
* Working in a team with people form very different backgrounds is very representative to the real world. This experience will certaintly help me in my future working career.<br />
As you can see, I'm glad I joined the project.<br />
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==== Nathalie ====<br />
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==== Jonas ====<br />
As a more modeling-aimed biochemist I've had the privilege of finding myself as some sort of ''corpus callosum'' ;) between the lab hemisphere on one hand and the modeling hemisphere on the other. This allowed me to fully enjoy and assist in the fantastic things that happened on both sides of the brain/team. Communicating between fields and keeping both teams on the same track was truly a very fulfilling experience.<br />
<br />
I also liked the many brainstorming sessions we had and spent a lot of my exam-time on the wiki brainstorm section. Creating genetic circuits with the desired properties by puzzling with genetic bricks allowed me to, fully and in an extremely creative manner, employ the things that I had learned during my education. It felt great to put this knowledge into practice.<br />
<br />
The thing that I will carry with me the longest however was the experience of working in our multidisciplinary team. 11 incredible people with completely different backgrounds combined and, as we say here, 'all with their noses pointed in the same direction'; creating one hell of a project.<br />
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==== Andim ====<br />
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==== Jan ====<br />
Earlier this year I got to know of "synthetic biology". The concept of building up your own biological system from basic biobricks immediately appealed to me. Also the idea to be part of the foundation of a relatively new discipline, that has gotten a burst of growth and attention the last years, seemed very exciting to me. Working at this with people with different skills would only contribute to a great project.<br />
<br />
As I'm a bio-enigineer, I was mainly occupied in the wetlab. In the beginning we had some failures to work through though. But we learned by experience and advice from our advisors and later on we circumvented or solved our earlier problems. The experience I acquired during those summer months was inexpensible. As our system was very big we didn't succeed in completing everything, neverthless we got a great lot done and working. <br />
<br />
At the start I thought the modelling people would have a pretty difficult task as the modelling of biological systems is also relatively new, so I could only be in awe for the great job they did in generating realistic models.<br />
<br />
Last but not least, it was a very enriching experience to work with an interdisciplinary team with such great and motivated people. I really learned things from everybody and everybody found something to do which he or she was comfortable with. Now I'm looking forward to the jamboree in november which will be the cherry on the cake we baked together.<br />
<br />
==== Benjamien ====<br />
When I first heard about iGEM, my first thought was:<br />
<blockquote>I want to contribute to this fascinating science and compete in this interesting competition!</blockquote><br />
And look, here I am. For me, this summer was an amazing experience, and I hope the adventure is not over yet. Not only a window on molecular biology and gene technology was created and my problem-solving abilities were sharpened in the synergy that arose between the engineers and me, a scientist.<br />
<br />
I hope to learn a lot more at the Jamboree, and that our team achieves a nice result there.<br />
<br />
==== Stefanie ====<br />
When I first heard about the project, I was thrilled. It was something I really wanted to contribute to. It was a great opportunity to get working experience in a real-life wet lab.<br />
<br />
My main contribution to the project as a bio-engineer was building our Dr. Coli in the wet lab. Together with my team members we were able to work out our concepts in a real living organism. I was extremely happy when the first fluorescent colonies were grown. We actually succeeded to build our own theoretically engineered system inside a bacteria!<br />
<br />
During the project I not only learned about the technical stuff directly linked to our system, but also a lot about myself. I'm now sure more than ever that my place is in the wet lab. I just love to be there and hopefully I once get the opportunity to do research in the field of synthetic biology.<br />
<br />
Working with people with different backgrounds was challenging in the beginning but at the end we ended up as good friends. Thanks to all of you for this great summer!<br />
<br />
==== Hanne ====<br />
Months ago, in June, when we were discussing what we wanted to do this summer, I was a bit worried how twelve people with such different backgrounds ever could work together. Don’t get me wrong, I was very excited about working in a multidisciplinary team, but I wondered how we could come to a symbiosis between wet and dry lab. After a few days I discovered that my worries were completely misplaced and I started to feel at ease within this diverse group. <br />
<br />
In the very beginning we had some brainstorms on what our project would be, and to my great surprise, I was one of the founders of Dr. Coli. Somewhere at the end of one of those meetings, I got the wild idea of a bacteria that could produce and regulate its own drug-production. The rest is history, as four months later, we’ve managed to create our Dr. Coli!<br />
<br />
As a biochemist I was really excited to get the chance to extend my lab skills and learn more about being an actual member of an exciting research. We had to cope with some great disappointments but luckily we achieved some new things too! It was nice to know that we weren’t on our own, as we could discuss our progress with our advisors during weekly meetings. They guided us and gave some practical guidance when we encountered difficulties. <br />
At the end of our period in the lab, I alternated my work overthere with some research on human practice and ethical aspects of synthetic biology. It was very interesting to get in touch with those problems, as when you are working so hard in the lab it is sometimes hard to think about possible consequences of your work.<br />
<br />
It was nice to see that the twelve of us, although so different, really started to form a group. Now I’m really looking forward to the Jamboree, it will be a nice ending of an amazing experience!<br />
<br />
==== Elke ====<br />
<br />
In these three months we worked together, I have gained a lot of respect for my team mates. All the things like modelling, building the wiki, engineering our bio-brick scheme, engineering primers,.... are all things I tried to help with, but other members of my team are a lot better in this because of their different background. But I watched, listened and learned a lot of them. <br />
<br />
As a bio-engineer, I spend most of my iGEM-time in the lab. It was very nice that we could do everything ourselves. The first month was a bit disappointing because the transformations and elektroporations didn't succeed. But then, things started to go well and we went wild when we had fluorescent colonies for the first time. It's an amazing feeling when an experiment you worked very hard on gives a good result.<br />
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==== Nick ====<br />
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At first I saw iGEM as a unique opportunity to get in touch with the latest scientific hype: synthetic biology. As a student in Mathematical Engineering it would be a real challenge to model something I've never done before: molecular biology. I also thought of it as good experience for my engineering career: learning to work with many people from different backgrounds to reach an extraordinary goal.<br />
<br />
During the project I learned that there's so much that you aren't taught in university and there still an enormous amount of knowledge out there, that was so new to me. I got to know the basics of molecular biology and learned to think in terms of transcription speed, dissociation constants, complexation reactions, ... All this was needed to build a realistic model of our project: Dr. Coli. Hundreds of simulations were run to check the working of our model, to analyze the results, to optimize our scheme. At the end of the summer, we reached our goal and delivered a working model with several simulations of Dr. Coli.<br />
<br />
When I look back to this summer @ KUL I can truly say that it was a rewarding experience that has taught me many things and hopefully we can win some prizes with our Dr. Coli!<br />
<br />
==== Antoine ====<br />
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Unaware of a large portion of biological concepts, I must say it wasn't that hard for me to work throught this project. IGEM embraces the spirit of bringing together distinctive disciplines and have them cooperate. Though my work was primarily restricted to modeling and IT-management, I got a taste of the real lab work. It was an experience worth trying and gave me a deep understanding of how our wet lab people had a tough nut to crack, given the vast complexity of our system on a biological level.<br />
<br />
Looking back, I believe as a civil engineer I got the opportunity to give my input towards the final model, meaning modeling isn't just an add-on in synthetic biology, but is capable of pointing out fundamental errors when it comes to functionality and behaviour of biological systems. I had memorable times working with biochemists and bio-engineers, in the end, we wouldn't have pulled it off without them, they truly formed a bridge between the wet and dry lab.<br />
<br />
In total, I got to taste the ideal world of modeling, the challenging task of working in the lab, and the more creative side of helping out with the wiki. Not to mention I've discovered a whole new array of delicious sandwiches, during the many many days we've spent on this project.<br />
<br />
==== Dries ====</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/MultiCellTeam:KULeuven/Model/MultiCell2008-10-08T17:23:03Z<p>Nickvd: /* Full Model - Part 2 */</p>
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== Multi-cell Modeling ==<br />
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[[Image:Multicell icon.PNG|right|300px]]<br />
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The output of our Invertimer, the LuxI protein, causes an accumulating amount of HSL molecules, which are in fact signaling molecules. This means that they are used by cells to communicate with each other by diffusing in the environment. <br />
<br />
At this point we have only simulated 1 Dr. Coli @ work. It might be a good idea to take this model to a higher level and simulate the behaviour of a colony of cells. At a later stage we can add a diffusive environment (medium), in which the signaling molecules can travel from one cell to a neighboring cell, and see what happens...<br />
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=== Full Model ===<br />
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A small example leads to a simple conclusion: this analysis is unnecessary. Even when there is possible diffusion of HSL molecules to the environment, it won't happen because of the exces amount of LuxR molecules. LuxR will immediately bind the available HSL molecules (very high association rate) and no HSL will diffuse.<br />
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[[Image:multicell.png|center|400px]]<br />
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=== Full Model - Part 2 ===<br />
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Because of the auto-inducible LuxR promotor there will certainly be diffusion into the medium (see [https://2008.igem.org/Team:KULeuven/Model/FullModel#Full_Model_-_Part_2 Model - Part2]): a deeper research needs to be done! Therefor we wrote a Matlab-script which is capable of interacting with the Simbiology Toolbox. This enables us to replicate cells in silico: we can simulate an increasing population of cells. A pretty visualisation is given below: each pop-up of a bar simulates the sudden presence of a new cell caused by the division of one of the available cells (starting population exists of 4 cells). This sudden pop-up effect is because we only simulate cell multiplication and not the growth of the new born cells: they are immediately at full size with about the same concentrations of the mother cell.<br />
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[[Image:Sim1.png|center|600px]]<br />
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Second, we also implemented some functions to be able to simulate the whole diagram with events and some other features which are present in the Simbiology Toolbox. At this point we are able to run simulations with a growing (Dr. Coli) cell population while they are susceptible to external signals (TetR-input).<br />
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MORE INFORMATION TO COME</div>Nickvdhttp://2008.igem.org/File:Multicell_ccdB1.pngFile:Multicell ccdB1.png2008-10-08T17:21:19Z<p>Nickvd: </p>
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<div></div>Nickvdhttp://2008.igem.org/File:Multicell_HSL1.pngFile:Multicell HSL1.png2008-10-08T17:20:23Z<p>Nickvd: </p>
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<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Team/PicturesTeam:KULeuven/Team/Pictures2008-09-18T08:35:14Z<p>Nickvd: </p>
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<h2>In the wet lab</h2><br />
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<a href="https://static.igem.org/mediawiki/2008/2/2a/Hanne_pcr.JPG" title="Hanne & the gel" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/2/2a/Hanne_pcr.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/8/8a/DSC00018.JPG" title="Andim at work" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/8/8a/DSC00018.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/d/d8/DSC00019.JPG" title="Gel with wells popping out. The girls were surprised when they saw it." rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/d/d8/DSC00019.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/e/e8/DSC00020.JPG" title="Gel with wells popping out. The girls were surprised when they saw it." rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/e/e8/DSC00020.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/e/e1/DSC00021.JPG" title="The horrible pipette-monster has seen a victim." rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/e/e1/DSC00021.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/3/33/DSC00022.JPG" title="The horrible pipette-monster reveales itself." rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/3/33/DSC00022.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/b/b3/DSC00023.JPG" title="Stefanie (lower left) and Hanne (upper right)." rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/b/b3/DSC00023.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/f/f8/DSC00024.JPG" title="Hanne and Stefanie." rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/f/f8/DSC00024.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/8/87/DSC00026.JPG" title="Notice the spirillium-ish mascotte" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/8/87/DSC00026.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/7/7f/DSC00027.JPG" title="Girls chatting up." rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/7/7f/DSC00027.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/6/60/KUL21.JPG" title="In the microscopy room" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/6/60/KUL21.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/1/16/KUL23.JPG" title="Stefanie checking out fluorescent colonies" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/1/16/KUL23.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/6/69/KUL26.JPG" title="Stefanie and Nathalie discussing the fluorescent colonies" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/6/69/KUL26.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/3/33/KUL27.JPG" title="Cosy gathering in the microscopy room" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/3/33/KUL27.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/f/f0/KUL28.JPG" title="Just remember, kids, drugs are bad business" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/f/f0/KUL28.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/f/fe/KUL29.JPG" title="The laboratory pigeon" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/f/fe/KUL29.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/3/32/KUL30.JPG" title="Fred, Kim, David and Hans, our true heroes! (especially the girl's)" rel="imagebox-wetlab"><img src="https://static.igem.org/mediawiki/2008/3/32/KUL30.JPG"></a><br />
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<h2>In the dry lab</h2><br />
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<a href="https://static.igem.org/mediawiki/2008/5/5b/KUL3.jpg" title="Two hands, therefore two computers" rel="imagebox-drylab"><img src="https://static.igem.org/mediawiki/2008/5/5b/KUL3.jpg"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/a/a1/KUL12.JPG" title="Antoine at work" rel="imagebox-drylab"><img src="https://static.igem.org/mediawiki/2008/a/a1/KUL12.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/8/8a/KUL13.JPG" title="Dries preparing for some nasty modeling" rel="imagebox-drylab"><img src="https://static.igem.org/mediawiki/2008/8/8a/KUL13.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/7/7e/KUL14.JPG" title="Nathalie en Hanne working hard" rel="imagebox-drylab"><img src="https://static.igem.org/mediawiki/2008/7/7e/KUL14.JPG"></a><br />
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<a href="https://static.igem.org/mediawiki/2008/7/7b/KUL24.JPG" title="Fire-alarm testing in the building" rel="imagebox-drylab"><img src="https://static.igem.org/mediawiki/2008/7/7b/KUL24.JPG"></a><br />
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<h2>Outside the lab</h2><br />
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<a href="https://static.igem.org/mediawiki/2008/0/07/KUL16.JPG" title="Under a tree hiding for the sun" rel="imagebox-nolab"><img src="https://static.igem.org/mediawiki/2008/0/07/KUL16.JPG"></a><br />
<br />
<a href="https://static.igem.org/mediawiki/2008/6/60/KUL19.JPG" title="Dries doing some strange move" rel="imagebox-nolab"><img src="https://static.igem.org/mediawiki/2008/6/60/KUL19.JPG"></a><br />
<br />
<a href="https://static.igem.org/mediawiki/2008/1/11/KUL22.JPG" title="Dries" rel="imagebox-nolab"><img src="https://static.igem.org/mediawiki/2008/1/11/KUL22.JPG"></a><br />
</div><br />
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</div><br />
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Post pictures here!!!</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/OverviewTeam:KULeuven/Model/Overview2008-09-15T09:18:02Z<p>Nickvd: /* Sensitivity Analysis */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
__NOTOC__<br />
<br />
=== Introduction ===<br />
<br />
[[Image:WhyWeNeedComputer.png|200px|right]]<br />
<br />
As an introduction to modeling we've made a small [https://static.igem.org/mediawiki/2008/4/4e/Modeling.ppt presentation] for the workout sessions of the first meeting. This presentation handles the following items: <br><br />
* some definitions<br />
* the difference between white box and black box models with an example<br />
* focus on the role of ODE's<br />
* the need for modeling<br />
* some modeling tools<br />
* and iGEM modeling<br />
<br />
This presentation is mainly based on the wiki of ETH Zürich 2006/2007.<br />
<br />
=== The Full Model ===<br />
<br />
[[Image:Superfinal.png|500px|center]]<br />
<br />
=== Modeling steps===<br />
<br />
==== Position in the system ====<br />
<br />
For each of the subsystems (compartments) we started with the idea of what it was supposed to do, considering it as a black-box system (as described in the [https://2008.igem.org/Team:KULeuven/Project project page]). To make sure that Dr. Coli was able to do his work properly, we had to design several subsystems and be well aware of the different interfaces between these subsystems. <br />
<br />
Then we tried to match species with these black-boxes, keeping in mind the working biobricks which have been made already. So we searched for existing components which could be able to perform the requested task.<br />
<br />
==== Describing the system ====<br />
<br />
The kinetic actions (transcription, translation, complexation, ...) that take place in the subsystems can be described by Ordinary Differential Equations (ODEs) like Mass-Action laws, Hill Kinetic laws and so on. An extensive search for parameters involved in these ODEs has resulted in the discovery of almost all necessary quantities for the simulations.<br />
<br />
For every subsystem, we made a PDF-file with all the ODEs involved in modeling the subsystem, together with a clear overview of the used parameters (with coherent links to our references).<br />
<br />
==== Models ====<br />
<br />
We implemented these ODEs in both [http://www.systems-biology.org/cd/ Celldesigner] and the [http://www.mathworks.com/access/helpdesk/help/toolbox/simbio/ MATLAB Symbiology Toolbox]. A nice tutorial for modeling in Celldesigner can be found on [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals Imperial College Computer Modelling Practicals Spring 2008]. These 2 environments offer a grapical user-interface which makes it easy to implement biochemical pathways (and the kinetic laws which govern these). In the pictures in each of the subsytems you can see clearly the influence of the different species: activation, repression, complexation, ... We also provide links to the actual implemented diagrams which can be freely downloaded to simulate the subsystems yourself.<br />
<br />
==== Simulation(s) ====<br />
<br />
The implemented models are simulated using inputs as close to reality as possible. In each simulation the typical assets of each subsystem are clearly visualized and described extensively. For example in the filter we simulate the influence of different noisy signals on the output of the filter (and on the output of the system).<br />
<br />
=== Sensitivity Analysis ===<br />
<br />
Good modeling practice requires that the modeler provides an evaluation of the confidence in the model, possibly assessing the uncertainties associated with the modeling process and with the outcome of the model itself. Uncertainty and Sensitivity Analysis offer valid tools for characterizing the uncertainty associated with a model. Uncertainty analysis (UA) quantifies the uncertainty in the outcome of a model. Sensitivity Analysis has the complementary role of ordering by importance the strength and relevance of the inputs in determining the variation in the output. Sensitivity analysis lets you calculate the time-dependent sensitivities of all the species states with respect to species initial conditions and parameter values in the model.<br />
<br />
A sensitivity analysis is needed e.g. when some of the parameter values are not known. The true value of a parameter is unimportant when the most essential species states are insensitive to the unknown parameter. Only for the sensitive unknown parameters are experiments needed to determine their true values. In our project we have been able to find hypothetical values for all used parameters, but a sensitivity analyses is nevertheless always valuable to detect critical parameters. These are the parameter values on which our project critically depends and which should be analyzed/characterized as exact as possible.<br />
<br />
Our analysis is based upon the following formulae where X is the output species that we look at and P is the parameter that is changed to 110% or 90% of its own value. The second term is for normalisation purposes. Results and discussions can be found in the [https://2008.igem.org/Team:KULeuven/Model/Sensitivity appropriate section].<br />
<br />
[[Image:Eqn1.png|center|250px]]<br />
<br />
[[Image:Eqn2.png|center|250px]]<br />
<br />
=== Important notes ===<br />
<br />
<b>1.</b> The idea of a pulsgenerator as reset mechanism has been cancelled for the following reasons: <br />
* it takes too long before the proposed system generates a pulse-like event<br />
* the pulse itself is too long <br />
* a constant lactonase production sequence generates enough lactonase to reset the timer<br />
More information about this problem and the solution can be found on [https://2008.igem.org/Team:KULeuven/Model/Reset Reset]-page.<br />
<br />
<b>2.</b> A mathematical analyses of the memory has been done to prove that it has 2 stable states and to describe the boundary which separates the trajectories leading to one of the steady states. <br />
<br />
More information about this analysis can be found on [https://2008.igem.org/Team:KULeuven/Model/Memory Memory]-page.</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/FullModelTeam:KULeuven/Model/FullModel2008-09-15T09:17:12Z<p>Nickvd: /* Sensitivity Analysis */</p>
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<div>{{:Team:KULeuven/Tools/Header}}<br />
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<br />
== Full Model ==<br />
<br />
=== Describing the system ===<br />
<br />
Dr. Coli produces a green fluorescent protein (drug) when it senses INPUT (certain disease signal in the human body). When Dr. Coli doesn't sense any INPUT anymore (the patient is cured), the invertimer will function as a molecular timer, counting towards the doctor's own demise: ccdB induced cell death. When INPUT (disease signal) reappers in time, the timer is reset. A filter ensures that the timer is not reset when only “noisy” INPUT signals are sensed. A memory device (stable switch) is included to ensure the clock only starts ticking when it is activated by the first input signal. <br />
<br />
==== ODE's ====<br />
<br />
<html><br />
<body><br />
<p><br />
<a href="https://static.igem.org/mediawiki/2008/7/73/Total.pdf"><br />
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60"><br />
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<br />
==== Parameters ====<br />
The parameters can be found in the sections about the simple parts of the system.<br />
<br />
=== Models ===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/6/66/Total_CellDesigner.zip SBML file]) ====<br />
[[Image:Total_CellDesigner.png|center|800px]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/5/5b/FullModel.sbproj.zip file]) ====<br />
[[Image:Final matlab.png|950px|center|Model]]<br />
<br />
=== Simulations ===<br />
<br />
[[Image:SystemInWork.png|850px|center]]<br />
<br />
Discussion of the simulation:<br />
<br />
* In the beginning the memory has status "0" and the simulation clearly shows that the timer isn't activated. This means that the bacteria can grow without any problem (no ccdB-production and hence no cell death) when they haven't sensed any desease marker in the beginning.<br />
* At t=50.000s the system is activated by a long lightpulse (simulating the insertion of the bacteria in the patient's body and sensing desease marker for the first time). This results in:<br />
** switching of the memory to status "1" --> activation of transcription of LuxR (green curve)<br />
** activation of the filter (desease marker is strong enough) which is reflected by the production of lactonase (blue curve), situated just after the filter mechanism.<br />
* At t=75.000 the lightpulse is switched off (simulating that there's no more desease marker: the patient is cured). This results in:<br />
** stopping the production of lactonase, which starts to degrade naturally (blue curve)<br />
** stopping the production of LacI, which stops repressing the transcription of LuxI. In this way HSL can be produced, but, since there's still lactonase present in the cell, there won't be a visible increase in HSL-LuxR-complex because the HSL is being transformed into hydroxyacid.<br />
* At t~=92.000 the lactonase is almost totally degraded which enables the HSL to form a complex with LuxR (yellow curve). This means that we have a timer that starts with a delay of +- 17.000s. At this point the HSL-LuxR-complex really starts to build up gradually (TIMER) for about 10.000s.<br />
* At t~=102.000s the HSL-LuxR-complex peaks, with at the same time (free) LuxR decreasing to almost zero. <br />
**At this point all the newly produced LuxR will go into complex with HSL and no free LuxR will remain. From this point on, the HSL-LuxR-complex will decrease to a steady state value which is equal to the production rate of LuxR-proteins. <br />
** BUT you can see clearly that the ccdB (red curve) also peaks (to a value of 10 to 20 molecules) which is enough to result in cell death.<br />
<br />
== Full Model - Part 2 ==<br />
<br />
=== Extension to the previous model ===<br />
<br />
During the summer we changed a lot of things to our grand scheme. This new system has quite some novelties:<br />
<br />
* Cell Death has also gotten an overhaul. Transcription now begins at a new hybrid promoter we made: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K145150 '''BBa_K145150''']. This promoter is repressed by c2 P22, which is produced by the memory in the OFF state, making premature activation and cell death impossible. Besides this repression, the promoter is activated by the HSL-LuxR complex originating from a previously activated timer. The promoter behaves as shown schematically below. <br />
<br />
[[Image:Hybrid_promotor.PNG|center]]<br />
<br />
* Second, LuxR is now no longer constitutively produced but is placed behind the beforementioned hybrid promoter. This construction mimicks more closely the natural system where LuxR is upregulated when a threshold amount of HSL is present. Plus it also increases the time it takes to activate ccdB, lengthening the timer. The system will now auto-activate if enough HSL is present and the memory is in the ON state.<br />
<br />
* Third, the ccdB coding region is also downstream of the hybrid promoter and is thus also subject to the regulation explained above; c2 P22 repression and HSL-LuxR auto-activation. One difference is that the polymerase must first read through a bad terminator with about 60% efficiency before reaching this coding region. Another difference is in the ribosome binding sites preceding both coding regions. Where LuxR can be translated from a RBS with a relative efficiency of 1.00, the ccdB frame can only be read from a 0.01 efficiency RBS.<br />
<br />
Because of this new organisation, we've also turned our attention towards [https://2008.igem.org/Team:KULeuven/Model/MultiCell multi cell] interactions and [https://2008.igem.org/Team:KULeuven/Model/Diffusion diffusion] of HSL in the medium again.<br />
<br />
=== Describing the system ===<br />
<br />
==== ODE's ====<br />
<br />
todo!!!<br />
<br />
==== Parameters ====<br />
The parameters can be found in the sections about the simple parts of the system.<br />
<br />
Extension: parameters of HSL-LuxR auto-activation can be found in [https://2008.igem.org/Team:KULeuven/Model/CellDeath#Extensions_to_previous_system Model:New Cell Death].<br />
<br />
=== Models ===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/c/c2/Total_CellDesigner2.zip SBML file])====<br />
Attention: this CellDesigner model is no longer up to date. For the final version, use the MATLAB model below!<br />
[[Image:TotalSystem celldesigner2.png|center|900px]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/f/fd/FullModel2.sbproj.zip file]) ====<br />
[[Image: NewTot.png|center|900px]]<br />
<br />
=== Simulations ===<br />
<br />
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<img src="https://static.igem.org/mediawiki/2008/0/09/FullSim1.png" style="float: left; width: 400px; height: 400px; margin: 0 5px;" /><br />
<img src="https://static.igem.org/mediawiki/2008/d/de/FullSim2.png" style="float: left; width: 400px; height: 400px; margin: 0 5px;" /><br />
<img src="https://static.igem.org/mediawiki/2008/5/59/FullSim3.png" style="float: left; width: 400px; height: 400px; margin: 0 5px;" /><br />
</div></div></div></html><br />
<br />
<br><br />
<br />
This simulation can already be seen as a very basic multicell simulation, since it is performed for 1000 cells growing in a microchemostat with a volume of 1000 . For more deailed information, please see our [https://2008.igem.org/Team:KULeuven/Model/MultiCell MultiCell] and [https://2008.igem.org/Team:KULeuven/Model/Diffusion Diffusion] modeling pages. If time is of the essence, the [https://2008.igem.org/Team:KULeuven/Model/Diffusion#Microchemostat Microchemostat subsection] should be most useful.<br />
<br />
==== Discussion of the simulation ====<br />
<br />
# In the absence of a disease market, the system starts of with a memory in the OFF state, this means the c2 P22 is produced which shuts down LuxR and ccdB production. LuxI production is also partially eliminated because the memory also outputs antisense LuxI. Put simple, the timer is not active and Dr. Coli can grow without worrying as there is no ccdB and hence no cell death.<br />
# At t=50.000s the system is activated by a long lightpulse (simulating the insertion of the doctor in the patient's body and sensing desease marker for the first time). This results in:<br />
## the switching of the memory to the ON state. This means cI 434 instead of c2 P22 so no more antisense LuxI or repression of LuxR and ccdB. (more specific switching simulations can be found in the corresponding [https://2008.igem.org/Team:KULeuven/Model/Memory#Simulations memory] pages).<br />
## With the memory in the ON state, LuxR as well as ccdB will rise to a background level. This level is extremely low for the latter but already significant for the former, because we want to make sure that auto-acivation is possible. <br />
## the activation of the filter (long pulse, the disease marker is strong enough). This is reflected in the production of lactonase, situated just after the filter mechanism.<br />
# At t=130.000s the lightpulse is switched of (simulating that there's no more disease marker: the patient is cured). This results in:<br />
## the shutting down of lactonase production, which continues to degrade naturally<br />
## the shutting down of LacI production, which stops repressing the transcription of LuxI. Slowly, LuxI is produced and thus also 3OC6HSL.<br />
# At t~=150.000, all the lactonase and the LacI are gone and it is possible to see LuxI and HSL increase. This means that the actual 'counting' only starts about 17.000s after the input is switched off. Part of the HSL diffuses outside of the cell, another part remains free but the third part associates with the background of Lux receptors (free LuxR drops).<br />
# This third part will auto-induce more LuxR receptors and upregulate ccdB.<br />
# When the timer has counted to about 50.000s after the input has gone dead, ccdB has reached the lethal amount of around 10-14 molecules per cell and Dr. Coli calls it a day.</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/SensitivityTeam:KULeuven/Model/Sensitivity2008-09-15T09:16:42Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Sensitivity Analysis ==<br />
<br />
=== Episode I: The MATLAB Menace ===<br />
<br />
Sensitivity analysis for Dr. Coli has been a pain in the ***. Our first attempts at this were done with the Sensitivity Analysis Tool that is included in MATLAB Simbiology. The problem here is that our model calls MATLAB's power fuction. Sensitivity analysis currently uses complex-step differentiation, which is currently not supported for this function. The computed sensitivities may not even approximate true sensitivities. So the value of this analyisis is doubtful.<br />
Nevertheless, below are some results of the calculated sensitivities for species in the system that precede any reaction that calls the power function.<br />
<br />
In these graphs, the 'parameters'-axis shows the parameters that are varied in the sensitivity analysis, while the ones along the states axis are the ones monitored as output. The z-axis is a measure for the sensitivity of the parameter under study.<br />
<br />
<br />
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<img src="https://static.igem.org/mediawiki/2008/7/7c/SensAmoreOFF.png" style="float: left; width: 500px; height: 400px; margin: 0 5px;" /><br />
<img src="https://static.igem.org/mediawiki/2008/d/d8/SensAmoreON.png" style="float: left; width: 500px; height: 400px; margin: 0 5px;" /><br />
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<br />
<br><br />
<br />
=== Episode IV: A New Hope ===<br />
<br />
We had come to the conclusion that the MATLAB sensitivity analysis just would not cut it for us, so we went on and started digging again. We tried a whole lot of different approaches, but nothing seemed to be appropriate for our system. (These attempts are episode II and III which we'll just skip here and forget about)<br />
Finally, we came up with the following. We define sensitivity in two different states, the ON state of the system and the OFF state The ON state receives maximal input during the entire simulation, while the OFF state only gets background signal.<br />
We come to the following formulae where X is the output species that we look at and P is the parameter that is changed to 110% or 90% of its own value. The second term is for normalisation purposes.<br />
<br />
[[Image:Eqn1.png|center|250px]]<br />
<br />
[[Image:Eqn2.png|center|250px]]<br />
<br />
A third situation has also been analysed. In the above two cases we constantly give 0 or 1 respectively. Our system however has a third and very important state: 0 - 1 - 0. In this state, the memory is ON and the timer can function. To simulate this, we used the same formula but we also created an event during the simulation.<br />
<br />
These attempts give us more helpful results. We can even interpret something stability-like for our memory now: how far can our parameterisation be off before the memory stops functioning as expected. The results obtained by using this method for sensitivity analysis can be seen depicted in the figures below.<br />
<br />
==== Output ====<br />
<br />
More as a control, the first figure depicts the sensitivity of our output GFP. It behaves completely as expected, clearly showing only dependencies for the degradation and synthesis rates of GFP while everything else is equal to zero. Also according to plan, the simulation gives exactly the same results for the two formulae above.<br />
<br />
[[Image:Sens_GFP_ON.png|800px|center]]<br />
<br />
<br />
==== Memory ====<br />
<br />
As mentioned before, we can use the sensitivity analysis of the memory to see how big our margins are on the arious parameters that make out our model. The first figure shows the sensitivity of c2 P22 for all system parameters in the OFF state. This means we use the second formula. The analysis shows all expected dependencies such as synthesis and degradation rates for c2 P22. But also for the affinity of cI 434 for the promoter in front of c2 P22, for the production/degradation rates of cI 434 with(out) LVA tag.<br />
<br />
[[Image:Sens_c2P22_OFF.png|800px|center]]<br />
<br />
For cI 434 in the OFF state, we see similar but distinct results. We see that all sensitivities appear to be bit higher and that some extra factors have appeared describing repression by and degradation of c2 P22 repressor. Once again logical results.<br />
<br />
[[Image:Sens_cI434_OFF.png|800px|center]]<br />
<br />
The next figure shows the sensitivities for c2 P22 in the ON state of the memory (where it plays a similar role as cI 434 (LVA) in the OFF state). We can even see that the figure is very similar to the one just above, except that the affinity of c2 P22 for the promoter controlling cI 434 (LVA) doesn't seem to matter anymore. This can be easily understood if you remember that we're simulating a continuous 1 signal here, where a lot of cI 434 (without LVA) is coming from the TetR promoter, making small contributions to the cI 434 concentration by the c2 P22 repressible promoter quite irrelevant in this case.<br />
<br />
[[Image:Sens_c2P22_ON.png|800px|center]]<br />
<br />
cI 434 (without LVA tag) during a continuous 1 signal is only dependent on the obvious synthesis, degradation rates as can be expected with the total amount of cI 434 being high enough to remove all c2 P22 from the system.<br />
<br />
[[Image:Sens_cI434_ON.png|800px|center]]<br />
<br />
A final figure shows the sensitivity of the same cI 434 without tag in a system that has been activated but is now without input. The switch appears to be so strong that we only detect the same sensitivities as in the above scenario of a continuous 1 signal.<br />
<br />
[[Image:Sens_cI434_event.png|800px|center]]<br />
<br />
==== Celldeath-related ====<br />
<br />
The first figure shows the sensitivities for Lactonase in the ON state (the first formula). They can all be expected; we clearly see the dependence on the filter (T7 as well as key-lock characteristics) as well as more obvious synthesis and degradation rates of lactonase itself.<br />
<br />
[[Image:Sens_aiiA_ON.png|800px|center]]<br />
<br />
This next one shows the sensitivities of LuxI in a 0 - 1 - 0 event situation. We clearly see the filter effect again but this time it appears to be reinforced by the LacI repressor of the inverter. The parameters for LacI repression are also nicely visible.<br />
<br />
[[Image:Sens_LuxI_event.png|800px|center]]<br />
<br />
By looking at HSL in the same 0 - 1 - 0 scenario, we see a very similar picture. All the same sensitivities are visible plus three significant new ones. The first is obvious, it is the rate of HSL synthesis by LuxI. The other two are less obvious, they are the cell volume and the volume of the medium. These are effects of the diffusion out of the cell and into the medium.<br />
<br />
[[Image:Sens_HSL_event.png|800px|center]]<br />
<br />
The final study is of ccdB, our final effector in the 0 - 1 - 0 scenario. We can see small sensitivities for the parameters characterising the HSL-LuxR complex such as affinity of the complex for the DNA, affinity of HSL for LuxR etc. The highest sensitivities we get for the properties of ccdB itself. The terminator efficiency and other synthesis and degradation rates.<br />
<br />
[[Image:Sens_ccdB_event.png|800px|center]]<br />
<br />
==== Further conclusions ====<br />
<br />
Our model seems to respond to these sensitivity analyses as suspected and at first glance appears to give us a bit of a margin on most of our parameters.</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Tools/Navigation_BarTeam:KULeuven/Tools/Navigation Bar2008-09-15T09:14:26Z<p>Nickvd: </p>
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</div><br />
</html></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/Cell_DeathTeam:KULeuven/Model/Cell Death2008-09-10T08:34:52Z<p>Nickvd: /* Extensions to previous system */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<div style="float: right;">[[Image:pictogram_celldeath.png|120px]]</div><br />
<br />
==Cell Death==<br />
<br />
=== Position in the system ===<br />
<br />
The Cell Death subsystem receives input from two other subsystems, namely:<br />
<br />
* [[Team:KULeuven/Model/Inverter | Inverter]]<br />
* [[Team:KULeuven/Model/Pulse_Generator | Pulse Generator]]<br />
<br />
LuxR is the component repressing the regulation of CcdB, the toxic product causing cell death. There the LuxR production is constitutive, no protein controls the gene regulation of LuxR, but the amount of LuxR available to repress the transcripion of the CcdB gene is controlled by HSL (Homoserine lactone).<br />
<br />
If the inverter subsystem produces HSL (occurs when no light is detectable), this will forms a complex with LuxR. This will diminish the amount of LuxR available to repress the CcdB transcription and initiate cell death. When waiting long enough the amount of HSL becomes critical.<br />
<br />
If however the pulse generator becomes active (by the filter), it will produce a pulse of lactonase, which will then bind to the HSL, reacting to an hydroxy-acid. As opposed to HSL, this hydroxy-acid will no longer form a complex with LuxR. This increase in LuxR lowers the CcdB production. The challenge is to generate a pulse of lactonase high enough to neutralise all HSL present in the cell.<br />
<br />
=== Describing the system ===<br />
<br />
[[Image:Cell_Death.jpg|center]]<br />
<br />
==== ODE's ====<br />
<br />
<html><br />
<body><br />
<p><br />
<a href="https://static.igem.org/mediawiki/2008/b/b8/Celldeath.pdf"><br />
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60"><br />
</a><br />
</p><br />
</body><br />
</html><br />
<br />
==== Parameters ====<br />
Remark: update parameters to repressive promotor<br />
{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"<br />
|+ ''Parameter values (Cell Death)''<br />
! width=15% | Name<br />
! width=15% | Value<br />
! width=40% | Comments<br />
! width=10% | Reference<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates<br />
|-<br />
| d<sub>LuxR</sub><br />
| 0.0010 s<sup>-1</sup><br />
|<br />
| <br />
|-<br />
| d<sub>LuxR_HSL</sub><br />
| 0.0010 s<sup>-1</sup><br />
| complex of HSL and LuxR degrades, giving back HSL<br />
|<br />
|-<br />
| d<sub>RNA_LuxR</sub><br />
| 0.00227 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>CcdB</sub><br />
| 7.7E-5 s<sup>-1</sup><br />
| <br />
| [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]<br />
|-<br />
| d<sub>RNA_CcdB</sub><br />
| 0.00231 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>HSL</sub><br />
| 1.02E-6 s<sup>-1</sup><br />
| <br />
| [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Association/Dissociation/Reaction Rates<br />
|-<br />
| k<sub>ass</sub> (HSL+LuxR)<br />
| 1E6 s<sup>-1</sup><br />
| association rate of HSL with LuxR. Chosen to be relatively (to the other rate constants) high and such that K<sub>diss</sub> (HSL + LuxR) equals 10<sup>-6</sup><br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL+LuxR)<br />
| 1 s<sup>-1</sup><br />
| dissociation rate of the HSL-LuxR complex<br />
| <br />
|-<br />
| k<sub>ass</sub> (HSL+lactonase)<br />
| 1E6 s<sup>-1</sup><br />
| association rate of HSL with lactonase<br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL+lactonase)<br />
| 446.5 s<sup>-1</sup><br />
| dissociation rate of the HSL-lactonase complex<br />
| <br />
|-<br />
| k<sub>cat</sub> (HSL:hydroxy-acid)<br />
| 29 s<sup>-1</sup><br />
| catalytic transformation of HSL to an hydroxy-acid, lactonase is the enzyme<br />
| [http://www.jbc.org/cgi/reprint/M311194200v1.pdf link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Constants<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 1E-6 [M]/L<br />
| k<sub>diss</sub> / k<sub>ass</sub> (HSL+LuxR)<br />
| [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 4.05E-6 [M]/L<br />
| binding HSL_LuxR on LuxPromotor<br />
| [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Hill Cooperativity<br />
|-<br />
| n<sub>HSL_LuxR</sub><br />
| 2.08<br />
| <br />
| [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates<br />
|-<br />
| k<sub>mRNA_LuxR</sub> (constitutive promotor)<br />
| 0.025 s<sup>-1</sup><br />
| see [[Team:KULeuven/Model/KineticConstants#Constitutive_promoters | Constitutive Promotors & E. coli transcription Rates]]<br />
|<br />
|-<br />
| k<sub>mRNA_CcdB</sub><br />
| 0.025 s<sup>-1</sup><br />
| maximal transcription rate for CcdB RNA (no LuxR repressor present)<br />
| <br />
|-<br />
|}<br />
<br />
[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6T39-3Y6HKD6-BK-1&_cdi=4941&_user=877992&_orig=search&_coverDate=08%2F30%2F1995&_sk=998379998&view=c&wchp=dGLbVtz-zSkzS&md5=49efd14150c71e668eabdef225220ce3&ie=/sdarticle.pdf This paper] says that synthesis of even a few molecules of the shorter CcdB protein is probably lethal.<br />
<br />
=== Models ===<br />
<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/3/37/CellDeath_CellDesigner.zip SBML file])====<br />
<br />
[[Image:CellDeath_CellDesigner.png|600px|center|Cell Death]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/4/45/CellDeath_Matlab.zip SBML file])====<br />
Remark: not yet up to date to latest (final) version <br />
[[Image:CellDeath_Matlab.jpg|600px|center|Cell Death]]<br />
<br />
== New Cell Death==<br />
<br />
===Extensions to previous system===<br />
<br />
During the summer we switched from the above system to a new one which you can see just below, take a look at this figure as it will help you understand the regulation that is present. This new system has a few novelties. <br />
<br />
* First of all, transcription begins at a new hybrid promoter we made: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K145150 '''BBa_K145150''']. This promoter is repressed by c2 P22, which is produced by the memory in the OFF state, making premature activation and cell death impossible. Besides this repression, the promoter is activated by the HSL-LuxR complex originating from a previously activated timer. The promoter behaves as shown schematically below. <br />
<br />
[[Image:Hybrid_promotor.PNG|center]]<br />
<br />
* Second, LuxR is now no longer constitutively produced but is placed behind the beforementioned hybrid promoter. This construction mimicks more closely the natural system where LuxR is upregulated when a threshold amount of HSL is present. Plus it also increases the time it takes to activate ccdB, lengthening the timer. The system will now auto-activate if enough HSL is present and the memory is in the ON state.<br />
<br />
* Third, the ccdB coding region is also downstream of the hybrid promoter and is thus also subject to the regulation explained above; c2 P22 repression and HSL-LuxR auto-activation. One difference is that the polymerase must first read through a bad terminator with about 60% efficiency before reaching this coding region. Another difference is in the ribosome binding sites preceding both coding regions. Where LuxR can be translated from a RBS with a relative efficiency of 1.00, the ccdB frame can only be read from a 0.01 efficiency RBS.<br />
<br />
===Describing the system===<br />
see also: [https://2008.igem.org/Team:KULeuven/Project/CellDeath Project:Cell Death]<br />
<br />
[[Image:Cell_Death_new.jpg|center]]<br />
<br />
====ODE's====<br />
<br />
todo!!!<br><br />
<br />
==== Parameters ====<br />
{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"<br />
|+ ''Parameter values (Cell Death)''<br />
! width=15% | Name<br />
! width=15% | Value<br />
! width=40% | Comments<br />
! width=10% | Reference<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates<br />
|-<br />
| d<sub>LuxR</sub><br />
| 9.627044174E-5 s<sup>-1</sup><br />
| no LVA tag, so longer lifetime<br />
| <br />
|-<br />
| d<sub>complex</sub><br />
| 9.627044174E-5 s<sup>-1</sup><br />
| complex of HSL and LuxR degrades, giving back HSL<br />
|<br />
|-<br />
| d<sub>RNA_LuxR</sub><br />
| 0.00227 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>ccdB</sub><br />
| 7.7E-5 s<sup>-1</sup><br />
| stable in the absence of ccdA<br />
| [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]<br />
|-<br />
| d<sub>RNA_ccdB</sub><br />
| 0.00231 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>HSL</sub><br />
| 1.02E-6 s<sup>-1</sup><br />
| very stable in the medium, average lifetime of 185h<br />
| [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Association/Dissociation/Reaction Rates<br />
|-<br />
| k<sub>ass</sub> (HSL+LuxR)<br />
| 0.002372 s<sup>-1</sup><br />
| association rate of HSL with LuxR (estimate from K<sub>M</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL-LuxR)<br />
| 1.0 s<sup>-1</sup><br />
| dissociation rate of the HSL-LuxR complex (estimate from K<sub>M</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>ass</sub> (HSL+lactonase)<br />
| 0.002372 s<sup>-1</sup><br />
| association rate of HSL with lactonase (estimate from K<sub>M</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL-lactonase)<br />
| 4470.0 s<sup>-1</sup><br />
| dissociation rate of the HSL-lactonase complex (estimate from K<sub>d</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>cat</sub> (HSL>>hydroxy-acid)<br />
| 29 s<sup>-1</sup><br />
| lactonase catalyzed transformation of HSL to a hydroxy-acid<br />
| [http://www.jbc.org/cgi/reprint/M311194200v1.pdf link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Constants<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 1E-6 [M]<br />
| HSL binding to LuxR<br />
| [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]<br />
|-<br />
| K<sub>HSL_LuxR-promoter</sub><br />
| 4.05E-6 [M]<br />
| binding of HSL_LuxR complex to the Lux Promotor<br />
| [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]<br />
|-<br />
| K<sub>HSL_lactonase</sub><br />
| 4.47E-3 [M]<br />
| K<sub>M</sub> of lactonase with 3OC6HSL<br />
| [http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Hybrid Promoter<br />
|-<br />
| K<sub>C2 P22</sub><br />
| 2.6E-10 [M]<br />
| Dissociation constant for P22 c2 promoter binding<br />
| [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&firstpage=10536&resourcetype=HWCIT link]<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 4.05E-6 [M]<br />
| Dissociation constant for HSL-LuxR complex promoter binding<br />
| [http://jb.asm.org/cgi/content/abstract/JB.01443-07v1 link]<br />
|-<br />
| Hill<br />
| 2<br />
| Hill coefficient for P22 c2 binding<br />
| [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&firstpage=10536&resourcetype=HWCIT link]<br />
|-<br />
| k<sub>leaky</sub><br />
| 5E-4 s<sup>-1</sup><br />
| transcription rate from the hybrid promoter in the '''unactivated''' ON state<br />
|<br />
|-<br />
| k<sub>max</sub><br />
| 0.0030 s<sup>-1</sup><br />
| maximal transcription rate for the fully activated ON hybrid promoter (might be higher)<br />
|<br />
|-<br />
| Terminator eff<br />
| 60.8%<br />
| percentage of transcription termination at the B0014 double terminator in front of ccdB<br />
| [http://partsregistry.org/Part:BBa_B0014 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates<br />
|-<br />
| k<sub>LuxR translation</sub><br />
| 0.556 s<sup>-1</sup><br />
| Translation rate for LuxR, B0034 RBS (relative efficiency 1.0)<br />
| [http://partsregistry.org/Part:BBa_B0034 link]<br />
|-<br />
| k<sub>ccdB translation</sub><br />
| 0.00556 s<sup>-1</sup><br />
| Translation rate for ccdB, B0033 RBS (relative efficiency 0.01)<br />
| [http://partsregistry.org/Part:BBa_B0033 link]<br />
|}<br />
<br />
===Models===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/1/14/Celldeath_CellDesigner_final.zip SBML file])====<br />
<br />
[[Image:CellDeath_CellDesigner_new.png|800px|center|Cell Death]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/3/36/CellDeath_Matlab_Final.zip SBML file])====<br />
<br />
[[Image:CellDeath_Matlab_Final.jpg|800px|center|Cell Death]]<br />
<br />
=== Simulations ===<br />
<br />
To simulate the cell death, the input signal TetR is all the time low (5E-5) except from 50000 till 80000 seconds,from 180000 till 190000 seconds and from 250000 till 270000 seconds (0.0125). The left figure shows us that a high input signal will lower the amount of HSL (the HSL will be converted into hydroxy acid by lactonase). This will increase the amount of free LuxR because there is not enough HSL to form the HSL-LuxR complex. During the pulse, the right figure shows us an increase of the amount of CcdB. Whenthe memory switches from state zero to state one, the amount of CIIP22 decreases which makes it possible to produce a small amount of CcdB (background signal). <br><br />
When the input signal is low again, the amount of HSL increases. This extra HSL will form with LuxR the complex which lowers the amount of free LuxR. The higher amount of the complex promotes the production of CcdB which increases to a (hopefully) deathly level. <br><br />
A new pulse lowers the amount of HSL and the complex and increases the amount of LuxR for the same reasons as before. The second pulse is smal in length and decreases the amount of CcdB only partially. The third pulse is long enough for a total reset of the entire system.<br />
<br />
<html><br />
<div class="center"><br />
<div class="noborder" style="overflow: auto; width: 800px; height: 420px;"><br />
<div class="noborder" style="width: 1250px;"> <br />
<img src="https://static.igem.org/mediawiki/2008/f/f4/Sim_celldeath.png" style="float: left; width: 600px; height: 400px; margin: 0 5px;" /><br />
<img src="https://static.igem.org/mediawiki/2008/9/9f/Sim_celldeath_total_2.png" style="float: left; width: 600px; height: 400px; margin: 0 5px;" /><br />
</div></div></div></html></div>Nickvdhttp://2008.igem.org/File:MultiCell_Toolbox.zipFile:MultiCell Toolbox.zip2008-09-09T15:03:44Z<p>Nickvd: uploaded a new version of "Image:MultiCell Toolbox.zip"</p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeXTeam:KULeuven/Software/Simbiology2LaTeX2008-09-09T14:54:08Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
We've written a small toolbox to convert the information in the Matlab Simbiology models to LaTeX-code. This code can be easily converted to a pdf-file with various open source programs (e.g. [http://www.texniccenter.org/index.php?id=20 TeXnicCenter for Windows]). The idea for this toolbox is based on the plugin [http://systems-biology.org/cd/plugins.html Squeezer] for CellDesigner.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
The program consists of GUI as interface between the user and the converting code. You can start the program by typing "Simbiology2Latex" in the Matlab console. The GUI looks like this:<br />
<br />
[[Image:Simbiology2Latex.png|center|GUI Preview]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1 ====<br />
The first thing you have to do is import the model. You can do this by clicking on the "Load Project File" button or by File > Load in the menu bar. After you imported the right model, you'll see some information about your project, like the project name, the number of compartments, reactions, ...<br />
<br />
==== Step 2 ====<br />
The second step is optional and consists of different substeps. With the button "Load Logo" you can import a logo (e.g. the team logo) that will be on the front page of your pdf-file. You can also give the name of the author, title and subtitle of the project.<br />
<br />
A result after step 1 and 2:<br />
[[Image:Simbiology2Latex_2.png|center|GUI Result]]<br />
<br />
==== Step 3 ====<br />
Push "RUN" to generate your TeX-file.<br />
<br />
==== Step 4 ====<br />
Open an Editor to convert the TeX-file into a pdf-file.<br />
<br />
== Problems ==<br />
<br />
*The formatted equations are sometimes too long.<br />
*There can only be one model in the project file. The first model will always the chosen one.<br />
<br />
== Remarks ==<br />
<br />
<html><center><div style="float:center;background:#5cc7dd;width:600px;height:170px" ><br />
<p><br />
The Simbiology2LaTeX Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the <a href="http://www.gnu.org/copyleft/gpl.html">GNU General Public License</a>, Simbiology2LaTeX Toolbox may not be used for commercial purposes without explicit written permission after contacting <a href="mailto:igem@kuleuven.be?SUBJECT=IGEM 2008:License Simbiology2LaTeX">igem@kuleuven.be</a>.<br />
</p><br />
<p> When reporting results obtained by Simbiology2LaTeX Toolbox, one should refer to </p><br />
<p> <center>iGEM2008/Team:KULeuven, Maarten Breckpot <br><br />
Simbiology2LaTeX Toolbox</center><br />
</p><br />
</div></center></html><br />
<br />
== File ==<br />
[https://static.igem.org/mediawiki/2008/9/9f/Simbiology2Latex.zip ZIP-file]<br />
<br />
== Features ==</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T14:53:12Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
[[Image:MCT Load.PNG|center]]<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
[[Image:MCT Reactions.PNG|center]]<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
[[Image:MCT Events.PNG|center]]<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
<html><center><div style="float:center;background:#5cc7dd;width:600px;height:170px" ><br />
<p><br />
The MultiCell Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the <a href="http://www.gnu.org/copyleft/gpl.html"> GNU General Public License</a>, MultiCell Toolbox may not be used for commercial purposes without explicit written permission after contacting <a href="mailto:igem@kuleuven.be?SUBJECT=IGEM 2008:License MultiCell Toolbox">igem@kuleuven.be</a>.<br />
</p><br />
<p> When reporting results obtained by MultiCell Toolbox, one should refer to </p><br />
<p> <center>iGEM2008/Team:KULeuven, Nick Van Damme <br><br />
MultiCell Toolbox </center><br />
</p><br />
</div></center></html><br />
<br />
== File ==<br />
<br />
[https://static.igem.org/mediawiki/2008/f/ff/MultiCell_Toolbox.zip Zip-File]<br />
<br />
To start the GUI: open GUI_start.fig or type GUI_start in MATLAB</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T14:51:03Z<p>Nickvd: /* Remarks */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
[[Image:MCT Load.PNG|center]]<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
[[Image:MCT Reactions.PNG|center]]<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
[[Image:MCT Events.PNG|center]]<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
<html><center><div style="float:center;background:#5cc7dd;width:600px;height:170px" ><br />
<p><br />
The MultiCell Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the GNU General Public License, MultiCell Toolbox may not be used for commercial purposes without explicit written permission after contacting <a href="mailto:igem@kuleuven.be?SUBJECT=IGEM 2008:License MultiCell Toolbox">igem@kuleuven.be</a>.<br />
</p><br />
<p> When reporting results obtained by MultiCell Toolbox, one should refer to </p><br />
<p> <center>iGEM2008/Team:KULeuven, Nick Van Damme <br><br />
MultiCell Toolbox </center><br />
</p><br />
</div></center></html><br />
<br />
== File ==<br />
<br />
[https://static.igem.org/mediawiki/2008/f/ff/MultiCell_Toolbox.zip Zip-File]<br />
<br />
To start the GUI: open GUI_start.fig or type GUI_start in MATLAB</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeXTeam:KULeuven/Software/Simbiology2LaTeX2008-09-09T14:50:07Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
We've written a small toolbox to convert the information in the Matlab Simbiology models to LaTeX-code. This code can be easily converted to a pdf-file with various open source programs (e.g. [http://www.texniccenter.org/index.php?id=20 TeXnicCenter for Windows]). The idea for this toolbox is based on the plugin [http://systems-biology.org/cd/plugins.html Squeezer] for CellDesigner.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
The program consists of GUI as interface between the user and the converting code. You can start the program by typing "Simbiology2Latex" in the Matlab console. The GUI looks like this:<br />
<br />
[[Image:Simbiology2Latex.png|center|GUI Preview]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1 ====<br />
The first thing you have to do is import the model. You can do this by clicking on the "Load Project File" button or by File > Load in the menu bar. After you imported the right model, you'll see some information about your project, like the project name, the number of compartments, reactions, ...<br />
<br />
==== Step 2 ====<br />
The second step is optional and consists of different substeps. With the button "Load Logo" you can import a logo (e.g. the team logo) that will be on the front page of your pdf-file. You can also give the name of the author, title and subtitle of the project.<br />
<br />
A result after step 1 and 2:<br />
[[Image:Simbiology2Latex_2.png|center|GUI Result]]<br />
<br />
==== Step 3 ====<br />
Push "RUN" to generate your TeX-file.<br />
<br />
==== Step 4 ====<br />
Open an Editor to convert the TeX-file into a pdf-file.<br />
<br />
== Problems ==<br />
<br />
*The formatted equations are sometimes too long.<br />
*There can only be one model in the project file. The first model will always the chosen one.<br />
<br />
== Remarks ==<br />
<br />
<html><center><div style="float:center;background:#5cc7dd;width:600px;height:170px" ><br />
<p><br />
The Simbiology2LaTeX Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the GNU General Public License, Simbiology2LaTeX Toolbox may not be used for commercial purposes without explicit written permission after contacting <a href="mailto:igem@kuleuven.be?SUBJECT=IGEM 2008:License Simbiology2LaTeX">igem@kuleuven.be</a>.<br />
</p><br />
<p> When reporting results obtained by Simbiology2LaTeX Toolbox, one should refer to </p><br />
<p> <center>iGEM2008/Team:KULeuven, Maarten Breckpot <br><br />
Simbiology2LaTeX Toolbox</center><br />
</p><br />
</div></center></html><br />
<br />
== File ==<br />
[https://static.igem.org/mediawiki/2008/9/9f/Simbiology2Latex.zip ZIP-file]<br />
<br />
== Features ==</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T14:46:50Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
[[Image:MCT Load.PNG|center]]<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
[[Image:MCT Reactions.PNG|center]]<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
[[Image:MCT Events.PNG|center]]<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
<html><center><div style="float:center;background:#5cc7dd;width:600px;height:170px" ><br />
<p><br />
The MultiCell Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the GNU General Public License, MultiCell Toolbox may not be used for commercial purposes without explicit written permission after contacting <a href="mailto:igem@kuleuven.be?SUBJECT=IGEM 2008">igem@kuleuven.be</a>.<br />
</p><br />
<p> When reporting results obtained by MultiCell Toolbox, one should refer to </p><br />
<p> <center>iGEM2008/Team:KULeuven, Nick Van Damme <br><br />
MultiCell Toolbox </center><br />
</p><br />
</div></center></html><br />
<br />
== File ==<br />
<br />
[https://static.igem.org/mediawiki/2008/f/ff/MultiCell_Toolbox.zip Zip-File]<br />
<br />
To start the GUI: open GUI_start.fig or type GUI_start in MATLAB</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T14:44:39Z<p>Nickvd: /* Remarks */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
[[Image:MCT Load.PNG|center]]<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
[[Image:MCT Reactions.PNG|center]]<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
[[Image:MCT Events.PNG|center]]<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
<html><div style="float:center;background:#5cc7dd;width:600px;height:170px" ><br />
<p><br />
The MultiCell Toolbox is made available for non commercial research purposes only under the GNU General Public License. However, notwithstanding any provision of the GNU General Public License, MultiCell Toolbox may not be used for commercial purposes without explicit written permission after contacting <a href="mailto:igem@kuleuven.be?SUBJECT=IGEM 2008">igem@kuleuven.be</a>.<br />
</p><br />
<p> When reporting results obtained by MultiCell Toolbox, one should refer to </p><br />
<p> iGEM2008/Team:KULeuven, Nick Van Damme </p><br />
<p> MultiCell Toolbox </p><br />
</p><br />
</div></html><br />
<br />
== File ==<br />
<br />
[https://static.igem.org/mediawiki/2008/f/ff/MultiCell_Toolbox.zip Zip-File]<br />
<br />
To start the GUI: open GUI_start.fig or type GUI_start in MATLAB</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T12:41:29Z<p>Nickvd: /* File */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
[[Image:MCT Load.PNG|center]]<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
[[Image:MCT Reactions.PNG|center]]<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
[[Image:MCT Events.PNG|center]]<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
3. Please refer to this page when using the MultiCell Toolbox.<br />
<br />
== File ==<br />
<br />
[https://static.igem.org/mediawiki/2008/f/ff/MultiCell_Toolbox.zip Zip-File]<br />
<br />
To start the GUI: open GUI_start.fig or type GUI_start in MATLAB</div>Nickvdhttp://2008.igem.org/File:MultiCell_Toolbox.zipFile:MultiCell Toolbox.zip2008-09-09T12:40:12Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/FullModelTeam:KULeuven/Model/FullModel2008-09-09T12:05:24Z<p>Nickvd: /* Extension to the previous model */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
<div style="float:right"><html><br />
<object width="250" height="250" ><br />
<param name="movie" value="docbl.swf"><br />
<embed src="https://static.igem.org/mediawiki/2008/c/ca/Docbl.swf" width="250" height="250" wmode="transparent"><br />
</embed><br />
</object><br />
</html><br />
</div><br />
<br />
== Full Model ==<br />
<br />
=== Describing the system ===<br />
<br />
Dr. Coli produces a green fluorescent protein (drug) when it senses INPUT (certain disease signal in the human body). When Dr. Coli doesn't sense any INPUT anymore (the patient is cured), the invertimer will function as a molecular timer, counting towards the doctor's own demise: ccdB induced cell death. When INPUT (disease signal) reappers in time, the timer is reset. A filter ensures that the timer is not reset when only “noisy” INPUT signals are sensed. A memory device (stable switch) is included to ensure the clock only starts ticking when it is activated by the first input signal. <br />
<br />
==== ODE's ====<br />
<br />
<html><br />
<body><br />
<p><br />
<a href="https://static.igem.org/mediawiki/2008/7/73/Total.pdf"><br />
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60"><br />
</a><br />
</p><br />
</body><br />
</html><br />
<br />
==== Parameters ====<br />
The parameters can be found in the sections about the simple parts of the system.<br />
<br />
=== Models ===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/6/66/Total_CellDesigner.zip SBML file]) ====<br />
[[Image:Total_CellDesigner.png|center|800px]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/5/5b/FullModel.sbproj.zip file]) ====<br />
[[Image:Final matlab.png|950px|center|Model]]<br />
<br />
=== Simulations ===<br />
<br />
[[Image:SystemInWork.png|850px|center]]<br />
<br />
Discussion of the simulation:<br />
<br />
* In the beginning the memory has status "0" and the simulation clearly shows that the timer isn't activated. This means that the bacteria can grow without any problem (no ccdB-production and hence no cell death) when they haven't sensed any desease marker in the beginning.<br />
* At t=50.000s the system is activated by a long lightpulse (simulating the insertion of the bacteria in the patient's body and sensing desease marker for the first time). This results in:<br />
** switching of the memory to status "1" --> activation of transcription of LuxR (green curve)<br />
** activation of the filter (desease marker is strong enough) which is reflected by the production of lactonase (blue curve), situated just after the filter mechanism.<br />
* At t=75.000 the lightpulse is switched of (simulating that there's no more desease marker: the patient is cured). This results in:<br />
** stopping the production of lactonase, which starts to degrade naturally (blue curve)<br />
** stopping the production of LacI, which stops repressing the transcription of LuxI. In this way HSL can be produced, but, since there's still lactonase present in the cell, there won't be a visible increase in HSL-LuxR-complex because the HSL is being transformed into hydroxyacid.<br />
* At t~=92.000 the lactonase is almost totally degraded which enables the HSL to form a complex with LuxR (yellow curve). This means that we have a timer that starts with a delay of +- 17.000s. At this point the HSL-LuxR-complex really starts to build up gradually (TIMER) for about 10.000s.<br />
* At t~=102.000s the HSL-LuxR-complex peaks, with at the same time (free) LuxR decreasing to almost zero. <br />
**At this point all the newly produced LuxR will go into complex with HSL and no free LuxR will remain. From this point on, the HSL-LuxR-complex will decrease to a steady state value which is equal to the production rate of LuxR-proteins. <br />
** BUT you can see clearly that the ccdB (red curve) also peaks (to a value of 10 to 20 molecules) which is enough to result in cell death.<br />
<br />
== Full Model - Part 2 ==<br />
<br />
=== Extension to the previous model ===<br />
<br />
During the summer we changed a lot of things to our grand scheme. This new system has quite some novelties:<br />
<br />
* Cell Death has also gotten an overhaul. Transcription now begins at a new hybrid promoter we made: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K145150 '''BBa_K145150''']. This promoter is repressed by c2 P22, which is produced by the memory in the OFF state, making premature activation and cell death impossible. Besides this repression, the promoter is activated by the HSL-LuxR complex originating from a previously activated timer. The promoter behaves as shown schematically below. <br />
<br />
[[Image:Hybrid_promotor.PNG|center]]<br />
<br />
* Second, LuxR is now no longer constitutively produced but is placed behind the beforementioned hybrid promoter. This construction mimicks more closely the natural system where LuxR is upregulated when a threshold amount of HSL is present. Plus it also increases the time it takes to activate ccdB, lengthening the timer. The system will now auto-activate if enough HSL is present and the memory is in the ON state.<br />
<br />
* Third, the ccdB coding region is also downstream of the hybrid promoter and is thus also subject to the regulation explained above; c2 P22 repression and HSL-LuxR auto-activation. One difference is that the polymerase must first read through a bad terminator with about 60% efficiency before reaching this coding region. Another difference is in the ribosome binding sites preceding both coding regions. Where LuxR can be translated from a RBS with a relative efficiency of 1.00, the ccdB frame can only be read from a 0.01 efficiency RBS.<br />
<br />
Because of this new organisation, we've also turned our attention towards [https://2008.igem.org/Team:KULeuven/Model/MultiCell multi cell] interactions and [https://2008.igem.org/Team:KULeuven/Model/Diffusion diffusion] of HSL in the medium again.<br />
<br />
=== Describing the system ===<br />
<br />
==== ODE's ====<br />
<br />
todo!!!<br />
<br />
==== Parameters ====<br />
The parameters can be found in the sections about the simple parts of the system.<br />
<br />
Extension: parameters of HSL-LuxR auto-activation can be found in [https://2008.igem.org/Team:KULeuven/Model/CellDeath#Extensions_to_previous_system Model:New Cell Death].<br />
<br />
=== Models ===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/c/c2/Total_CellDesigner2.zip SBML file])====<br />
[[Image:TotalSystem celldesigner2.png|center|900px]]<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/f/fd/FullModel2.sbproj.zip file]) ====<br />
[[Image: NewTot.png|center|900px]]<br />
<br />
=== Simulations ===</div>Nickvdhttp://2008.igem.org/Talk:Team:KULeuven/Model/FullModelTalk:Team:KULeuven/Model/FullModel2008-09-09T12:05:16Z<p>Nickvd: New page: * First of all, the parameters were reinvestigated and doublechecked since errors can have large effects as we've learned throughout this summer. * Second, we decided to upgrade our filte...</p>
<hr />
<div>* First of all, the parameters were reinvestigated and doublechecked since errors can have large effects as we've learned throughout this summer.<br />
<br />
* Second, we decided to upgrade our filter to contain a more efficient key-lock system. We finally found these parts after seriously digging through the [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain Berkeley 2006 pages] and the [http://partsregistry.org/Main_Page Registry]. This new system with its improved efficiency can be seen reflected in the parameters of the new key-lock system.</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/FullModelTeam:KULeuven/Model/FullModel2008-09-09T12:02:37Z<p>Nickvd: /* Sensitivity Analysis */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
<div style="float:right"><html><br />
<object width="250" height="250" ><br />
<param name="movie" value="docbl.swf"><br />
<embed src="https://static.igem.org/mediawiki/2008/c/ca/Docbl.swf" width="250" height="250" wmode="transparent"><br />
</embed><br />
</object><br />
</html><br />
</div><br />
<br />
== Full Model ==<br />
<br />
=== Describing the system ===<br />
<br />
Dr. Coli produces a green fluorescent protein (drug) when it senses INPUT (certain disease signal in the human body). When Dr. Coli doesn't sense any INPUT anymore (the patient is cured), the invertimer will function as a molecular timer, counting towards the doctor's own demise: ccdB induced cell death. When INPUT (disease signal) reappers in time, the timer is reset. A filter ensures that the timer is not reset when only “noisy” INPUT signals are sensed. A memory device (stable switch) is included to ensure the clock only starts ticking when it is activated by the first input signal. <br />
<br />
==== ODE's ====<br />
<br />
<html><br />
<body><br />
<p><br />
<a href="https://static.igem.org/mediawiki/2008/7/73/Total.pdf"><br />
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60"><br />
</a><br />
</p><br />
</body><br />
</html><br />
<br />
==== Parameters ====<br />
The parameters can be found in the sections about the simple parts of the system.<br />
<br />
=== Models ===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/6/66/Total_CellDesigner.zip SBML file]) ====<br />
[[Image:Total_CellDesigner.png|center|800px]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/5/5b/FullModel.sbproj.zip file]) ====<br />
[[Image:Final matlab.png|950px|center|Model]]<br />
<br />
=== Simulations ===<br />
<br />
[[Image:SystemInWork.png|850px|center]]<br />
<br />
Discussion of the simulation:<br />
<br />
* In the beginning the memory has status "0" and the simulation clearly shows that the timer isn't activated. This means that the bacteria can grow without any problem (no ccdB-production and hence no cell death) when they haven't sensed any desease marker in the beginning.<br />
* At t=50.000s the system is activated by a long lightpulse (simulating the insertion of the bacteria in the patient's body and sensing desease marker for the first time). This results in:<br />
** switching of the memory to status "1" --> activation of transcription of LuxR (green curve)<br />
** activation of the filter (desease marker is strong enough) which is reflected by the production of lactonase (blue curve), situated just after the filter mechanism.<br />
* At t=75.000 the lightpulse is switched of (simulating that there's no more desease marker: the patient is cured). This results in:<br />
** stopping the production of lactonase, which starts to degrade naturally (blue curve)<br />
** stopping the production of LacI, which stops repressing the transcription of LuxI. In this way HSL can be produced, but, since there's still lactonase present in the cell, there won't be a visible increase in HSL-LuxR-complex because the HSL is being transformed into hydroxyacid.<br />
* At t~=92.000 the lactonase is almost totally degraded which enables the HSL to form a complex with LuxR (yellow curve). This means that we have a timer that starts with a delay of +- 17.000s. At this point the HSL-LuxR-complex really starts to build up gradually (TIMER) for about 10.000s.<br />
* At t~=102.000s the HSL-LuxR-complex peaks, with at the same time (free) LuxR decreasing to almost zero. <br />
**At this point all the newly produced LuxR will go into complex with HSL and no free LuxR will remain. From this point on, the HSL-LuxR-complex will decrease to a steady state value which is equal to the production rate of LuxR-proteins. <br />
** BUT you can see clearly that the ccdB (red curve) also peaks (to a value of 10 to 20 molecules) which is enough to result in cell death.<br />
<br />
== Full Model - Part 2 ==<br />
<br />
=== Extension to the previous model ===<br />
<br />
During the summer we changed a lot of things to our grand scheme. This new system has quite some novelties.<br />
<br />
* First of all, the parameters were reinvestigated and doublechecked since errors can have large effects as we've learned throughout this summer.<br />
<br />
* Second, we decided to upgrade our filter to contain a more efficient key-lock system. We finally found these parts after seriously digging through the [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain Berkeley 2006 pages] and the [http://partsregistry.org/Main_Page Registry]. This new system with its improved efficiency can be seen reflected in the parameters of the new key-lock system.<br />
<br />
* Cell Death has also gotten an overhaul. Transcription now begins at a new hybrid promoter we made: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K145150 '''BBa_K145150''']. This promoter is repressed by c2 P22, which is produced by the memory in the OFF state, making premature activation and cell death impossible. Besides this repression, the promoter is activated by the HSL-LuxR complex originating from a previously activated timer. The promoter behaves as shown schematically below. <br />
<br />
[[Image:Hybrid_promotor.PNG|center]]<br />
<br />
* Fourth, LuxR is now no longer constitutively produced but is placed behind the beforementioned hybrid promoter. This construction mimicks more closely the natural system where LuxR is upregulated when a threshold amount of HSL is present. Plus it also increases the time it takes to activate ccdB, lengthening the timer. The system will now auto-activate if enough HSL is present and the memory is in the ON state.<br />
<br />
* The ccdB coding region is also downstream of the hybrid promoter and is thus also subject to the regulation explained above; c2 P22 repression and HSL-LuxR auto-activation. One difference is that the polymerase must first read through a bad terminator with about 60% efficiency before reaching this coding region. Another difference is in the ribosome binding sites preceding both coding regions. Where LuxR can be translated from a RBS with a relative efficiency of 1.00, the ccdB frame can only be read from a 0.01 efficiency RBS.<br />
<br />
* Because of this new organisation, we've also turned our attention towards [https://2008.igem.org/Team:KULeuven/Model/MultiCell multi cell] interactions and [https://2008.igem.org/Team:KULeuven/Model/Diffusion diffusion] of HSL in the medium again.<br />
<br />
=== Describing the system ===<br />
<br />
==== ODE's ====<br />
<br />
todo!!!<br />
<br />
==== Parameters ====<br />
The parameters can be found in the sections about the simple parts of the system.<br />
<br />
Extension: parameters of HSL-LuxR auto-activation can be found in [https://2008.igem.org/Team:KULeuven/Model/CellDeath#Extensions_to_previous_system Model:New Cell Death].<br />
<br />
=== Models ===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/c/c2/Total_CellDesigner2.zip SBML file])====<br />
[[Image:TotalSystem celldesigner2.png|center|900px]]<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/f/fd/FullModel2.sbproj.zip file]) ====<br />
[[Image: NewTot.png|center|900px]]<br />
<br />
=== Simulations ===</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/Cell_DeathTeam:KULeuven/Model/Cell Death2008-09-09T12:01:58Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<div style="float: right;">[[Image:pictogram_celldeath.png|120px]]</div><br />
<br />
==Cell Death==<br />
<br />
=== Position in the system ===<br />
<br />
The Cell Death subsystem receives input from two other subsystems, namely:<br />
<br />
* [[Team:KULeuven/Model/Inverter | Inverter]]<br />
* [[Team:KULeuven/Model/Pulse_Generator | Pulse Generator]]<br />
<br />
LuxR is the component repressing the regulation of CcdB, the toxic product causing cell death. There the LuxR production is constitutive, no protein controls the gene regulation of LuxR, but the amount of LuxR available to repress the transcripion of the CcdB gene is controlled by HSL (Homoserine lactone).<br />
<br />
If the inverter subsystem produces HSL (occurs when no light is detectable), this will forms a complex with LuxR. This will diminish the amount of LuxR available to repress the CcdB transcription and initiate cell death. When waiting long enough the amount of HSL becomes critical.<br />
<br />
If however the pulse generator becomes active (by the filter), it will produce a pulse of lactonase, which will then bind to the HSL, reacting to an hydroxy-acid. As opposed to HSL, this hydroxy-acid will no longer form a complex with LuxR. This increase in LuxR lowers the CcdB production. The challenge is to generate a pulse of lactonase high enough to neutralise all HSL present in the cell.<br />
<br />
=== Describing the system ===<br />
<br />
[[Image:Cell_Death.jpg|center]]<br />
<br />
==== ODE's ====<br />
<br />
<html><br />
<body><br />
<p><br />
<a href="https://static.igem.org/mediawiki/2008/b/b8/Celldeath.pdf"><br />
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60"><br />
</a><br />
</p><br />
</body><br />
</html><br />
<br />
==== Parameters ====<br />
Remark: update parameters to repressive promotor<br />
{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"<br />
|+ ''Parameter values (Cell Death)''<br />
! width=15% | Name<br />
! width=15% | Value<br />
! width=40% | Comments<br />
! width=10% | Reference<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates<br />
|-<br />
| d<sub>LuxR</sub><br />
| 0.0010 s<sup>-1</sup><br />
|<br />
| <br />
|-<br />
| d<sub>LuxR_HSL</sub><br />
| 0.0010 s<sup>-1</sup><br />
| complex of HSL and LuxR degrades, giving back HSL<br />
|<br />
|-<br />
| d<sub>RNA_LuxR</sub><br />
| 0.00227 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>CcdB</sub><br />
| 7.7E-5 s<sup>-1</sup><br />
| <br />
| [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]<br />
|-<br />
| d<sub>RNA_CcdB</sub><br />
| 0.00231 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>HSL</sub><br />
| 1.02E-6 s<sup>-1</sup><br />
| <br />
| [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Association/Dissociation/Reaction Rates<br />
|-<br />
| k<sub>ass</sub> (HSL+LuxR)<br />
| 1E6 s<sup>-1</sup><br />
| association rate of HSL with LuxR. Chosen to be relatively (to the other rate constants) high and such that K<sub>diss</sub> (HSL + LuxR) equals 10<sup>-6</sup><br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL+LuxR)<br />
| 1 s<sup>-1</sup><br />
| dissociation rate of the HSL-LuxR complex<br />
| <br />
|-<br />
| k<sub>ass</sub> (HSL+lactonase)<br />
| 1E6 s<sup>-1</sup><br />
| association rate of HSL with lactonase<br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL+lactonase)<br />
| 446.5 s<sup>-1</sup><br />
| dissociation rate of the HSL-lactonase complex<br />
| <br />
|-<br />
| k<sub>cat</sub> (HSL:hydroxy-acid)<br />
| 29 s<sup>-1</sup><br />
| catalytic transformation of HSL to an hydroxy-acid, lactonase is the enzyme<br />
| [http://www.jbc.org/cgi/reprint/M311194200v1.pdf link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Constants<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 1E-6 [M]/L<br />
| k<sub>diss</sub> / k<sub>ass</sub> (HSL+LuxR)<br />
| [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 4.05E-6 [M]/L<br />
| binding HSL_LuxR on LuxPromotor<br />
| [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Hill Cooperativity<br />
|-<br />
| n<sub>HSL_LuxR</sub><br />
| 2.08<br />
| <br />
| [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription Rates<br />
|-<br />
| k<sub>mRNA_LuxR</sub> (constitutive promotor)<br />
| 0.025 s<sup>-1</sup><br />
| see [[Team:KULeuven/Model/KineticConstants#Constitutive_promoters | Constitutive Promotors & E. coli transcription Rates]]<br />
|<br />
|-<br />
| k<sub>mRNA_CcdB</sub><br />
| 0.025 s<sup>-1</sup><br />
| maximal transcription rate for CcdB RNA (no LuxR repressor present)<br />
| <br />
|-<br />
|}<br />
<br />
[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6T39-3Y6HKD6-BK-1&_cdi=4941&_user=877992&_orig=search&_coverDate=08%2F30%2F1995&_sk=998379998&view=c&wchp=dGLbVtz-zSkzS&md5=49efd14150c71e668eabdef225220ce3&ie=/sdarticle.pdf This paper] says that synthesis of even a few molecules of the shorter CcdB protein is probably lethal.<br />
<br />
=== Models ===<br />
<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/3/37/CellDeath_CellDesigner.zip SBML file])====<br />
<br />
[[Image:CellDeath_CellDesigner.png|600px|center|Cell Death]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/4/45/CellDeath_Matlab.zip SBML file])====<br />
Remark: not yet up to date to latest (final) version <br />
[[Image:CellDeath_Matlab.jpg|600px|center|Cell Death]]<br />
<br />
== New Cell Death==<br />
<br />
===Extensions to previous system===<br />
<br />
* During the summer we switched from the above system to a new one which you can see just below, take a look at this figure as it will help you understand the regulation that is present. This new system has a few novelties. First of all, transcription begins at a new hybrid promoter we made: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K145150 '''BBa_K145150''']. This promoter is repressed by c2 P22, which is produced by the memory in the OFF state, making premature activation and cell death impossible. Besides this repression, the promoter is activated by the HSL-LuxR complex originating from a previously activated timer. The promoter behaves as shown schematically below. <br />
<br />
[[Image:Hybrid_promotor.PNG|center]]<br />
<br />
* Second, LuxR is now no longer constitutively produced but is placed behind the beforementioned hybrid promoter. This construction mimicks more closely the natural system where LuxR is upregulated when a threshold amount of HSL is present. Plus it also increases the time it takes to activate ccdB, lengthening the timer. The system will now auto-activate if enough HSL is present and the memory is in the ON state.<br />
<br />
* Third, the ccdB coding region is also downstream of the hybrid promoter and is thus also subject to the regulation explained above; c2 P22 repression and HSL-LuxR auto-activation. One difference is that the polymerase must first read through a bad terminator with about 60% efficiency before reaching this coding region. Another difference is in the ribosome binding sites preceding both coding regions. Where LuxR can be translated from a RBS with a relative efficiency of 1.00, the ccdB frame can only be read from a 0.01 efficiency RBS.<br />
<br />
===Describing the system===<br />
see also: [https://2008.igem.org/Team:KULeuven/Project/CellDeath Project:Cell Death]<br />
<br />
[[Image:Cell_Death_new.jpg|center]]<br />
<br />
====ODE's====<br />
<br />
todo!!!<br><br />
<br />
==== Parameters ====<br />
{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"<br />
|+ ''Parameter values (Cell Death)''<br />
! width=15% | Name<br />
! width=15% | Value<br />
! width=40% | Comments<br />
! width=10% | Reference<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates<br />
|-<br />
| d<sub>LuxR</sub><br />
| 9.627044174E-5 s<sup>-1</sup><br />
| no LVA tag, so longer lifetime<br />
| <br />
|-<br />
| d<sub>complex</sub><br />
| 9.627044174E-5 s<sup>-1</sup><br />
| complex of HSL and LuxR degrades, giving back HSL<br />
|<br />
|-<br />
| d<sub>RNA_LuxR</sub><br />
| 0.00227 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>ccdB</sub><br />
| 7.7E-5 s<sup>-1</sup><br />
| stable in the absence of ccdA<br />
| [http://www.ncbi.nlm.nih.gov/pubmed/8022284?dopt=abstract link]<br />
|-<br />
| d<sub>RNA_ccdB</sub><br />
| 0.00231 s<sup>-1</sup><br />
| <br />
| [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link]<br />
|-<br />
| d<sub>HSL</sub><br />
| 1.02E-6 s<sup>-1</sup><br />
| very stable in the medium, average lifetime of 185h<br />
| [http://aem.asm.org/cgi/content/abstract/71/3/1291 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Association/Dissociation/Reaction Rates<br />
|-<br />
| k<sub>ass</sub> (HSL+LuxR)<br />
| 0.002372 s<sup>-1</sup><br />
| association rate of HSL with LuxR (estimate from K<sub>M</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL-LuxR)<br />
| 1.0 s<sup>-1</sup><br />
| dissociation rate of the HSL-LuxR complex (estimate from K<sub>M</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>ass</sub> (HSL+lactonase)<br />
| 0.002372 s<sup>-1</sup><br />
| association rate of HSL with lactonase (estimate from K<sub>M</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>diss</sub> (HSL-lactonase)<br />
| 4470.0 s<sup>-1</sup><br />
| dissociation rate of the HSL-lactonase complex (estimate from K<sub>d</sub> but recalculated to remove molar dimension)<br />
| <br />
|-<br />
| k<sub>cat</sub> (HSL>>hydroxy-acid)<br />
| 29 s<sup>-1</sup><br />
| lactonase catalyzed transformation of HSL to a hydroxy-acid<br />
| [http://www.jbc.org/cgi/reprint/M311194200v1.pdf link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Dissociation Constants<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 1E-6 [M]<br />
| HSL binding to LuxR<br />
| [http://jb.asm.org/cgi/content/full/189/11/4127?view=long&pmid=17400743 link]<br />
|-<br />
| K<sub>HSL_LuxR-promoter</sub><br />
| 4.05E-6 [M]<br />
| binding of HSL_LuxR complex to the Lux Promotor<br />
| [http://parts.mit.edu/igem07/index.php/Tokyo/AHL_assay link]<br />
|-<br />
| K<sub>HSL_lactonase</sub><br />
| 4.47E-3 [M]<br />
| K<sub>M</sub> of lactonase with 3OC6HSL<br />
| [http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Hybrid Promoter<br />
|-<br />
| K<sub>C2 P22</sub><br />
| 2.6E-10 [M]<br />
| Dissociation constant for P22 c2 promoter binding<br />
| [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&firstpage=10536&resourcetype=HWCIT link]<br />
|-<br />
| K<sub>HSL_LuxR</sub><br />
| 4.05E-6 [M]<br />
| Dissociation constant for HSL-LuxR complex promoter binding<br />
| [http://jb.asm.org/cgi/content/abstract/JB.01443-07v1 link]<br />
|-<br />
| Hill<br />
| 2<br />
| Hill coefficient for P22 c2 binding<br />
| [http://www.jbc.org/cgi/content/abstract/258/17/10536?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&firstpage=10536&resourcetype=HWCIT link]<br />
|-<br />
| k<sub>leaky</sub><br />
| 5E-4 s<sup>-1</sup><br />
| transcription rate from the hybrid promoter in the '''unactivated''' ON state<br />
|<br />
|-<br />
| k<sub>max</sub><br />
| 0.0030 s<sup>-1</sup><br />
| maximal transcription rate for the fully activated ON hybrid promoter (might be higher)<br />
|<br />
|-<br />
| Terminator eff<br />
| 60.8%<br />
| percentage of transcription termination at the B0014 double terminator in front of ccdB<br />
| [http://partsregistry.org/Part:BBa_B0014 link]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates<br />
|-<br />
| k<sub>LuxR translation</sub><br />
| 0.556 s<sup>-1</sup><br />
| Translation rate for LuxR, B0034 RBS (relative efficiency 1.0)<br />
| [http://partsregistry.org/Part:BBa_B0034 link]<br />
|-<br />
| k<sub>ccdB translation</sub><br />
| 0.00556 s<sup>-1</sup><br />
| Translation rate for ccdB, B0033 RBS (relative efficiency 0.01)<br />
| [http://partsregistry.org/Part:BBa_B0033 link]<br />
|}<br />
<br />
===Models===<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/1/14/Celldeath_CellDesigner_final.zip SBML file])====<br />
<br />
[[Image:CellDeath_CellDesigner_new.png|800px|center|Cell Death]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/3/36/CellDeath_Matlab_Final.zip SBML file])====<br />
<br />
[[Image:CellDeath_Matlab_Final.jpg|800px|center|Cell Death]]<br />
<br />
=== Simulations ===<br />
<br />
To simulate the cell death, the input signal TetR is all the time low (5E-5) except from 50000 till 80000 seconds,from 180000 till 190000 seconds and from 250000 till 270000 seconds (0.0125). The left figure shows us that a high input signal will lower the amount of HSL (the HSL will be converted into hydroxy acid by lactonase). This will increase the amount of free LuxR because there is not enough HSL to form the HSL-LuxR complex. During the pulse, the right figure shows us an increase of the amount of CcdB. Whenthe memory switches from state zero to state one, the amount of CIIP22 decreases which makes it possible to produce a small amount of CcdB (background signal). <br><br />
When the input signal is low again, the amount of HSL increases. This extra HSL will form with LuxR the complex which lowers the amount of free LuxR. The higher amount of the complex promotes the production of CcdB which increases to a (hopefully) deathly level. <br><br />
A new pulse lowers the amount of HSL and the complex and increases the amount of LuxR for the same reasons as before. The second pulse is smal in length and decreases the amount of CcdB only partially. The third pulse is long enough for a total reset of the entire system.<br />
<br />
<html><br />
<div class="center"><br />
<div class="noborder" style="overflow: auto; width: 800px; height: 420px;"><br />
<div class="noborder" style="width: 1250px;"> <br />
<img src="https://static.igem.org/mediawiki/2008/f/f4/Sim_celldeath.png" style="float: left; width: 600px; height: 400px; margin: 0 5px;" /><br />
<img src="https://static.igem.org/mediawiki/2008/9/9f/Sim_celldeath_total_2.png" style="float: left; width: 600px; height: 400px; margin: 0 5px;" /><br />
</div></div></div></html></div>Nickvdhttp://2008.igem.org/Talk:Team:KULeuven/Model/InverterTalk:Team:KULeuven/Model/Inverter2008-09-09T12:01:08Z<p>Nickvd: New page: === Sensitivity Analysis === center</p>
<hr />
<div>=== Sensitivity Analysis ===<br />
<br />
[[Image:Sens Inverter.png|center]]</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/InverterTeam:KULeuven/Model/Inverter2008-09-09T12:00:57Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
<div style="float: right;">[[Image:pictogram_inverter.png|120px]]</div><br />
==Invertimer==<br />
<br />
=== Position in the system ===<br />
<br />
The invertimer subsystem receives its input from the filter, T7. The invertimer's function is to '''produce''' HSL when '''no''' input is present, so a low T7 input gives rise to a high HSL output and vice versa. The production of HSL means that the cell will start a timer that eventually will be used in the celldeath-subsystem to produce ccdB. In this way the cell will die off if no desease remains present.<br />
<br />
=== Describing the system ===<br />
see also: [https://2008.igem.org/Team:KULeuven/Project/Inverter Project:Invertimer]<br />
<br />
[[Image:Inverter_BioBrick.jpg|center]]<br />
<br />
==== ODE's ====<br />
<br />
<html><br />
<body><br />
<p><br />
<a href="https://static.igem.org/mediawiki/2008/b/be/Inverter.pdf"><br />
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60"><br />
</a><br />
</p><br />
</body><br />
</html><br />
<br />
==== Parameters ====<br />
<br />
{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"<br />
|+ ''Parameter values (Inverter)''<br />
! width=15% | Name<br />
! width=15% | Value<br />
! width=40% | Comments<br />
! width=10% | Reference<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation Rates<br />
|- <br />
| d<sub>LuxI</sub><br />
| d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup><br />
| LVA-tag reduces lifetime to 40 minutes<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html> [7<html>]</html>]<br />
|-<br />
| d<sub>RNA_LuxI</sub><br />
| 0.0025 s<sup>-1</sup><br />
| <br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [5<html>]</html>]<br />
|-<br />
| d<sub>LuxI_antimRNA</sub><br />
| 0.0045303737 s<sup>-1</sup><br />
| estimate: because this RNA isn't translated, it degrades faster <br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [5<html>]</html>]<br />
|-<br />
| d<sub>LacI</sub><br />
| d<sub>LVA</sub> = 2.814E-4 s<sup>-1</sup><br />
| LVA-tag reduces lifetime to 40 minutes<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html> [7<html>]</html>]<br />
|-<br />
| d<sub>closed mRNA LacI</sub><br />
| 0.0046209812 s<sup>-1</sup><br />
| estimate: because this mRNA isn't translated, it degrades faster <br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [5<html>]</html>]<br />
|-<br />
| d<sub>open mRNA LacI</sub><br />
| 0.0023104906 s<sup>-1</sup><br />
| <br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [5<html>]</html>]<br />
|-<br />
| d<sub>open mRNA LacI complex</sub><br />
| 0.0023104906 s<sup>-1</sup><br />
| <br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [5<html>]</html>]<br />
|-<br />
| d<sub>HSL</sub><br />
| 1.02E-6 s<sup>-1</sup><br />
| very stable in the medium, lifetime around 185h<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [11<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | LuxI catalysis<br />
|-<br />
| k<sub>cat</sub><br />
| 0.0166666667 s<sup>-1</sup><br />
| Estimated to be about 90% of V<sub>max</sub> in LB medium.<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [4<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | T7 Transcription<br />
|-<br />
| K<sub>T7</sub><br />
| 421<br />
| dissociation constant, recalculated to remove units<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [10<html>]</html>]<br />
|-<br />
| k<sub>max</sub><br />
| 0.044 s<sup>-1</sup><br />
| maximal T7 transcription rate<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [10<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Key-Lock constants<br />
|-<br />
| K<sub>eq 1</sub><br />
| 0,015 [M]<br />
| between closed and open T7 mRNA, modeled for competition, experimental<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html>]<br />
|-<br />
| K<sub>eq 2</sub><br />
| 0.0212 [M]<br />
| between closed T7 mRNA and key unlocked mRNA complex, modeled for competition, experimental<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html>]<br />
|-<br />
| k<sub>dis2</sub><br />
| 0.00416 s<sup>-1</sup><br />
| derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html>]<br />
|-<br />
| k<sub>complex2</sub><br />
| 0.00237 s<sup>-1</sup><br />
| derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html>]<br />
|-<br />
| k<sub>closed</sub><br />
| 500 s<sup>-1</sup><br />
| derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html>]<br />
|-<br />
| k<sub>open</sub><br />
| 7.5 s<sup>-1</sup><br />
| derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | LacI repression<br />
|-<br />
| K<sub>LacI</sub><br />
| 1.0E-10 M<sup>-1</sup><br />
| Dissociation constant<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [3<html>]</html>]<br />
|- <br />
| n<sub>LacI</sub><br />
| 2.0<br />
| Hill coefficient for LacI<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [3<html>]</html>]<br />
|-<br />
| k_trans_LacI <br />
| 0.0025 s<sup>-1</sup><br />
| Estimated maximal transcription rate from R0011<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [9<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Antisense LuxI<br />
|-<br />
| k_complex3<br />
| 0.00237 s<sup>-1</sup><br />
| rate constant for formation of asRNA - LuxI mRNA duplex<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [3<html>]</html>]<br />
|-<br />
| K<sub>mRNA_LuxI:antisense_mRNA</sub><br />
| 4.22E14 <br />
| Complex of LuxI mRNA with antisense mRNA<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [1<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Translation Rates<br />
|-<br />
| k<sub>transl LuxI</sub><br />
| 0.167 s<sup>-1</sup><br />
| translation rate for B0032 RBS (0.3 relative efficiency)<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [8<html>]</html>]<br />
|-<br />
| k<sub>transl LacI</sub><br />
| 0.167 s<sup>-1</sup><br />
| lock defined translation rate for LacI<br />
| [https://2008.igem.org/Team:KULeuven/Model/Inverter#References [2<html>]</html>]<br />
|}<br />
<br />
=== Models ===<br />
<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/9/9e/Inverter_CellDesigner.zip SBML file])====<br />
<br />
[[Image:Inverter_CellDesigner.png|800px|center|Inverter]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/0/00/Inverter_Matlab.zip SBML file])====<br />
[[Image:Inverter_Matlab.jpg|700px|center|Inverter]]<br />
<br />
=== Simulations ===<br />
<br />
{| class="wikitable"<br />
|-<br />
! Time span<br />
! Input (TetR)<br />
! Results<br />
|-<br />
| A<br />
| 0.0125<br />
| The amount LacI increases from state zero to state one because both mRNA_RIBOKEY and pT7_tag are present. This results in a repression of LuxI which decreases to zero: the input signal (TetR) is inverted. <br />
|-<br />
| B<br />
| 5E-5<br />
| The amount LacI decreases back to state zero. The amount LuxI remains the same (state zero). <br />
|-<br />
| C<br />
| 5E-5<br />
| LuxI changes from state zero to state one. Time span B and C form together the transient behaviour of the inverter when the input signal changes from one to zero.<br />
|-<br />
| D<br />
| 5E-5<br />
| LuxI remains in state one: the input signal is once again inverted.<br />
|-<br />
| E<br />
| 0.0125<br />
| A short pulse of 1000 seconds has a influence a steep decrease of LuxI.<br />
|-<br />
| F & G<br />
| 5E-5<br />
| During time span F and G, LuxI decreases further for a while and increases back to state one.<br />
|-<br />
| H<br />
| 5E-5<br />
| LuxI is back in state one.<br />
|}<br />
<br />
The simulation shows a working inverter (left figure). A small disadvantage is the transient behaviour of the inverter: a small pulse of 1000 seconds results in a transient behaviour of +- 30000 seconds. Also for a long pulse (10000 seconds) is a long transient behaviour noticeable (40000 seconds). The effect of the inverter on the timer aspect is visuable in the right figure: a long pulse ( from 10000 till 11000) resets the timer (HSL drecreases till zero). After this pulse and the transient behaviour of the inverter, the timer restarts counting. The short pulse (from 200000 till 201000 seconds) only partially resets the timer.<br />
<br />
<html><br />
<div class="center"><br />
<div class="noborder" style="overflow: auto; width: 800px; height: 520px;"><br />
<div class="noborder" style="width: 1200px;"> <br />
<img src="https://static.igem.org/mediawiki/2008/d/d1/Sim_inverter_1.png" style="float: left; width: 550px; height: 500px; margin: 0 5px;" /><br />
<img src="https://static.igem.org/mediawiki/2008/2/27/HSL.png" style="float: left; width: 600px; height: 500px; margin: 0 5px;" /><br />
</div></div></div></html><br />
<br />
=== References ===<br />
<br />
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/><br />
<title>Bibliography</title><br />
</head><br />
<body><br />
<table style="border-collapse:collapse;line-height:1.1em;"><br />
<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">A. E G H Wagner and R W Simons, “Antisense RNA Control in Bacteria, Phages, and Plasmids,” Nov. 2003; http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.mi.48.100194.003433.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">“Berkeley2006-RiboregulatorsMain - IGEM”; http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<br />
<tr style="vertical-align:top;"><td>[3]</td><td style="padding-left:4pt;">“ETHZ/Parameters - IGEM07”; http://parts.mit.edu/igem07/index.php/ETHZ/Parameters.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">“Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein,” Sep. 1996; http://www.pnas.org/content/93/18/9505.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[5]</td><td style="padding-left:4pt;">J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” <span style="font-style:italic;">Proceedings of the National Academy of Sciences of the United States of America</span>, vol. 99, Jul. 2002, pp. 9697–9702. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1073/pnas.112318199&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Global%20analysis%20of%20mRNA%20decay%20and%20abundance%20in%20Escherichia%20coli%20at%20single-gene%20resolution%20using%20two-color%20fluorescent%20DNA%20microarrays&amp;rft.jtitle=Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20of%20the%20United%20States%20of%20America&amp;rft.stitle=Proc%20Natl%20Acad%20Sci%20U%20S%20A.%20&amp;rft.volume=99&amp;rft.issue=15&amp;rft.aufirst=Jonathan%20A.&amp;rft.aulast=Bernstein&amp;rft.au=Jonathan%20A.%20Bernstein&amp;rft.au=Arkady%20B.%20Khodursky&amp;rft.au=Pei-Hsun%20Lin&amp;rft.au=Sue%20Lin-Chao&amp;rft.au=Stanley%20N.%20Cohen&amp;rft.date=2002-07-23&amp;rft.pages=9697%E2%80%939702"></span></td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[6]</td><td style="padding-left:4pt;">W. Hsieh et al., “Influence of sequence and distance between two operators on interaction with the lac repressor,” <span style="font-style:italic;">J. Biol. Chem.</span>, vol. 262, Oct. 1987, pp. 14583-14591. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Influence%20of%20sequence%20and%20distance%20between%20two%20operators%20on%20interaction%20with%20the%20lac%20repressor&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=262&amp;rft.issue=30&amp;rft.aufirst=WT&amp;rft.aulast=Hsieh&amp;rft.au=WT%20Hsieh&amp;rft.au=PA%20Whitson&amp;rft.au=KS%20Matthews&amp;rft.au=RD%20Wells&amp;rft.date=1987-10-25&amp;rft.pages=14583-14591"></span></td></tr><br />
<br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[7]</td><td style="padding-left:4pt;">J.B. Andersen et al., “New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria,” <span style="font-style:italic;">Applied and Environmental Microbiology</span>, vol. 64, Jun. 1998, pp. 2240–2246. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=New%20Unstable%20Variants%20of%20Green%20Fluorescent%20Protein%20for%20Studies%20of%20Transient%20Gene%20Expression%20in%20Bacteria&amp;rft.jtitle=Applied%20and%20Environmental%20Microbiology&amp;rft.stitle=Appl%20Environ%20Microbiol.%20&amp;rft.volume=64&amp;rft.issue=6&amp;rft.aufirst=Jens%20Bo&amp;rft.aulast=Andersen&amp;rft.au=Jens%20Bo%20Andersen&amp;rft.au=Claus%20Sternberg&amp;rft.au=Lars%20Kongsbak%20Poulsen&amp;rft.au=Sara%20Petersen%20Bj%C3%B8rn&amp;rft.au=Michael%20Givskov&amp;rft.au=S%C3%B8ren%20Molin&amp;rft.date=1998-06&amp;rft.pages=2240%E2%80%932246"></span></td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[8]</td><td style="padding-left:4pt;">“Part:BBa B0032 - partsregistry.org”; http://partsregistry.org/Part:BBa_B0032.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[9]</td><td style="padding-left:4pt;">“Part:BBa R0011 - partsregistry.org”; http://partsregistry.org/Part:BBa_R0011.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[10]</td><td style="padding-left:4pt;">G.M. Skinner et al., “Promoter Binding, Initiation, and Elongation By Bacteriophage T7 RNA Polymerase: A SINGLE-MOLECULE VIEW OF THE TRANSCRIPTION CYCLE,” <span style="font-style:italic;">J. Biol. Chem.</span>, vol. 279, Jan. 2004, pp. 3239-3244. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1074/jbc.M310471200&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Promoter%20Binding%2C%20Initiation%2C%20and%20Elongation%20By%20Bacteriophage%20T7%20RNA%20Polymerase%3A%20A%20SINGLE-MOLECULE%20VIEW%20OF%20THE%20TRANSCRIPTION%20CYCLE&amp;rft.jtitle=J.%20Biol.%20Chem.&amp;rft.volume=279&amp;rft.issue=5&amp;rft.aufirst=Gary%20M.&amp;rft.aulast=Skinner&amp;rft.au=Gary%20M.%20Skinner&amp;rft.au=Christoph%20G.%20Baumann&amp;rft.au=Diana%20M.%20Quinn&amp;rft.au=Justin%20E.%20Molloy&amp;rft.au=James%20G.%20Hoggett&amp;rft.date=2004&amp;rft.pages=3239-3244"></span></td></tr><br />
<br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[11]</td><td style="padding-left:4pt;">Y. Wang and J.R. Leadbetter, “Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils,” <span style="font-style:italic;">Appl. Environ. Microbiol.</span>, vol. 71, Mar. 2005, pp. 1291-1299. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1128/AEM.71.3.1291-1299.2005&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Rapid%20Acyl-Homoserine%20Lactone%20Quorum%20Signal%20Biodegradation%20in%20Diverse%20Soils&amp;rft.jtitle=Appl.%20Environ.%20Microbiol.&amp;rft.volume=71&amp;rft.issue=3&amp;rft.aufirst=Ya-Juan&amp;rft.aulast=Wang&amp;rft.au=Ya-Juan%20Wang&amp;rft.au=Jared%20Renton%20Leadbetter&amp;rft.date=2005-03-01&amp;rft.pages=1291-1299"></span></td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
</table></body><br />
</html></div>Nickvdhttp://2008.igem.org/Talk:Team:KULeuven/Model/FilterTalk:Team:KULeuven/Model/Filter2008-09-09T12:00:17Z<p>Nickvd: </p>
<hr />
<div>{| align="center"<br />
|[[Image:Sim_filter_short.jpg|450px]]<br />
|[[Image:Sim_filter_long.jpg|450px]]<br />
|}<br />
<br />
<br />
=== Sensitivity Analysis ===<br />
<br />
[[Image:Sens Filter.png|center]]</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/FilterTeam:KULeuven/Model/Filter2008-09-09T12:00:02Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
<div style="float: right;">[[Image:pictogram_filter.png|120px]]</div><br />
<br />
== Filter ==<br />
<br />
=== Position in the system ===<br />
<br />
The filter is positioned immediately after the input, because its job is to filter out possible noise signals or background signals that aren't caused by the "desease". It is the starting piece of the whole system, situated before the invertimer- and the reset-subsystem.<br />
<br />
=== Describing the system ===<br />
see also: [https://2008.igem.org/Team:KULeuven/Project/Filter Project:Filter]<br />
<br />
[[Image:Filter_BioBrick.jpg|center]]<br />
<br />
==== ODE's ====<br />
<br />
<html><br />
<body><br />
<p><br />
<a href="https://static.igem.org/mediawiki/2008/a/a4/Filter.pdf"><br />
<img border="0" src="https://2008.igem.org/wiki/skins/common/images/icons/fileicon-pdf.png" width="65" height="60"><br />
</a><br />
</p><br />
</body><br />
</html><br />
<br />
==== Parameters ====<br />
<br />
{| width=80% style="border: 1px solid #003E81; background-color: #EEFFFF;"<br />
|+ ''Parameter values Filter''<br />
! width=15% | Name<br />
! width=15% | Value<br />
! width=40% | Comments<br />
! width=10% | Reference<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation rates<br />
|-<br />
| d<sub>pT7 tag</sub><br />
| 0.00155 s<sup>-1</sup><br />
| UmuD tag added to speed up degradation of otherwise too stable T7 polymerase<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [4<html>]</html> [5<html>]</html> [8<html>]</html>]<br />
|-<br />
| d<sub>mRNA RIBOKEY</sub><br />
| 0.00462 s<sup>-1</sup><br />
| estimate: because this RNA isn't translated, it degrades faster<br />
|[https://2008.igem.org/Team:KULeuven/Model/Filter#References [3<html>]</html>]<br />
|-<br />
| d<sub>closed mRNA T7</sub><br />
| 0.00462 s<sup>-1</sup><br />
| estimate: because this mRNA isn't translated, it degrades faster<br />
|[https://2008.igem.org/Team:KULeuven/Model/Filter#References [3<html>]</html>]<br />
|-<br />
| d<sub>open mRNA T7</sub><br />
| 0.00231 s<sup>-1</sup><br />
| <br />
|[https://2008.igem.org/Team:KULeuven/Model/Filter#References [3<html>]</html>]<br />
|-<br />
| d<sub>open mRNA T7 complex</sub><br />
| 0.00231 s<sup>-1</sup><br />
| <br />
|[https://2008.igem.org/Team:KULeuven/Model/Filter#References [3<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Equilibrium constants<br />
|-<br />
| K<sub>eq 1</sub><br />
| 0,015 [M]<br />
| between closed and open T7 mRNA, models competition, experimental<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [1<html>]</html> [2<html>]</html>]<br />
|-<br />
| K<sub>eq 2</sub><br />
| 0.0212 [M]<br />
| between closed T7 mRNA and key unlocked mRNA complex, models competition, experimental<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [1<html>]</html> [2<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Rate constants<br />
|-<br />
| k<sub>dis</sub><br />
| 0.00416 s<sup>-1</sup><br />
| estimate derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [1<html>]</html>]<br />
|-<br />
| k<sub>complex</sub><br />
| 0.00237 s<sup>-1</sup><br />
| estimate derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [1<html>]</html>]<br />
|-<br />
| k<sub>closed</sub><br />
| 500 s<sup>-1</sup><br />
| estimate derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [1<html>]</html>]<br />
|-<br />
| k<sub>open</sub><br />
| 7.5 s<sup>-1</sup><br />
| estimate derived from experimental values<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [1<html>]</html>]<br />
|-<br />
| k<sub>translation</sub><br />
| 0.167 s<sup>-1</sup><br />
| lock defined translation rate for T7 RNA pol<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [7<html>]</html>]<br />
|-<br />
! colspan="4" style="border-bottom: 1px solid #003E81;" | Transcription rates<br />
|-<br />
| TetR_var_transcr_rate<br />
| p(TetR) dependent <br />
| (RiboKey) between 5E-5 and 0.0125 s<sup>-1</sup> ~ [aTc]<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [6<html>]</html>]<br />
|-<br />
| k<sub>mRNA T7</sub><br />
| 0,0011 s<sup>-1</sup><br />
| weak constitutive promoter J23109<br />
| [https://2008.igem.org/Team:KULeuven/Model/Filter#References [7<html>]</html>]<br />
|}<br />
<br />
<b>Remark:</b> The key-lock system has been enhanced to 0.3%-14% (new parameters have been added)<br />
<br />
=== Models ===<br />
<br />
==== CellDesigner ([https://static.igem.org/mediawiki/2008/1/10/Filter_CellDesigner.zip SBML file])====<br />
<br />
[[Image:Filter_CellDesigner.png|800px|center|filter]]<br />
<br />
==== Matlab ([https://static.igem.org/mediawiki/2008/c/ce/Filter_Matlab.zip SBML file])====<br />
<br />
[[Image:Filter_Matlab.jpg|center]]<br />
<br />
=== Simulations ===<br />
<br />
[[Image:Sim_filter_1.png|800px|center|filter]]<br />
<br />
[[Image:Filter 1.PNG|right]]<br />
<br />
====1. AND gate of the filter====<br />
<br />
In the simulation we can clearly see this series of events:<br />
* when dark blue(ribokey) starts to increase, red (T7) also starts to increase, giving rise to an increasing amount of lactonase (blue) = AND-GATE.<br />
* when dark blue(ribokey) starts to decrease, red (T7) also starts to decrease, but much slower. The lactonase also starts to decrease, as it should be.<br />
The short lifetime of the ribokey compared to the lifetime of the T7-protein, guarantees that the AND-GATE always works perfectly fine: when there's no more input, the ribokey will rapidly decrease (and disappear) and makes sure that the AND-GATE is not activated anymore, even when the T7-protein is slowly decreasing.<br />
<br />
====2. Filtering in practice====<br />
<br />
In the simulation three kinds of inputpulses have been used:<br />
<br />
*First pulse: 300s<br />
**small peak of lactonase<br />
**no influence on the timer<br />
<br />
*Second pulse: 1000s<br />
**medium peak of lactonase<br />
**influences the timer by levelling the timing capabilities, but it doesn't reset the timer<br />
<br />
*Third pulse: 5000s<br />
**huge peak of lactonase<br />
**reset of the timer: amount of complex goes to zero<br />
<br />
====3. Proof of filtering capacities====<br />
<br />
As proof of the filtering capacities, we'll compare the maximum amount of GFP with the maximum amount of Lactonase as a function of the pulse length of TetR. We've chosen Lactonase and GFP because they differ only in the absence or presence of the filter, all other parameters are identical (eg. degradation rate). The model used here consists only of the filter, the output and the lactonase productions subsystems.<br />
<br />
The left figures shows us a clear difference between the amount of GFP and lactonase for almost every pulse length. The explanation for the (almost constant) big difference for pulses longer than 1000 seconds is the following. For such long pulses, the filter can be considered as fully active, such that the only differences between the output and the lactonase production are characteristics of the ribokey and the difference in transcription rates between E. coli's RNA polymerase II and phage T7's polymerase. <br />
For a pulse shorter than 1000 seconds the filter is not fully active. This creates a filtering effect. If we just look at the first 1000 seconds (right figures), we see that the amount of Lactonase remains more or less the same while the amount of GFP increases very fast.<br />
<html><br />
<div class="center"><br />
<div class="noborder" style="overflow: auto; width: 800px; height: 520px;"><br />
<div class="noborder" style="width: 1050px;"> <br />
<img src="https://static.igem.org/mediawiki/2008/1/18/Filter_amount_vs_pulse.png" style="float: left; width: 500px; height: 500px; margin: 0 5px;" /><br />
<img src="https://static.igem.org/mediawiki/2008/3/32/Filter_amount_vs_pulse_zoomed.png" style="float: left; width: 500px; height: 500px; margin: 0 5px;" /><br />
</div></div></div></html><br />
<br />
Another way to see the filtering effect is to look at the ratio of GFP to Lactonase. This figure clearly shows the disproportionality between GFP and lactonase for the pulses shorter than 1000 seconds. The best filtering effect occurs for pulses around 100 seconds. This figure also shows that placing the filter in front of a signal wil lower this signal with a factor of at least 25. This base factor should be multiplied with +-7 for pules around 100 seconds.<br />
[[Image:GFP_Lactonase.png|center|550px]]<br />
<br />
=== References ===<br />
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/><br />
<title>Bibliography</title><br />
</head><br />
<body><br />
<table style="border-collapse:collapse;line-height:1.1em;"><br />
<tr style="vertical-align:top;"><td>[1]</td><td style="padding-left:4pt;">“Berkeley2006-RiboregulatorsMain - IGEM”; http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[2]</td><td style="padding-left:4pt;">F.J. Isaacs et al., “Engineered riboregulators enable post-transcriptional control of gene expression,” <span style="font-style:italic;">Nat Biotech</span>, vol. 22, Jul. 2004, pp. 841-847. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1038/nbt986&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Engineered%20riboregulators%20enable%20post-transcriptional%20control%20of%20gene%20expression&amp;rft.jtitle=Nat%20Biotech&amp;rft.stitle=Nat%20Biotech&amp;rft.volume=22&amp;rft.issue=7&amp;rft.aufirst=Farren%20J&amp;rft.aulast=Isaacs&amp;rft.au=Farren%20J%20Isaacs&amp;rft.au=Daniel%20J%20Dwyer&amp;rft.au=Chunming%20Ding&amp;rft.au=Dmitri%20D%20Pervouchine&amp;rft.au=Charles%20R%20Cantor&amp;rft.au=James%20J%20Collins&amp;rft.date=2004-07&amp;rft.pages=841-847&amp;rft.issn=1087-0156"></span></td></tr><br />
<br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[3]</td><td style="padding-left:4pt;">J.A. Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays,” <span style="font-style:italic;">Proceedings of the National Academy of Sciences of the United States of America</span>, vol. 99, Jul. 2002, pp. 9697–9702. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1073/pnas.112318199&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Global%20analysis%20of%20mRNA%20decay%20and%20abundance%20in%20Escherichia%20coli%20at%20single-gene%20resolution%20using%20two-color%20fluorescent%20DNA%20microarrays&amp;rft.jtitle=Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20of%20the%20United%20States%20of%20America&amp;rft.stitle=Proc%20Natl%20Acad%20Sci%20U%20S%20A.%20&amp;rft.volume=99&amp;rft.issue=15&amp;rft.aufirst=Jonathan%20A.&amp;rft.aulast=Bernstein&amp;rft.au=Jonathan%20A.%20Bernstein&amp;rft.au=Arkady%20B.%20Khodursky&amp;rft.au=Pei-Hsun%20Lin&amp;rft.au=Sue%20Lin-Chao&amp;rft.au=Stanley%20N.%20Cohen&amp;rft.date=2002-07-23&amp;rft.pages=9697%E2%80%939702"></span></td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[4]</td><td style="padding-left:4pt;">“IGEM:Tsinghua/2007/Projects/RAP - OpenWetWare”; http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[5]</td><td style="padding-left:4pt;">M. Gonzalez et al., “Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues required for proteolysis,” <span style="font-style:italic;">Genes Dev.</span>, vol. 12, Dec. 1998, pp. 3889-3899. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1101/gad.12.24.3889&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Lon-mediated%20proteolysis%20of%20the%20Escherichia%20coli%20UmuD%20mutagenesis%20protein%3A%20in%20vitro%20degradation%20and%20identification%20of%20residues%20required%20for%20proteolysis&amp;rft.jtitle=Genes%20Dev.&amp;rft.volume=12&amp;rft.issue=24&amp;rft.aufirst=Martin&amp;rft.aulast=Gonzalez&amp;rft.au=Martin%20Gonzalez&amp;rft.au=Ekaterina%20G.%20Frank&amp;rft.au=Arthur%20S.%20Levine&amp;rft.au=Roger%20Woodgate&amp;rft.date=1998-12-15&amp;rft.pages=3889-3899"></span></td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<br />
<tr style="vertical-align:top;"><td>[6]</td><td style="padding-left:4pt;">M. Bon, S.J. McGowan, and P.R. Cook, “Many expressed genes in bacteria and yeast are transcribed only once per cell cycle,” <span style="font-style:italic;">FASEB J.</span>, vol. 20, Aug. 2006, pp. 1721-1723. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1096/fj.06-6087fje&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Many%20expressed%20genes%20in%20bacteria%20and%20yeast%20are%20transcribed%20only%20once%20per%20cell%20cycle&amp;rft.jtitle=FASEB%20J.&amp;rft.volume=20&amp;rft.issue=10&amp;rft.aufirst=Michael&amp;rft.aulast=Bon&amp;rft.au=Michael%20Bon&amp;rft.au=Simon%20J.%20McGowan&amp;rft.au=Peter%20R.%20Cook&amp;rft.date=2006-08-01&amp;rft.pages=1721-1723"></span></td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[7]</td><td style="padding-left:4pt;">“Part:BBa J23109 - partsregistry.org”; http://partsregistry.org/Part:BBa_J23109.</td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
<tr style="vertical-align:top;"><td>[8]</td><td style="padding-left:4pt;">J.P. McDonald et al., “Regulation of UmuD cleavage: role of the amino-terminal tail,” <span style="font-style:italic;">Journal of Molecular Biology</span>, vol. 282, Oct. 1998, pp. 721-730. <span class="Z3988" title="url_ver=Z39.88-2004&amp;ctx_ver=Z39.88-2004&amp;rft_id=info%3Adoi/10.1006/jmbi.1998.2044&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Regulation%20of%20UmuD%20cleavage%3A%20role%20of%20the%20amino-terminal%20tail&amp;rft.jtitle=Journal%20of%20Molecular%20Biology&amp;rft.volume=282&amp;rft.issue=4&amp;rft.aufirst=John%20P&amp;rft.aulast=McDonald&amp;rft.au=John%20P%20McDonald&amp;rft.au=Erinn%20E%20Maury&amp;rft.au=Arthur%20S%20Levine&amp;rft.au=Roger%20Woodgate&amp;rft.date=1998-10-02&amp;rft.pages=721-730"></span></td></tr><br />
<tr><td colspan="2">&nbsp;</td></tr><br />
</table></body><br />
<br />
</html></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/Kinetic_ConstantsTeam:KULeuven/Model/Kinetic Constants2008-09-09T10:49:39Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
===ETHZ list of parameters===<br />
* [http://parts.mit.edu/igem07/index.php/ETHZ/Parameters ETHZ list of parameters]<br />
===mRNA decay===<br />
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays]<br />
<br />
===T7 RNAP===<br />
*[http://www.jbc.org/cgi/reprint/267/4/2640 Initiation of Transcription by T7 RNA Polymerase at Its Natural Promoters]<br />
*[http://pubs.acs.org/cgi-bin/article.cgi/bichaw/2002/41/i11/pdf/bi0158472.pdf Kinetic and Thermodynamic Basis of Promoter Strength: Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence]<br />
*[http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP data T7 team Tsinghua 2007]<br />
*[http://www.jbc.org/cgi/reprint/281/47/35677 Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase]<br />
*[http://www.jbc.org/cgi/content/full/279/5/3239#FIG2 Single molecule studies of T7 RNA polymerase]<br />
<br />
===LacI - LuxI===<br />
* [http://www.tam.cornell.edu/tam/cms/manage/upload/Strogatz_20coupled_repressilators_PNAS.pdf Coupled repressilators]<br />
<br />
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]<br />
<br />
===LuxI, LuxR, mRNALuxI, mRNALuxR decay===<br />
<br />
*[http://bioinformatics.oxfordjournals.org/cgi/content/full/21/11/2722#E11 Noise-induced cooperative behavior in a multicell system]<br />
<br />
*[http://www.pnas.org/content/93/18/9505 LuxI kinetics]<br />
<br />
===HSL stuff===<br />
<br />
*[http://aem.asm.org/cgi/content/abstract/71/3/1291 Rapid Acyl-Homoserine Lactone Quorum Signal Biodegradation in Diverse Soils] Fig 6: half-life 185 h ==> decay rate 1.02 * 10^-6 s^-1 ==> 0.00889 nM/h<br />
<br />
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-457D0X9-9&_user=877992&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000047079&_version=1&_urlVersion=0&_userid=877992&md5=36d07f326b2c2e55c4de05a1ab426e09 Kinetics of the AHL Regulatory System in a Model Biofilm System]<br />
<br />
*[http://www.pnas.org/content/96/8/4360.full HSL lactone synthesis kinetics by a LuxI-related enzyme]<br />
<br />
*[http://www.jbc.org/cgi/content/full/279/14/13645#TBL2 Lactonase mediated HSL degradation (hydrolysis)]<br />
<br />
====Diffusion====<br />
<br />
*[http://jb.asm.org/cgi/content/full/185/5/1485 AHL diffusion model]<br />
<br />
*[http://jb.asm.org/cgi/content/full/185/5/1485 AHL diffusion constants & stuff]<br />
<br />
===OmpR, OmpF===<br />
*[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=543474&blobtype=pdf A simulation model of Escherichia coli osmoregulatory switch using E-CELL system] (Relevance: High), bekijk pg.11/13<br />
*[http://www.jbc.org/cgi/reprint/281/25/17114 Transcription Regulation of ompF and ompC by a Single Transcription Factor, OmpR] (Relevance: Medium)<br />
*[http://jb.oxfordjournals.org/cgi/reprint/111/6/707.pdf Transmembrane Signal Transduction and Osmoregulation in Escherichia coli: Functional Importance of the Transmembrane Regions of Membrane-Located Protein Kinase, EnvZ] (Relevance:?), geen toegang tenzij account<br />
*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=209999 DNA-Binding Properties of the Transcription Activator (OmpR) for the Upstream Sequences of ompF in Escherichia coli Are Altered by envZ Mutations and Medium Osmolarity] (Relevance: Low)<br />
*[http://jb.asm.org/cgi/reprint/176/5/1309 A Distant Upstream Site Involved in the Negative Regulation of the Escherichia coli ompF Gene] (Relevance: ?), voor repressor regulatie van OmpF door OmpR<br />
*[http://jb.asm.org/cgi/reprint/176/16/5005.pdf micF Antisense RNA Has a Major Role in Osmoregulation of OmpF in Escherichia coli] (Relevance: Low), invloed ''''Antisense RNA'''' op OmpF regulatie, hmm...<br />
<br />
===Psid met P2ogr promotor===<br />
*[http://parts.mit.edu/igem07/index.php/Cambridge/Amplifier_project Cambridge amplifier project, combinatie van verschillende promotoren met verschillende activatoren, experimenteel amplification factor bepaald met GFP reporter]<br />
<br />
*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=178405 P<sub>sid</sub> promotor with different activators]<br />
<br />
===Constitutive promoters===<br />
*Estimated transcription rate for J23105:[http://parts.mit.edu/igem07/index.php?title=ETHZ/Parameters]<br />
*Scale other transcription rate with table in parts registry.<br />
<br />
* Estimate the rate of transcription from a constitutive promotor family member.<br />
[[Image:Const_pro_strength.png|center|400px|thumb|Estimates for the rate of transcription from the constitutive promotor family members. X is the GFP fluorescence in arbitrary units according to the Registry. Y is the number of mRNA's produced per second from that promotor]]<br />
<br />
===E. coli transcription rates===<br />
[http://www.fasebj.org/cgi/content/summary/20/10/1721 Paper about the calculated transcription rates for every E.coli ORF] <br><br />
[http://users.path.ox.ac.uk/~pcook/data/catalogs.html Tables with the calculated transcription rates for every E.coli ORF]</div>Nickvdhttp://2008.igem.org/Talk:Team:KULeuven/Model/OverviewTalk:Team:KULeuven/Model/Overview2008-09-09T10:48:14Z<p>Nickvd: New page: Good modeling practice requires that the modeler provides an evaluation of the confidence in the model, possibly assessing the uncertainties associated with the modeling process and with t...</p>
<hr />
<div>Good modeling practice requires that the modeler provides an evaluation of the confidence in the model, possibly assessing the uncertainties associated with the modeling process and with the outcome of the model itself. Uncertainty and Sensitivity Analysis offer valid tools for characterizing the uncertainty associated with a model. Uncertainty analysis (UA) quantifies the uncertainty in the outcome of a model. Sensitivity Analysis has the complementary role of ordering by importance the strength and relevance of the inputs in determining the variation in the output. Sensitivity analysis lets you calculate the time-dependent sensitivities of all the species states with respect to species initial conditions and parameter values in the model.</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Model/OverviewTeam:KULeuven/Model/Overview2008-09-09T10:48:00Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
__NOTOC__<br />
<br />
=== Introduction ===<br />
<br />
[[Image:WhyWeNeedComputer.png|200px|right]]<br />
<br />
As an introduction to modeling we've made a small [https://static.igem.org/mediawiki/2008/4/4e/Modeling.ppt presentation] for the workout sessions of the first meeting. This presentation handles the following items: <br><br />
* some definitions<br />
* the difference between white box and black box models with an example<br />
* focus on the role of ODE's<br />
* the need for modeling<br />
* some modeling tools<br />
* and iGEM modeling<br />
<br />
This presentation is mainly based on the wiki of ETH Zürich 2006/2007.<br />
<br />
=== The Full Model ===<br />
<br />
[[Image:Superfinal.png|500px|center]]<br />
<br />
=== Modeling steps===<br />
<br />
==== Position in the system ====<br />
<br />
For each of the subsystems (compartments) we started with the idea of what it was supposed to do, considering it as a black-box system (as described in the [https://2008.igem.org/Team:KULeuven/Project project page]). To make sure that Dr. Coli was able to do his work properly, we had to design several subsystems and be well aware of the different interfaces between these subsystems. <br />
<br />
Then we tried to match species with these black-boxes, keeping in mind the working biobricks which have been made already. So we searched for existing components which could be able to perform the requested task.<br />
<br />
==== Describing the system ====<br />
<br />
The kinetic actions (transcription, translation, complexation, ...) that take place in the subsystems can be described by Ordinary Differential Equations (ODEs) like Mass-Action laws, Hill Kinetic laws and so on. An extensive search for parameters involved in these ODEs has resulted in the discovery of almost all necessary quantities for the simulations.<br />
<br />
For every subsystem, we made a PDF-file with all the ODEs involved in modeling the subsystem, together with a clear overview of the used parameters (with coherent links to our references).<br />
<br />
==== Models ====<br />
<br />
We implemented these ODEs in both [http://www.systems-biology.org/cd/ Celldesigner] and the [http://www.mathworks.com/access/helpdesk/help/toolbox/simbio/ MATLAB Symbiology Toolbox]. A nice tutorial for modeling in Celldesigner can be found on [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals Imperial College Computer Modelling Practicals Spring 2008]. These 2 environments offer a grapical user-interface which makes it easy to implement biochemical pathways (and the kinetic laws which govern these). In the pictures in each of the subsytems you can see clearly the influence of the different species: activation, repression, complexation, ... We also provide links to the actual implemented diagrams which can be freely downloaded to simulate the subsystems yourself.<br />
<br />
==== Simulation(s) ====<br />
<br />
The implemented models are simulated using inputs as close to reality as possible. In each simulation the typical assets of each subsystem are clearly visualized and described extensively. For example in the filter we simulate the influence of different noisy signals on the output of the filter (and on the output of the system).<br />
<br />
==== Sensitivity Analysis ====<br />
<br />
A sensitivity analysis is needed e.g. when some of the parameter values are not known. The true value of a parameter is unimportant when the most essential species states are insensitive to the unknown parameter. Only for the sensitive unknown parameters are experiments needed to determine their true values. In our project we have been able to find hypothetical values for all used parameters, but a sensitivity analyses is nevertheless always valuable to detect critical parameters. These are the parameter values on which our project critically depends and which should be analyzed/characterized as exact as possible.<br />
<br />
=== Important notes ===<br />
<br />
<b>1.</b> The idea of a pulsgenerator as reset mechanism has been cancelled for the following reasons: <br />
* it takes too long before the proposed system generates a pulse-like event<br />
* the pulse itself is too long <br />
* a constant lactonase production sequence generates enough lactonase to reset the timer<br />
More information about this problem and the solution can be found on [https://2008.igem.org/Team:KULeuven/Model/Reset Reset]-page.<br />
<br />
<b>2.</b> A mathematical analyses of the memory has been done to prove that it has 2 stable states and to describe the boundary which separates the trajectories leading to one of the steady states. <br />
<br />
More information about this analysis can be found on [https://2008.igem.org/Team:KULeuven/Model/Memory Memory]-page.</div>Nickvdhttp://2008.igem.org/Team:KULeuven/9_September_2008Team:KULeuven/9 September 20082008-09-09T10:45:12Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Lab Work ==<br />
<br />
=== Wet Lab ===<br />
<br />
=== Dry Lab ===<br />
<br />
==== Modeling ====<br />
<br />
Finished the MultiCell Toolbox and edited its [https://2008.igem.org/Team:KULeuven/Software/MultiCell Wiki-page].<br />
<br />
==== Wiki ====<br />
<br />
Last edits were conducted to the picture gallery, so it doesn't look like... well you know what, no more. Wiki finished.<br />
<br />
== Remarks ==<br />
<br />
We discovered on the [https://2008.igem.org/Special:Statistics iGEM - Statistics] page that our website is ranked n°2 in the list of Most Viewed Pages (with a n°1 place for the iGEM home page).<br />
<br />
[[Image:Views.PNG|center]]<br />
<br />
<br />
<br />
<br />
<br />
{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}</div>Nickvdhttp://2008.igem.org/Team:KULeuven/9_September_2008Team:KULeuven/9 September 20082008-09-09T10:42:19Z<p>Nickvd: /* Modeling */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Lab Work ==<br />
<br />
=== Wet Lab ===<br />
<br />
=== Dry Lab ===<br />
<br />
==== Modeling ====<br />
<br />
Finished the MultiCell Toolbox and edited its Wiki-page.<br />
<br />
==== Wiki ====<br />
<br />
Last edits were conducted to the picture gallery, so it doesn't look like... well you know what, no more. Wiki finished.<br />
<br />
== Remarks ==<br />
<br />
We discovered on the [https://2008.igem.org/Special:Statistics iGEM - Statistics] page that our website is ranked n°2 in the list of Most Viewed Pages (with a n°1 place for the iGEM home page).<br />
<br />
[[Image:Views.PNG|center]]<br />
<br />
<br />
<br />
<br />
<br />
{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T10:39:07Z<p>Nickvd: /* Step 1: Load Project */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
[[Image:MCT Load.PNG|center]]<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
[[Image:MCT Reactions.PNG|center]]<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
[[Image:MCT Events.PNG|center]]<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
3. Please refer to this page when using the MultiCell Toolbox.<br />
<br />
== File ==<br />
<br />
COMING SOON</div>Nickvdhttp://2008.igem.org/File:MCT_Load.PNGFile:MCT Load.PNG2008-09-09T10:37:59Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T10:32:05Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
[[Image:MCT Reactions.PNG|center]]<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
[[Image:MCT Events.PNG|center]]<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
3. Please refer to this page when using the MultiCell Toolbox.<br />
<br />
== File ==<br />
<br />
COMING SOON</div>Nickvdhttp://2008.igem.org/File:MCT_Events.PNGFile:MCT Events.PNG2008-09-09T10:29:28Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/File:MCT_Reactions.PNGFile:MCT Reactions.PNG2008-09-09T10:27:42Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T10:18:22Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data about your project: the number of compartments, species and reactions. After loading your project, it will be checked to conform to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
1. The loaded projectfile needs to conform to some standards to be able to simulate with the Multi Cell Toolbox:<br />
<br />
* There must be a compartment with the name 'system', which encomprises everything.<br />
* There must be a compartment with the name 'cell1', which represents the basic cell that will be used for cell replication/division. Its 'Owner' must be the 'system'-compartment.<br />
<br />
2. The cell division process is very simplified in this toolbox. It keeps track of the age of the cells and when the time is right for division, the mothercell is divided in 2 new cells: a 'reïncarnation' of the mothercell (with adjusted initial conditions) and a new cell (with initial conditions adjusted to the mothercell). In this stage of the toolbox we don't take into account the possibility of cell growth or other events during the cell division process (extensions in a future release...).<br />
<br />
3. Please refer to this page when using the MultiCell Toolbox.<br />
<br />
== File ==<br />
<br />
COMING SOON</div>Nickvdhttp://2008.igem.org/Team:KULeuven/Software/MultiCellTeam:KULeuven/Software/MultiCell2008-09-09T09:53:22Z<p>Nickvd: </p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Introduction ==<br />
<br />
Have you ever wanted to simulate the effects of your MATLAB Symbiology project in a multicellular environment? This toolbox enables you to expand your 'what happens in 1 cell'-model into a network of interconnected cells with the full abilities of a growing population of cells. It delivers you an easy-to-use graphical interface to configure the simulation settings and with just 1 click an extensive simulation is started.<br />
<br />
== The Program ==<br />
<br />
=== GUI ===<br />
<br />
[[Image:MultiCellToolbox.PNG|center]]<br />
<br />
=== Use ===<br />
<br />
==== Step 1: Load Project ====<br />
<br />
Push the button to load your '1cell'-project. In the Project Properties panel the name of your project will appear together with some crucial data of your project: the number of compartments, species and reactions. After loading your project, it will be checked for conforming to the requested standards of the toolbox (see [https://2008.igem.org/Team:KULeuven/Software/MultiCell#Remarks Remarks]) and a note will appear in the Control panel.<br />
<br />
==== Step 2: Fill in simulation parameters ====<br />
<br />
In the Simulation Properties panel you can enter all the necessary parameters for the simulation: <br />
* Simulation Time: duration of the simulation (with cell division action)<br />
* System Equilibrium time: time the system needs to reach its equilibrium state (first simulation starts with Species.InitialCondition equal to their initial condition in the project)<br />
*Initial Population: the amount of cells before the simulation starts (with cell division action)<br />
*Division Time (mean): mean time for 1 cell till (next) division<br />
*Division Time (spread): possible spread around the mean time for 1 cell till (next) division<br />
<br />
You also need to enter the reactions that involve species in 'cell1' and have to be copied to their daughter cells. This can be done by clicking the Reactions button and selecting these reactions.<br />
<br />
==== Step 3: Add events to simuation ====<br />
<br />
One of the pros of this toolbox is the included possibility of introducing events (just like in MATLAB). Select the starting time (trigger), the specie involved and the amount of the specie and then click 'Add...'. The other buttons also speak for themselves.<br />
<br />
==== Step 4: RUN ====<br />
<br />
After configuring all the necessary settings, you're now ready to run the application!<br />
<br />
<br />
== Remarks ==<br />
<br />
<br />
== File ==<br />
<br />
COMING SOON<br />
<br />
== Features ==</div>Nickvdhttp://2008.igem.org/File:MultiCellToolbox.PNGFile:MultiCellToolbox.PNG2008-09-09T09:22:54Z<p>Nickvd: uploaded a new version of "Image:MultiCellToolbox.PNG"</p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/File:MultiCellToolbox.PNGFile:MultiCellToolbox.PNG2008-09-09T09:06:29Z<p>Nickvd: uploaded a new version of "Image:MultiCellToolbox.PNG"</p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/9_September_2008Team:KULeuven/9 September 20082008-09-09T09:00:24Z<p>Nickvd: New page: {{:Team:KULeuven/Tools/Header}} == Lab Work == === Wet Lab === === Dry Lab === ==== Modeling ==== ==== Wiki ==== == Remarks == We discovered on the [https://2008.igem.org/Special:Sta...</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Lab Work ==<br />
<br />
=== Wet Lab ===<br />
<br />
=== Dry Lab ===<br />
<br />
==== Modeling ====<br />
<br />
==== Wiki ====<br />
<br />
== Remarks ==<br />
<br />
We discovered on the [https://2008.igem.org/Special:Statistics iGEM - Statistics] page that our website is ranked n°2 in the list of Most Viewed Pages (with a n°1 place for the iGEM home page).<br />
<br />
[[Image:Views.PNG|center]]<br />
<br />
== Comic of the day ==<br />
<br />
<br />
<br />
<br />
<br />
{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}</div>Nickvdhttp://2008.igem.org/File:Views.PNGFile:Views.PNG2008-09-09T08:59:04Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/8_September_2008Team:KULeuven/8 September 20082008-09-08T14:12:02Z<p>Nickvd: New page: {{:Team:KULeuven/Tools/Header}} == Lab Work == === Wet Lab === Final scheme: 600px Parallel scheme 600px === Dr...</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Lab Work ==<br />
<br />
=== Wet Lab ===<br />
<br />
Final scheme:<br />
<br />
[[Image:8sept final.PNG|center|600px]]<br />
<br />
Parallel scheme<br />
<br />
[[Image:8sept parallel.PNG|center|600px]]<br />
<br />
<br />
=== Dry Lab ===<br />
<br />
==== Modeling ====<br />
<br />
==== Wiki ====<br />
<br />
== Remarks ==<br />
<br />
== Comic of the day ==<br />
<br />
<br />
<br />
<br />
<br />
{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}</div>Nickvdhttp://2008.igem.org/File:8sept_parallel.PNGFile:8sept parallel.PNG2008-09-08T14:08:19Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/File:8sept_final.PNGFile:8sept final.PNG2008-09-08T14:07:09Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/Tools/Navigation_BarTeam:KULeuven/Tools/Navigation Bar2008-09-07T11:47:49Z<p>Nickvd: </p>
<hr />
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<ul><br />
<li><br />
<a href="https://2008.igem.org/Team:KULeuven">Home</a><br />
</li><br />
<li><br />
<a>The Team</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Team/LabsandGroups">Research Labs and Groups</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Team/Students">Students</a><br />
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<a href="https://2008.igem.org/Team:KULeuven/Team/Pictures">Pictures</a><br />
</div><br />
</li><br />
<li><br />
<a>The Project</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Project">Summary</a><br />
<span><br />
<a>Components</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Project/Input">Input</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Project/Output">Output</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Project/Filter">Filter</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Project/Reset">Reset</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Project/CellDeath">Cell Death</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Project/Memory">Memory</a><br />
</div><br />
</span><br />
<a href="https://2008.igem.org/Team:KULeuven/Literature">Literature</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Brainstorm">Brainstorm</a><br />
</div><br />
</li><br />
<li><br />
<a>Ethics</a><br />
<div><br />
<br />
</div><br />
</li><br />
<li><br />
<a>Submitted Parts</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Parts">Listing</a><br />
<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a><br />
</div><br />
</li><br />
<li><br />
<a>Modeling</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a><br />
<span><br />
<a>Components</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/Output">Output</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a><br />
</div><br />
</span><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a><br />
</div><br />
</li><br />
<li><br />
<a>Data Analysis</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a><br />
<span><br />
<a>New Parts</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a><br />
</div><br />
</span><br />
<span><br />
<a>Components</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Input">Input</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Output">Output</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a><br />
</div><br />
</span><br />
<a href="https://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a><br />
</div><br />
</li><br />
<li><br />
<a>Software</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a><br />
</div><br />
</li><br />
<li><br />
<a>Notebook</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a><br />
<a href="https://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Meeting Reports">Reports</a><br />
<span><br />
<a>Lab Data</a><br />
<div><br />
<a href="https://2008.igem.org/Team:KULeuven/Freezer">Freezer</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Primers">Primers</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Ligation">Ligation</a><br />
</div><br />
</span><br />
<a href="https://2008.igem.org/Team:KULeuven/Tools">Tools</a><br />
<a href="https://2008.igem.org/Team:KULeuven/Press">Press</a><br />
<br />
</div><br />
</li><br />
<br />
</ul><br />
</div><br />
</div><br />
</html></div>Nickvdhttp://2008.igem.org/Team:KULeuven/5_September_2008Team:KULeuven/5 September 20082008-09-05T16:15:26Z<p>Nickvd: /* Wet Lab */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Lab Work ==<br />
<br />
=== Wet Lab ===<br />
<br />
Succes in the Wet Lab: we constructed the OUTPUT-subsystem with GFP with and without LVA-tag, as can be seen in this picture. On the left side GFP with LVA tag (our part K145015): less fluorescent. On the right side GFP without LVA tag (part E0042): more fluorescent.<br />
<br />
[[Image:DSC02957.JPG|center|800px]]<br />
<br />
Final Scheme till so far:<br />
<br />
[[Image:5sept final.PNG|center|700px]]<br />
<br />
Parallel Scheme till so far:<br />
<br />
[[Image:5sept parallel.PNG|center|700px]]<br />
<br />
<br />
NOT THAT MUCH MORE PARTS TO FINISH!!!!<br />
<br />
=== Dry Lab ===<br />
<br />
Dr. Coli and his danger, ethics, ethics, ethics...<br />
<br />
==== Modeling ====<br />
<br />
SimBiology2Latex Toolbox has been finalized and can be found on the wiki.<br />
<br />
MultiCell Toolbox has entered it's final design stages. A preview of the GUI can be found on the wiki.<br />
<br />
Some more work on diffusion has been done. Sensitivity Analyses is still a pain in the ***.<br />
<br />
==== Wiki ====<br />
<br />
Homepage has been revamped, removing a lot of bugs. IE fixes still need to follow. Components bar has been fixed.<br />
<br />
== Remarks ==<br />
<br />
== Strip of the day ==<br />
<br />
<br />
{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}</div>Nickvdhttp://2008.igem.org/File:5sept_parallel.PNGFile:5sept parallel.PNG2008-09-05T16:14:28Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/File:5sept_final.PNGFile:5sept final.PNG2008-09-05T16:13:48Z<p>Nickvd: </p>
<hr />
<div></div>Nickvdhttp://2008.igem.org/Team:KULeuven/5_September_2008Team:KULeuven/5 September 20082008-09-05T15:54:23Z<p>Nickvd: /* Modeling */</p>
<hr />
<div>{{:Team:KULeuven/Tools/Header}}<br />
<br />
== Lab Work ==<br />
<br />
=== Wet Lab ===<br />
<br />
Succes in the Wet Lab: we constructed the OUTPUT-subsystem with GFP with and without LVA-tag, as can be seen in this picture. On the left side GFP with LVA tag (our part K145015): less fluorescent. On the right side GFP without LVA tag (part E0042): more fluorescent.<br />
<br />
[[Image:DSC02957.JPG|center|800px]]<br />
<br />
=== Dry Lab ===<br />
<br />
Dr. Coli and his danger, ethics, ethics, ethics...<br />
<br />
==== Modeling ====<br />
<br />
SimBiology2Latex Toolbox has been finalized and can be found on the wiki.<br />
<br />
MultiCell Toolbox has entered it's final design stages. A preview of the GUI can be found on the wiki.<br />
<br />
Some more work on diffusion has been done. Sensitivity Analyses is still a pain in the ***.<br />
<br />
==== Wiki ====<br />
<br />
Homepage has been revamped, removing a lot of bugs. IE fixes still need to follow. Components bar has been fixed.<br />
<br />
== Remarks ==<br />
<br />
== Strip of the day ==<br />
<br />
<br />
{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}</div>Nickvd