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Team:KULeuven/Evaluation
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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. | 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. | ||
| - | 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 was finished during the first six - seven weeks. During these weeks the model was gradually built and updated several times. A | + | 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. |
| - | Every subsystem was extensively tested and simulated before we | + | 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. |
| - | While the modelling team was busy | + | 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: |
| - | * punching the | + | * punching the bricks: ... |
| - | * 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 have | + | * 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. |
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. | 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. | ||
* ... | * ... | ||
| - | Despite these obstacles, the lab team could finish different parts which resulted in some biobricks | + | Despite these obstacles, the lab team could finish different parts which resulted in some great biobricks. |
TODO: hier nog iets zeggen over de behaalde resultaten in het labo | TODO: hier nog iets zeggen over de behaalde resultaten in het labo | ||
| - | 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 | + | 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... |
TODO: nog iets over grand prizes? | TODO: nog iets over grand prizes? | ||
Revision as of 11:41, 11 October 2008
UNDER CONSTRUCTION
Contents |
Our road towards the golden dream ...
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.
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. 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.
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:
- punching the bricks: ...
- 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.
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.
- ...
Despite these obstacles, the lab team could finish different parts which resulted in some great biobricks.
TODO: hier nog iets zeggen over de behaalde resultaten in het labo
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...
TODO: nog iets over grand prizes?
Personal Evaluation
Students
Maarten
A once in a life time opportunity broadening my view in different aspects
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:
- 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.
- This project was a nice introduction into the world of synthetic biology which was unknown to me.
- 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.
As you can see, I'm glad I joined the project.
Nathalie
Jonas
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.
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.
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.
