Team:KULeuven/Road Map

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{|style="font color="#000000"; background-color:#ffffff; border-spacing:6px; text-align:center" width="960px"
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{{:Team:KULeuven/Tools/Styling}}
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven|<font color="#ffffff">Home</font>]]
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{{:Team:KULeuven/Tools/Scripting}}
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Team|<font color="#ffffff">The Team</font>]]
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{{:Team:KULeuven/Tools/Header}}
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Road Map|<font color="#ffffff">Road Map</font>]]
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Project|<font color="#ffffff">The Project</font>]]
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Parts|<font color="#ffffff">Parts Submitted to the Registry</font>]]
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Modeling|<font color="#ffffff">Modeling</font>]]
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!style="text-align:center; background-color:#003E81; border-width:0px; padding:3px;"|[[Team:KULeuven/Notebook|<font color="#ffffff">Notebook</font>]]
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|}
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[[Image:kulbanner.jpg|960px]]
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This page contains information on meetings and schedules, on practical stuff, and some suggestions on background reading.<br><br>Brainstorm ideas for the project have been moved to the '''[[Team:KULeuven/Brainstorm|brainstorm page]]'''.
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<br><br> Spelen met de wiki doe je in de [[Team:KULeuven/Zandbak|zandbak]], vragen stellen of suggesties doen op de [[Team:KULeuven/Discussion|discussiepagina]].
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= To do =
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* check for international passport
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* design a team t-shirt ('''Could someone check whether we can use Jan Fabre's Totem?''')
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* book flights and hotel
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* '''can someone check out how to work with the notebook?'''
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<br><br>
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= Meetings =
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== May 22nd ==
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students and instructors brainstorm @ ESAT 01.57
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<br>
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present: all students, SDK, LVA, YM, JR, GG, IT
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* Each student [[Team:KULeuven/Project|presented]] his/her 3 favourite projects of previous iGEMs. All project brainstorm ideas are moved to the [[Team:KULeuven/Project|project page]]. There, you can add links to your favourite projects and/or upload your presentation.
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* The group picture is on our [[Team:KULeuven/Team|team page]].
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* Vote [[Team:KULeuven/Discussion|here]] for the logo you like best (thanks Jonas for the logo and Benjamien for the Zandbak and Discussiepagina idea!).
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* To make a summer schedule, '''please indicate your holiday plans below''' (Practical stuff - Planned summer holidays). The last exam is on June 27th.
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* Since the engineers want to see what's going on in the lab, and the biologists/bio-engineers want to learn about modeling, we'll organize some introductory tutorials in the beginning of the summer holidays.
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* Put ideas and suggestions for the wiki [[Team:KULeuven/Discussion|here]].
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* Inge will inform whether the students can stay at the Studentenwijk Arenberg during the summer holidays.
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* You are all welcome to join the [http://www.kuleuven.be/bioscenter/ BioSCENTer launch event] (Wednesday 28th, Max Weber auditorium, Parkstraat 51). Our iGEM participation will be presented between 15.35 and 15.45.
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* Check out the [http://www.kuleuven.be/bioscenter/igem iGEM website] at [http://www.kuleuven.be/bioscenter BioSCENTer].
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<br>
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* Good luck with the exams!
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== June 10th ==
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present: SDK, KM, AC, JR, LVO, IT
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'''Teachers workshop'''
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(Inge)<br>
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Tom Knight, Randy Rettberg and Meagan Lizarazo organised the Europe teachers workshop.
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I'll summarize the most important things.<br><br>
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''On the project:''
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* Try to divide the project into subparts in such a way that the whole project does not fail if one subpart fails / aim for intermediate goals and aim further if remaining time allows
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* iGEM is about doing synthetic biology based on standard parts, not about freestyle synthetic biology, however great that can be
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* They encourage to use existing BioBricks and improve their characterization and work further on previous projects - provide proper acknowledgement! ("Can someone completely own an idea?")
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''On sponsors:''
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* Matlab will sponsor!
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* DNA synthesis by GeneArt (0.25/bp + 35 sample transport) - takes 4-6 weeks!
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''BioBrick practicalities:''
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* protocols can be found on openwetware (will be included in the iGEM website soon)
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* plasmids in the Registry can be found by looking for ccdB (P1010) - available in a variety of plasmids
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* document your parts! take your time for this, documentation is extremely important (cfr. [https://2008.igem.org/Judging judging page]).
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* The organisation has put a lot of work in quality checking the BioBricks spring 2008 distrubution, BUT, there still can be mistakes, so always check whether the BioBrick is indeed the one you were looking for!
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* [http://partsregistry.org/Measurement Measurement] is important - we received Jason's measurement kit by mail!
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* Meagan gave a [http://partsregistry.org/Help:Team_experience_tutorial tutorial] on how to input a part in the registry
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* every team has a sandbox and a favorite parts section: the judges will only look at the parts in the favorite parts section!
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* each sent in BioBrick should be provided in a standard BioBrick plasmid
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* there are no rules on modeling (yet)
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''General:''
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* what's the overall goal? impress iGEM ;)
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* Over lunch, each instructor had to present his/her team [https://2008.igem.org/Europe_Teachers_Workshop/Team_reports short report].
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* As part of the competition, we have to answer the questions on the [https://2008.igem.org/Safety safety page].
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* We're supposed to have fun :) If we don't, we can call them and they'll tell us a joke
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<br>
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'''Project Brainstorm'''
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The ideas that came up are on the [[Team:KULeuven/Brainstorm|brainstorm page]].
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== June 17th ==
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present: SDK, KM, JVDL, YM, LVO, JR, AC, IT
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The ideas that came up are on the [[Team:KULeuven/Brainstorm|brainstorm page]].
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Marianne Heselmans, journalist for LifeSciences (Netherlands) and Mens&Molecule (Belgium) contacted us for an interview! She has written an article on iGEM and the Dutch and Belgian teams that are participating.
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== June 23rd ==
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present: SDK, LVO, KM, JW, YM, JVDL, IT
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The ideas that came up are on the [[Team:KULeuven/Brainstorm|brainstorm page]].
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== June 30th ==
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This meeting will be in '''room 01.08''' instead of room 01.213 (CMPG, Landbouwinstituut)!
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Please let me know if you cannot attend. The doodle for these meetings is [http://www.doodle.ch/d3mfvkme93p6n7th here]. If possible, it would be nice if most students could attend. -[[User:Ingethijs|Ingethijs]]
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<br>
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'''meeting agenda'''
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* set the final project idea(s)
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* things to think about:
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** good lab practice & safety training?
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** lab coats?
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** lab organisation: eg. do we order enzymes, disposables etc. especially for iGEM? how much space is there - can we divide the team over the labs or can everyone work in the CMPG lab?
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** do we organise tutorials? if yes, which? - the students could do this themselves: prepare a subject in groups in the week of June 30th and present this on Monday July 7th to the team (interesting topics: basic molecular biology - basic gene technology - basic modeling --> have a look at the teaching resources below for inspiration)
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** fund raising?
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** contact press - which?
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* set-up summer planning:
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** the week of June 30th to July 1st is "orientation week" --> can for instance be used to carefully assess the possibility of the project idea(s)
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** full speed iGEM from July 7th to September 19th
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** I'm making an overview of all summer agenda's - ensure continuity in lab guidance
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** room 91.13 of the LBI is reserved for iGEM for the whole summer holiday
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** should we fix a weekly meeting day+hour?
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= Practical stuff =
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nickvd: I propose to start working on the project the first week of July (read: Monday 7th). In that way we can get some rest after the exams, recharge our batteries so we can start working with a clear mind and full of motivation!
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*That would be excellent, because I' m going to Werchter... So I'm available starting from Monday 7th --[[User:Hanne|Hanne]] 20:05, 22 May 2008 (UTC)
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* I am also back on the 7th. --[[user:andim|Andim]]
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* ...
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Are there people that can start on Monday 30th of June or somewhere that week? For instance because they have few exams, don't like holidays... ;) For some BioBricks playing-around, preliminary testing, toy-modeling etc. --Inge
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* My last exam is on the 25th... I'll have a headache for the first two days and then I would like to review certain things on PID-controllers and Matlab, so I figure I should be able to start soon. --[[User:Avdmeers|Antoine]]
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* I can start the 3rd of July (and perhaps the 1st also) [[user:Bmoeyaert|Benjamien]]
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* I should be able to start the 1st of July. [[user:BNathalie|Nathalie]]
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* Normally I can also start the 30th of june [[user:Jotaro|Jan]]
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* I don't mind messing about a bit that first week, so no problem for me [[user:Zeunas|Jonas]]
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== Planned summer holidays==
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* IT: August 2nd-17th
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* [[User:Bmoeyaert|Benjamien]]: August 2nd-17th
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* nickvd: no holiday plans, only moving plans the first week of July. I would also prefer to end somewhere around September 10th to get some rest before my thesis year.
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* Stefanie: no holiday plans, only moving plans the first week of July.
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* [[User:Hanne|Hanne]]: August 11th-17th, August 6th, and a short minibreak.
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* [[User:Zeunas|Jonas]]: I'm out of town September 15-21 and end of july, no other plans yet
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* Elke: September 12th-19th
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* [[User:Jotaro|Jan]]: In the beginning of september I'm probably expected to start in the lab with my thesis, but maybe I can also work a week for my thesis in august so I can also participate a week in IGEM in september. I'll try to arrange what fits with my promotor, but it's too early to say. I don't have holiday plans yet, but if there's a gap when there's no work for IGEM, I'll probably go on holiday :)
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* [[User:BNathalie|Nathalie]]: I only planned something from June 28th until July 1st. So normally, I will be available all the time.
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* [[User:maarten|maarten]]: no holiday plans so far, but like nick I would also prefer to end somewhere around September 10th so I can relax a bit before I start working on my thesis
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* [[User:Avdmeers|Antoine]]: 3 short breaks in August, not planned yet though
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*[[User:andim|Andim]]: June 24th- July7th I will be at home in Istanbul, then the weekend after I am not here.
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* Dries: August 20th-31th
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= Interesting reads =
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<!--  biblio werkt nog niet <biblio> -->
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<!-- #paper 1 pmid=10659857 -->
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== Teaching resources ==
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* [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology Imperial College Introduction to Synthetic Biology Spring 2008]
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* [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals Imperial College Computer Modelling Practicals Spring 2008]
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* [http://openwetware.org/wiki/Intertech:iSB2008 Valencia Introduction to Synthetic Biology 2008]
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* [https://andersonlab.qb3.berkeley.edu/Tutorials/Computational_iGEM.html Berkeley course on Synthetic Biology]
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* [http://www.openwetware.org/wiki/Harvard:Synthetic_Biology_Nanocourse/2007 Harvard Synthetic Biology Nanocourse 2007]
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== Software resources ==
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* [http://en.wikipedia.org/wiki/Wikipedia:Tutorial A wiki tutorial that can be very useful]
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* [http://sbml.org SBML]
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* [http://www.systems-biology.org/cd/index.html CellDesigner]
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== General ==
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* [http://www.nature.com/nature/comics/syntheticbiologycomic/index.html synthetic biology comic]
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* [http://gardnerlab.bu.edu/publications/Gardner.TS_PhDThesis_2000.pdf PhD thesis Timothy Gardner (toggle switch!)]
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== iGEM and BioBricks ==
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* [http://parts.mit.edu/wiki/index.php/Resources introductory resources on the iGEM competition]
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* [http://partsregistry.org/wiki/index.php/Help:Team_experience_tutorial iGEM tutorial]
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* [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses example of an iGEM model - Imperial 2006]
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* [http://parts.mit.edu/igem07/index.php/Taipei wiki of Taipei 2007, interesting links]
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* [http://openwetware.org/wiki/IGEM:Projects_categorized all previous iGEM projects categorized, feel free to add]
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<br>
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* [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]
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* [http://partsregistry.org/Help:IGEM_08_DNA_distribution BioBricks 2008 spring distribution]
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* [http://partsregistry.org/Measurement BioBricks measurement]
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* [http://openwetware.org/wiki/Parts_characterization parts characterization]
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* [http://partsregistry.org/wiki/index.php/Help:Contents BioBricks help]
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<br>
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* PMID 16978856: Chris Voigt 2006 review on synthetic biology parts (sensors, switches etc.) ! very useful to use in tutorials !
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* PMID 18410688: BioBrick vectors
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== Original research papers and reviews ==
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* PMID 10659857
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* PMID 10659856
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* PMID 15858574
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* PMID 17700541
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* PMID 16330045
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* PMID 18410688
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* PMID 16306983
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<!-- </biblio> -->
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Latest revision as of 15:42, 19 October 2008

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