From 2008.igem.org

Revision as of 07:02, 1 July 2008

This page contains information on meetings and schedules, on practical stuff, and some suggestions on background reading.

Brainstorm ideas for the project have been moved to the brainstorm page.

Spelen met de wiki doe je in de zandbak, vragen stellen of suggesties doen op de discussiepagina.

To do

• check for international passport
• design a team t-shirt (Could someone check whether we can use Jan Fabre's Totem?)
• book flights and hotel
• can someone check out how to work with the notebook?

Meetings

May 22nd

students and instructors brainstorm @ ESAT 01.57

present: all students, SDK, LVA, YM, JR, GG, IT

• Each student presented his/her 3 favourite projects of previous iGEMs. All project brainstorm ideas are moved to the project page. There, you can add links to your favourite projects and/or upload your presentation.
• The group picture is on our team page.
• Vote here for the logo you like best (thanks Jonas for the logo and Benjamien for the Zandbak and Discussiepagina idea!).
• To make a summer schedule, please indicate your holiday plans below (Practical stuff - Planned summer holidays). The last exam is on June 27th.
• 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.
• Put ideas and suggestions for the wiki here.
• Inge will inform whether the students can stay at the Studentenwijk Arenberg during the summer holidays.
• 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.
• Check out the [http://www.kuleuven.be/bioscenter/igem iGEM website] at [http://www.kuleuven.be/bioscenter BioSCENTer].

• Good luck with the exams!

June 10th

present: SDK, KM, AC, JR, LVO, IT

Teachers workshop (Inge)
Tom Knight, Randy Rettberg and Meagan Lizarazo organised the Europe teachers workshop. I'll summarize the most important things.

On the project:

• 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
• iGEM is about doing synthetic biology based on standard parts, not about freestyle synthetic biology, however great that can be
• 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?")

On sponsors:

• Matlab will sponsor!
• DNA synthesis by GeneArt (0.25/bp + 35 sample transport) - takes 4-6 weeks!

BioBrick practicalities:

• protocols can be found on openwetware (will be included in the iGEM website soon)
• plasmids in the Registry can be found by looking for ccdB (P1010) - available in a variety of plasmids
• document your parts! take your time for this, documentation is extremely important (cfr. judging page).
• 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!
• [http://partsregistry.org/Measurement Measurement] is important - we received Jason's measurement kit by mail!
• Meagan gave a [http://partsregistry.org/Help:Team_experience_tutorial tutorial] on how to input a part in the registry
• every team has a sandbox and a favorite parts section: the judges will only look at the parts in the favorite parts section!
• each sent in BioBrick should be provided in a standard BioBrick plasmid
• there are no rules on modeling (yet)

General:

• what's the overall goal? impress iGEM ;)
• Over lunch, each instructor had to present his/her team short report.
• As part of the competition, we have to answer the questions on the safety page.
• We're supposed to have fun :) If we don't, we can call them and they'll tell us a joke

Project Brainstorm

The ideas that came up are on the brainstorm page.

June 17th

present: SDK, KM, JVDL, YM, LVO, JR, AC, IT

The ideas that came up are on the brainstorm page.

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.

June 23rd

present: SDK, LVO, KM, JW, YM, JVDL, IT

The ideas that came up are on the brainstorm page.

June 30th

present: Benjamien, Hanne, Elke, Jan, Antoine, Dries, Nick, Stefanie, Jonas, Nathalie, Liesbeth, Sigrid, Astrid, Joris, Johan, Jos, Inge

getting started

• the students prepare tutorials and present these on Monday July 7th to the team (have a look at the teaching resources below for inspiration) --> room 00.210 from 10h to 15h, we'll go to Alma at noon
  • introduction to synthetic biology (goal, examples...): Benjamien, Nathalie
  • basic molecular biology and gene technology: Hanne, Jonas
  • BioBricks (how to work with them - standard cloning procedures - measurement...): Elke, Jan
  • modeling (what for? how? eg. Matlab simbiology etc.) + iGEM modeling (go through last years modeling parts to get an idea of iGEM modeling): Maarten, Nick
• wet lab
  • the team will work in the CMPG labs
  • ensure lab guidance continuity (to do Inge and Sigrid: make list of responsables)
  • all students have lab coats
  • yet to decide how the costs will be arranged (also, do we order enzymes, disposables etc. especially for iGEM?)
• dry lab
  • a desktop pc will be installed in room 91.13 (internet available)
  • Jonas and Antoine explore the possibilities of the wiki (a.o. notebook, templates (eg. digest, PCR... cfr [http://parts.mit.edu/igem07/index.php/Going_through_our_wiki Paris 2007]), ...)
  • during iGEM, everyone is responsible for the wiki
• meeting arrangements
  • room 91.13 of the LBI is reserved for iGEM for the whole summer holiday --> to do: clean + writing board + check who has access
  • weekly meeting at Friday from 12h to 14h in room 00.42 of the LBI. You can order a sandwich by mailing to Inge before Thursday 16h. Students fill out the form by Thursday 16 (still have to put this online) - First meeting is Friday July 18th!
• summer planning
  • week of June 30th to July 1st = "orientation week"
    • prepare tutorials
    • assess the possibility of the project ideas
    • check that we're not repeating previous years' work
    • fill in the details of the project (interesting BioBricks to use, adapt, make...)
    • ...
  • full speed iGEM from July 7th to September 19th

the project
During orientation week, the timer project (PI control of drug production and timer for cell death) and the D project (with regulator and sRNA or with stable/unstable - gfp/TEV protease) will be assessed carefully (see the brainstorm page for an overview of these ideas).

things to think about

• fund raising?
• contact press - which? (Hanne has connections at Het Nieuwsblad)

Practical stuff

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!

• That would be excellent, because I' m going to Werchter... So I'm available starting from Monday 7th --Hanne 20:05, 22 May 2008 (UTC)
• I am also back on the 7th. --Andim
• ...

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

• 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. --Antoine
• I can start the 3rd of July (and perhaps the 1st also) Benjamien
• I should be able to start the 1st of July. Nathalie
• Normally I can also start the 30th of june Jan
• I don't mind messing about a bit that first week, so no problem for me Jonas

Planned summer holidays

• IT: August 2nd-17th
• Benjamien: August 2nd-17th
• 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.
• Stefanie: no holiday plans, only moving plans the first week of July.
• Hanne: August 11th-17th, August 6th, and a short minibreak.
• Jonas: I'm out of town September 15-21 and end of july, no other plans yet
• Elke: September 12th-19th
• 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 :)
• Nathalie: I only planned something from June 28th until July 1st. So normally, I will be available all the time.
• 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
• Antoine: 3 short breaks in August, not planned yet though
• Andim: June 24th- July7th I will be at home in Istanbul, then the weekend after I am not here.
• Dries: July 11, August 20th-31th

Interesting reads

Teaching resources

• [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology Imperial College Introduction to Synthetic Biology Spring 2008]
• [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology/Computer_Modelling_Practicals Imperial College Computer Modelling Practicals Spring 2008]
• [http://openwetware.org/wiki/Intertech:iSB2008 Valencia Introduction to Synthetic Biology 2008]
• Berkeley course on Synthetic Biology
• [http://www.openwetware.org/wiki/Harvard:Synthetic_Biology_Nanocourse/2007 Harvard Synthetic Biology Nanocourse 2007]

Software resources

• [http://en.wikipedia.org/wiki/Wikipedia:Tutorial A wiki tutorial that can be very useful]
• [http://sbml.org SBML]
• [http://www.systems-biology.org/cd/index.html CellDesigner]

General

• [http://www.nature.com/nature/comics/syntheticbiologycomic/index.html synthetic biology comic]
• [http://gardnerlab.bu.edu/publications/Gardner.TS_PhDThesis_2000.pdf PhD thesis Timothy Gardner (toggle switch!)]

iGEM and BioBricks

• [http://parts.mit.edu/wiki/index.php/Resources introductory resources on the iGEM competition]
• [http://partsregistry.org/wiki/index.php/Help:Team_experience_tutorial iGEM tutorial]
• [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses example of an iGEM model - Imperial 2006]
• [http://parts.mit.edu/igem07/index.php/Taipei wiki of Taipei 2007, interesting links]
• [http://openwetware.org/wiki/IGEM:Projects_categorized all previous iGEM projects categorized, feel free to add]

• [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]
• [http://partsregistry.org/Help:IGEM_08_DNA_distribution BioBricks 2008 spring distribution]
• [http://partsregistry.org/Measurement BioBricks measurement]
• [http://openwetware.org/wiki/Parts_characterization parts characterization]
• [http://partsregistry.org/wiki/index.php/Help:Contents BioBricks help]

• PMID 16978856: Chris Voigt 2006 review on synthetic biology parts (sensors, switches etc.) ! very useful to use in tutorials !
• PMID 18410688: BioBrick vectors

Original research papers and reviews

• PMID 10659857
• PMID 10659856
• PMID 15858574
• PMID 17700541
• PMID 16330045
• PMID 18410688
• PMID 16306983

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