Team:TUDelft/Meetings

Meeting 17

• Wednesday August 28 12:30-13:30
• Kluyverlab room C

Agenda

• Progress on experimental and modeling work
• Outcomes of the meeting with Peter Leon
• Comments for

Meeting 16

• Wednesday August 20 12:30-13:30
• Kluyverlab room C

Agenda/Minutes

• Stabs: ordered, received (9 stabs), already growing in a culture, the plasmids of which is going to be isolated. (courtesy of Ruud)
• Transformation: final checks to make sure sure that the problems are on the DNA. (+) control works fine, (the problem is not on the transformation protocol) put the DNA in a gel, got unclear/weird images. It looks like with the IGEM protocol (includes a heating step up to 42oc), you loose DNA but many impurities under the form of chopped off protein. In time DNA denaturates. Plans: There is one more thing to test: to transform the DNA we received to test promotor strength.
• PCR: Ruud is setting up/checking available PCR protocol. 95-50-75 protocol with Taq polymerase seems expectedly working. Plans: Put the genes into a vector (from stabs)
• New sequence design: Bastiaan made an additional sequence design that would allow to be activated starting from ~27oC. He got the green light to order it together with an additional sequence (to be activated at ~32oC). Where to order? (Action man:Bastiaan)
• How to test the temperature? We have a meeting with Peter Leon Hagedoorn. The outcomes of this meeting will be reported.
• Modeling work: The coloring pathway is curated. Found a parameter set for which the system is stable. Bifurcation analysis is carried out to find out parameter regions for which the system is locally stable. BRENDA is checked for nominal values of the a number of parameters in the pathway. Most values lie between 0.001-0.034. Matlab freaks have practical problems in generating random numbers within this region. Plans: make the enzyme variable, (currently constant). Check the literature for temperature enzyme activity relations.
• Questions: -What is actually in the vector? (from Steven to the Pipette nerds)

-How do you plan to integrate (plug in/adapt not Runge-Kutta), the Temperature dependence of the enzyme activity? Put a switch.

• Additional remarks: Janine said: "Disregard my remarks".

Three distinct words from Domenico: Document, document, document

Meeting 15

• Wednesday August 13 12:30-13:30
• Kluyverlab room C

Agenda/Action Points in the meeting:

• Trip to Groningen: it was a nice, introductory meeting with the Groningen team. we'll arrange a similar one somewhere in September.
• Webpage: Ethics sub-part is nicely filled (courtesy of Steven). Lab-notebook should be filled (almost) day-by-day. Separate remarks made for Experimental-Modeling wiki sub-parts.
• New advisor: Ali Mesbah is the new advisor. He will supervise/advise the modeling works, mostly ODE modeling part
• Orders: Having problems in the transformations, stabs will be ordered (Action man: Ruud). Further oligos will be ordered since these are delivered faster (Action man: Bas).
• Project Proposal: This version is highly improved (courtesy of Ruud). Marco still had comments.
• Travel: We are staying in Holiday-Inn Somerville

Meeting 14

• Wednesday August 6 12:30-13:30
• Kluyverlab room C

Agenda:

• progress of lab work
• modeling
• travel arrangements

Meeting 13

• Thursday July 31 12:30-13:30
• Kluyverlab room C

Agenda:

• progress of lab work
• project description
• modeling

Meeting 12

• Thursday July 24 12:30-13:30
• Kluyverlab room C

Agenda:

• Modeling fo the RNA switches. Planning of the experimental work.

Meeting 11

• Wednesday July 16 12:30-13:30
• Kluyverlab room D

Agenda:

• We got final a project. We have now to work it out...

Meeting 10

• Wednesday July 9 12:30-13:30
• Kluyverlab room C

Agenda:

• Final Brainstorming (... the previous one was not that final after all...).

Meeting 9

• Wednesday July 2 12:30-13:30
• Kluyverlab room B

Agenda:

• Final Brainstorming.

Meeting 8

• Thursday June 26 12:30-13:30
• Kluyverlab room C

Agenda:

• Brainstorming with the advisors.

Meeting 7

• Wednesday June 18 12:30-13:30
• Kluyverlab room B

Agenda:

Discussion with Ibo van der Poel on value sensitive design and related ethical issues.

Meeting 6

• Wednesday June 11 12:30-13:30
• Kluyverlab room B

Agenda:

• Brainstorming with the advisors.

Meeting 5

• Wednesday June 4 12:30-13:30
• Kluyverlab room D

Agenda:

• Primer on Molecular biology and modeling in a nutshel.
• Report about the teacher'workshop in Paris (Domenico).
• Update on systematic classification of previous year iGEM projects.

Report:

• Primer on Molecular biology and modeling in a nutshel.

The team members in "need" will have a separate session. Valencia link for some courses: [http://openwetware.org/wiki/Intertech:iSB2008:Materials Synthetic biology course-Valencia]. Nice course organized in 3 parts: training for biologists, training for engineers and training in syntetic biology. The students will meet tomorrow at 14:00.

• Report about the teacher'workshop in Paris (Bastiaan).

Everyone was very motivated, we also met members of the team from Groningen (NL). An introduction was given in which we were told we are at the beginning of a new era. We should not exppect to solve large problems like cancer but start out slow and easy. Some teams are larger than ours (12 members) and some are already working with parts in the wet lab.

The main wiki page should be the WiKi on iGEM. Two weeks before the Jamboree this will be locked! If nothing is there it will not be evaluated! Also be sure we have all information on the wiki before this closing date.

In general: Documentation is one of the most important parts of the iGEM project!

Beware errors are possible in the current DNA archive. Be sure to check by restriction analysis if you have the correct construct! If we foind an eronous construct the correct one can be dsipatched quicklly

www.partsregistry.org : large source of information on the parts, also protocols for extracting the DNA from the provides folder and making compentent cells. Registering parts: Start registration from the start of developement or even generation of the idea.

We have to impress/stunn/amaze the Judges: generate a novel and original idea (poineering, cutting edge, ambitious). Split the idea in steps/milestones and work on one step at the time (kind of modular organisation of the project).

Teams are invited to contribute to an inter-lab comparisson within iGEM.

Many protocols can be found on openwetware, however be aware the ones in the iGEM registry are tested and proven to work, using other protocols are on your own account (if you do, document/report)

Building on previous projects is encouraged, as long as you document it well and be sure to refer/acknowledge iGEM and the specific team.

• Update on systematic classification of previous year iGEM projects.

Most of them are done.

• Brainstorming next week

As a starting point use the classification of the previous iGEM projects. Members should present ideas to the advisors next meeting, prepare a few ppt slides/wiki entries.

Meeting 4

• Wednesday May 28 12:30-13:30
• Kluyverlab room D

Action points:

• Systematic classification of iGEM projects of previous year. Apparently a webpage already exists on openwetware that has initiated this effort; therefore we will add on that. Bastiaan will take the lead: he will assign each student a bunch of projects to claasify. This will facilitate the discussion with the advisors.
• Add a description of your competences/expertise on the wiki, so that it is clear what is your contribution to the project (Ruud, Rad, Farzad, Steven).
• A planning will be posted on the webpage so that we know when everyone is available (Oscar). (*Filippo Menolascina 05:19, 29 May 2008 (EDT): we could use gmail calendar integration supplied by OWW to work out this...some other users have implemented it. Oscar, if you need help tell me!)
• Have a look at the synthetic biology course of the [http://openwetware.org/wiki/Imperial_College/Courses/Spring2008/Synthetic_Biology Imperial College] (all).
• Have a look at the experimental protocols for DNA extraction (Ruud).

Meeting 3

• Thursday May 22 12:30-13:30
• Location: let us meet at room D. From there we will head to the garden since no room is available... :)

Meeting 2

• Wednesday May 14 12:30-13:30
• Kluyverlab room D

Meeting 1

• Thursday May 8 12:30-13:30
• Kluyverlab room D

Introduction meeting

• Thursday April 24 17:00-18:00
• Kluyverlab room D