IGEM:IMPERIAL/2006/ProjectCalendar/2006-8-9

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Open questions to co-ordinators

(each co-ordinator should edit and answer his/her section)

Assembly

  • What is the status of the different constructs (validated/finished/in construction) ?
    • See Ligation Chart as well as Lab Status Page. We have already started Stage 3 ligations and are awaiting some parts to create the AiiA construct.
  • For those in construction, when are they supposed to be ready ?

    • J37015 - ready
    • J37015RS - ready by Friday
    • J37015Cre - awaiting successful Cre addition, hopefully by next Friday
    • J37016 - ready by Friday
    • J37019 - ready
    • J37020 - ready by next Tuesday
    • J37022 - hopefully in 2 weeks
    • J37023 - awaiting successful FLAG addition, hopefully by next Tuesday
    • J37024 - once J37023 is ready, should be ready in 2 days
    • J37025 - once J37025 is ready, should be ready in 2 days (aiming for 2 weeks)
  • What is the current experience of using PCR to validate successful ligation ?

    • Currently PCR is not working, we have been trying several times, if all else fails, Dr. Mann will intervene

  • Are there any other issues ?

    • Currently no other issues to be raised.

Testing

  • List all the test constructs to be tested and specify the status of the corresponding testing protocol (validated/need feedbacks/unfinished/to be done) + add link to wiki
    • click here for the complete list
  • For each experiment, is it clear how we will use experimental results ?
    • No at the moment, we need modelling team to define parameters in their proposed models
  • Do we still need to validate the Zinc hypothesis in relation to the activity of aiiA ?
    • Yes, after we have constructed J37022

Modelling

  • test constructs
    • Define the level of maturity of the models for each test construct (validated/need feedbacks/unfinished/to be done) + link to wiki
    • Will the experiments help us to specify all the parameters of the different models ?
  • Lotka-Volterra
    • What is our current knowledge of the model ?
    • What is the strategy applied ?
  • Full system
    • Do we have a model for the full system ?
    • Is it working ?

The test construct are as they were previously. Christin and I (Farah) have been working on the overall system model and looking at the individual test construct models to see how they compare. Once we have checked that we are extracting the correct parameters from our test constructs we can then refine the protocols, if necessary, according to our findings. We aim to produce a document tomorrow to track our progress. We'll pass the document on to the rest of the group and Vincent for feedback.

For the LV model, thanks to Matthieu Bultelle's talk today, we have a systematic approach to run ODEs and study the sensitivity and general behaviour of the LV system.

Documentation

  • Do we have an updated version on the WIKI of all the information cited above ?
    • The lab notebook is up to date as of today
    • The skeletons for all the testing protocols are in place. They being refined at the moment and J37015 should be done tomorrow and we plan the rest to be finshed by the end of the week
    • The modelling is not quite complete, however Farah and Christin are looking at the overall model and should have something finished by tomorrow (Thursday). Documentation for the Lotka-Volterra is up on the WIKI.
  • Do we have an updated Gantt chart for the project ?
    • We don't have an updated Gantt chart at present. At the moment we are writing down our targets for the week on the Monday and then, in the debrief, working out what everyone is doing the next day. We plan to put this information down as more formal documentation, but whether this will be in the form of a Gantt chart is yet to be decided.

Others

  • What is the current status on the Biosensor ?
    • Please see Biosensor we are currently trying to find enzymes for implementation of a tri-enzyme electrode, which is able to measure nM ! (link to paper)
  • Are our contacts aware of the current status ?
    • We are in constant correspondance with Anna. Please see link above.
  • Do you still have debriefs ? When ?
    • Yes, we do again - every day at 5pm.

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