Team:Newcastle/Meetings/30 April 2009

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Contents 1 Instructor Meeting 30 April 2009 1.1 Agenda of the Meeting 1.2 Last Meeting’s Action Points 1.3 Questions about Modelling 1.4 Check Action Points from Previous Meetings 1.5 Set a date for laboratory refresher session 1.6 BioBrick Tutorial 1.7 Review iGem Logos 1.8 NEW ACTION POINTS 1.9 PRIORITIES 1.10 AGENDA FOR 07/05/09:

Instructor Meeting 30 April 2009

Chairperson – Arun Minutes – Mathew R

PRESENT: Neil, Jen, Dan, Morgan, Jess, Goksel, Hanny, James, Arun, MathewR APOLOGIES: Craig, Matthew P

Agenda of the Meeting

• Last meeting's action points
• Questions about modelling
• Check action points from previous meetings
• Set a date for the Lab Refresher session in June
• Ask about the Lab Work start date
• Briefly look at the timeline
• BioBrick tutorial after the meeting
• Review new logos

Last Meeting’s Action Points

• People assigned responsibilities for different tasks – This has been done! A page has been created on the wiki called ‘Meeting structures’ laying out structures for both Internal and General meetings. The order of chairperson and minutes-taker is also listed.
• Start on Modelling – Ongoing
• Model the metal intake – James has been searching for equations to use. Has started to put structure together. Will need to develop structure first and then play with values and parameters. Will also need to organise a modelling tutorial for clarity. Will need to look at CellML repository for examples (especially BioModels)
• Model the ComK system – Jane has looked at equations on Goksel’s suggested paper but needs to confer with lecturer about it. Managed to get a simulation working for next meeting!
• Model Sin Operon – Goksel has constructed a map with all of the elements involved in the sin operon. Has also written equations in CellML. In addition, Goksel has attempted to write equations for ComK in CellML. Needs to get this stochastic switch model simulation up and running.
• Investigate if Sigma A is turned off during sporulation – Jess has put a paper on wiki under ‘Useful Links.’ The researchers found Sigma A in the spores but were unsure whether it wasn’t used until germination. Sigma A is used in early spore formation. Needs to research a more recent paper concerning Sigma A and sporulation as paper researched is from 1999. Dan has offered help if needed.
• Calculate cost of synthesizing promoter library – Arun has consulted GeneWorks for costs. Needs to now find consensus sequence for promoter and submit them to the company. Also needs to decide degeneracies because degeneracies cost money!
• Contact Leendert Hamoen to register to iGem wiki – have done so but he is unable to confirm his place as advisor for the iGem team.
• Contact Nigel Robinson concerning metallisation – have done so and got a good response. However the right question has not been answered and so another email will be needed with the question better clarified (with examples just to make sure the right question has been asked). Also another question needs to be asked: Can certain promoters be inhibited by metals?
• Take Pictures of meetings – Needs to be done on Monday’s meeting!

Questions about Modelling

Need to install MatLab once contact to the company has been made. Also need to look iGem Website for discounts (e.g. GeneWorks) for synthesizing promoter libraries.

Check Action Points from Previous Meetings

Looked at timetable for previous action points

• Still need to consider making flyers for sponsors
• Still need to implement modelling but it is ongoing
• Need to transfer files from internal wiki to external wiki.
• Review of modelling tasks – ongoing
• Review of BioBrick standards – going to be covered later today

Need to consider population modelling. Also need to have page on wiki listing all of the genes along with constructs and reasons for selection for the project. Need to also design a few experiments demonstrating ‘cool’ concepts, e.g. stochastic switch – this is to prove that several elements of our project work and that our idea could also fit together. For next week, we will need to look at Gold Award checklist!

Set a date for laboratory refresher session

Looked at timetable at proposed time for lab refresher session and agreed it was feasible – 15th June 2009.

BioBrick Tutorial

Conducted after this meeting – involved refreshing our knowledge on microbial genetics along with the concept and structure of a BioBrick.

Review iGem Logos

Hanny presented a set of logos she had created – all of them with similar layout but differing in some properties. Needs to possibly integrate the project name ‘Bac-Man’ into the logo.

NEW ACTION POINTS

1. Model of Metal Intake – need to develop structure of model first and then play with values and parameters.
2. Model of Metal Intake – need to organise a modelling tutorial for clarity on what modelling involves.
3. Model of Metal Intake – look at SBML repository for examples of models especially BioModels.
4. Model Sin Operon – Get the stochastic switch model simulation up and running.
5. Sigma A – need to research more recent papers concerning Sigma A and sporulation.
6. Promoter Library – need to now find consensus sequence for promoter and submit it to company.
7. Promoter Library – need to decide on degeneracies as degeneracies cost money!
8. Contacting Nigel Robinson – resubmit query with a little more clarity!
9. Contacting Nigel Robinson – Send question: Can certain promoters be inhibited by metals?
10. Modelling – need to install MatLab once contact with company has been made.
11. Modelling – look on iGem website for discounts (e.g. GeneArt) for synthesizing promoter libraries
12. Previous action points – still need to consider making flyers for sponsors
13. Previous action points – still need to implement modelling (ongoing)
14. Previous action points – need to transfer files from internal wiki to external wiki
15. Previous action points – review modelling tasks (ongoing)
16. Previous action points – review of BioBrick standards
17. Need to consider population modelling
18. Need to have page on wiki listing all of the genes along with constructs and reasons why the genes were selected.
19. Design a few experiments demonstrating ‘cool’ concepts e.g. stochastic switch
20. FOR NEXT WEEK – look at Gold Award checklist!
21. Possibly integrate the project name ‘Bac-Man’ into the logo.

PRIORITIES

1. GERMINATION
2. Model of Metal Intake – need to develop structure of model first and then play with values and parameters (James)
3. Model of Metal Intake – need to organise a modelling tutorial for clarity on what modelling involves.(James)
4. Model of Metal Intake – look at CellML repository for examples of model (components) especially BioModels. (James)
5. Model Sin Operon – Get the stochastic switch model simulation up and running. (Goksel)
6. Modelling – need to install MatLab once contact with company has been made. (Goksel)
7. Sigma A – need to research more recent papers concerning Sigma A and sporulation. (Jess)
8. Need to have page on wiki listing all of the genes along with constructs and reasons why the genes were selected. (Mathew)
9. Promoter Library – need to now find consensus sequence for promoter and submit it to company. (Arun)
10. Promoter Library – need to decide on degeneracies as degeneracies cost money! (Arun)

AGENDA FOR 07/05/09:

• Review previous meeting’s action points.
• Organise a modelling tutorial date.
• Revision week?
• What other teams are doing.
• Priorities strategy.