Newcastle University/3 July 2008

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Latest revision as of 14:52, 11 July 2008

iGEM Minutes 03/07/2008

Minutes

Minute Taker = Mark Wappett

Action Plan for next Week

Group

• Start writing up Thesis introduction section.

• Go through the .gb file for the BioBrick and add/edit metadata to meet iGEM specifications

• JDBC tutorial – learn how to use. This will be held at 10am on Monday morning

• Interface coding – will take place on Tuesday when Matthew has time – probably will be Tuesday Afternoon.

Megan

• Continue coding up part models

• Work on database and JDBC

• Present Thesis writing at first group writing meeting on Thursday

Mark

• Continue developing EA – adding multiple Mapping functionality and separate hidden layer node promoter scoring

• Print promoter strengths and add to tab-delimited files

• Look at CellML parsing and simulation – CellML needs to be added as fitness function.

• E-mail Jan-Willem about Fridays in the lab over August

Time:

14:30 – 15:30 (followed by discussion and drinks with Neil at the Northern Stage)

Attended by:

Anil Wipat - Supervisor

Jen Hallinan – Supervisor

Matthew Pocock – Supervisor

Mark Wappett – Project 3

Megan Aylward – Project 1

Not Attended by:

Morgan Taschuk

Nina Neilson-Dzumhur

Jan-Willem

Meeting Content:

Jen starts with the Edinburgh trip and Meeting. Brings up the e-mail discussing the itinery of the stay. Accommodation will be provided free in student Dorms, and we will be setting off by Train on the morning of the 15th of July. Need to put some though into what to tell them – essentially now everything as we have nothing left to hide. We need to prepare a presentation that will be around 20 minutes in length leaving 10 minutes at the end for questions. This really needs to be looked at in the coming week and discussed at length in the next meeting.

Jen suggests getting the control Biobrick submitted to the repository prior to the Edinburgh meeting so we have something to show when we go up there. This involves us meeting up and going through the Genbank file Jan-Willem created and editing the Metadata so that it meets the iGEM specifications Altering miscellaneous features would be a good idea.

Flights have been booked for the 7th November. We will be flying over to Amsterdam before connecting to Boston. We will be flying with KLM.

We may have to book a Hostel while we are over there as Hotels are ridiculously priced – i.e. up to $350 US a night. Need to look at Hostels on the HostelWorld website, although there is only one in the centre. If we can find one outside the centre close to a T light railway station we could potentially book that one.

Jen and Matt turn the discussion to write-ups. We have started our own writing group. Others outside the iGEM project are more than welcome to join in so ask Matt, Kathryn, Jay, Shree, William etc.

Start with the Introduction, background or even the methods section as this may still be fresh in everyones minds.

Point made that we really need to be all coded up over the next four weeks so this is really crunch time.

Mark outlines a few problems/issues with the EA design. Most were addressed in the previous meeting with Jen. However the issue is with what exactly to swap.

Matt makes the point that any sequence part that could be changed can be – i.e. you would not change a ribosome you would change a Ribosome binding site for example.

It was agreed that primarily the EA will be concerned with the switching of Promoter sites based on their strengths, however this will be extended to transcription factors and ribosome binding sites as time moves on. There is also scope for the adding and removal of parts to the data.

Megan starts to discuss some of the problems she is having with building parts in CellML and getting real numerical values on things such as promoter strengths.

Jen points out that unfortunately Biologists are not interested in researching and therefore publishing in the literature what we are often interested in. This makes our research much more difficult as a result of this.

Megan then brings up the issue of JDBC and getting database objects to plug into Java. Matt suggests a tutorial for this on Monday at 10am where we can learn how to use this. The feature will make up an important part of the Interface between the Parts repository and the EA.

Matt queries how we have been getting on with the Interface. Mark and Megan state what they have done. Matt suggests that this is taken onto the next stage by an interface coding session on Tuesday Afternoon.

The normal iGEM meeting will be moved to 3:30 directly after the Writing group meeting from now on.

2:30 Meeting concludes and group moves down to Northern Stage to meet with Neil.

AOB – Discussed at Northern Stage

CellML simulation problems. Neil has e-mailed Mike and James about solving this problem. May have to jump ship to SPML if this problem cannot be solved.

Still £1,000 up for grabs for another person to come on board in the lab with Rea. Mark suggests his friend Jess.

@@ Line 1: / Line 1: @@
-  [[Team:Newcastle University/Notebook|Back to Calendar]]
+iGEM Minutes 03/07/2008
+'''Minutes'''
+Minute Taker = Mark Wappett
+Action Plan for next Week
+'''Group'''
+•	Start writing up Thesis introduction section.
+•	Go through the .gb file for the BioBrick and add/edit metadata to meet iGEM specifications
+•	JDBC tutorial – learn how to use.  This will be held at 10am on Monday morning
+•	Interface coding – will take place on Tuesday when Matthew has time – probably will be Tuesday Afternoon.
+''Megan''
+•	Continue coding up part models
+•	Work on database and JDBC
+•	Present Thesis writing at first group writing meeting on Thursday
+'''Mark'''
+•	Continue developing EA – adding multiple Mapping functionality and separate hidden layer node promoter scoring
+•	Print promoter strengths and add to tab-delimited files
+•	Look at CellML parsing and simulation – CellML needs to be added as fitness function.
+•	E-mail Jan-Willem about Fridays in the lab over August
+'''Time:'''
+:30 – 15:30 (followed by discussion and drinks with Neil at the Northern Stage)
+'''Attended by:'''
+Anil Wipat - Supervisor
+Jen Hallinan – Supervisor
+Matthew Pocock – Supervisor
+Mark Wappett – Project 3
+Megan Aylward – Project 1
+'''Not Attended by:'''
+Morgan Taschuk
+Nina Neilson-Dzumhur
+Jan-Willem
+Meeting Content:
+Jen starts with the Edinburgh trip and Meeting.  Brings up the e-mail discussing the itinery of the stay.
+Accommodation will be provided free in student Dorms, and we will be setting off by Train on the morning of the 15th of July.
+Need to put some though into what to tell them – essentially now everything as we have nothing left to hide.
+We need to prepare a presentation that will be around 20 minutes in length leaving 10 minutes at the end for questions.  This really needs to be looked at in the coming week and discussed at length in the next meeting.
+Jen suggests getting the control Biobrick submitted to the repository prior to the Edinburgh meeting so we have something to show when we go up there.  This involves us meeting up and going through the Genbank file Jan-Willem created and editing the Metadata so that it meets the iGEM specifications
+Altering miscellaneous features would be a good idea.
+Flights have been booked for the 7th November.  We will be flying over to Amsterdam before connecting to Boston.  We will be flying with KLM.
+We may have to book a Hostel while we are over there as Hotels are ridiculously priced – i.e. up to $350 US a night.  Need to look at Hostels on the HostelWorld website, although there is only one in the centre.  If we can find one outside the centre close to a T light railway station we could potentially book that one.
+Jen and Matt turn the discussion to write-ups.  We have started our own writing group.  Others outside the iGEM project are more than welcome to join in so ask Matt, Kathryn, Jay, Shree, William etc.
+Start with the Introduction, background or even the methods section as this may still be fresh in everyones minds.
+Point made that we really need to be all coded up over the next four weeks so this is really crunch time.
+Mark outlines a few problems/issues with the EA design.  Most were addressed in the previous meeting with Jen.  However the issue is with what exactly to swap.
+Matt makes the point that any sequence part that could be changed can be – i.e. you would not change a ribosome you would change a Ribosome binding site for example.
+It was agreed that primarily the EA will be concerned with the switching of Promoter sites based on their strengths, however this will be extended to transcription factors and ribosome binding sites as time moves on.  There is also scope for the adding and removal of parts to the data.
+Megan starts to discuss some of the problems she is having with building parts in CellML and getting real numerical values on things such as promoter strengths.
+Jen points out that unfortunately Biologists are not interested in researching and therefore publishing in the literature what we are often interested in.  This makes our research much more difficult as a result of this.
+Megan then brings up the issue of JDBC and getting database objects to plug into Java.  Matt suggests a tutorial for this on Monday at 10am where we can learn how to use this.  The feature will make up an important part of the Interface between the Parts repository and the EA.
+Matt queries how we have been getting on with the Interface.  Mark and Megan state what they have done.  Matt suggests that this is taken onto the next stage by an interface coding session on Tuesday Afternoon.
+The normal iGEM meeting will be moved to 3:30 directly after the Writing group meeting from now on.
+:30 Meeting concludes and group moves down to Northern Stage to meet with Neil.
+AOB – Discussed at Northern Stage
+CellML simulation problems.  Neil has e-mailed Mike and James about solving this problem.  May have to jump ship to SPML if this problem cannot be solved.
+Still £1,000 up for grabs for another person to come on board in the lab with Rea.
+Mark suggests his friend Jess.