Newcastle University/3 July 2008

From 2008.igem.org

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[[Team:Newcastle University/Notebook|Back to Calendar]]
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iGEM Minutes 03/07/2008
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'''Minutes'''
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Minute Taker = Mark Wappett
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'''Minutes IGEM'''
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Action Plan for next Week
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Date: 03/04/08
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'''Group'''
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Place: CT. 601
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Time: 15.30-17.00
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Attendees: 8/9
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• Start writing up Thesis introduction section.
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• Go through the .gb file for the BioBrick and add/edit metadata to meet iGEM specifications
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Guest: Jan Willem-Venning
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• JDBC tutorial – learn how to use.  This will be held at 10am on Monday morning
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Supervisors:
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• Interface coding – will take place on Tuesday when Matthew has time – probably will be Tuesday Afternoon.
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Dr Anil Wipat (anil.wipat@newcastle.ac.uk), Dr Jennifer Hallinan (j.s.hallinan@newcastle.ac.uk), Dr Matthew Pocock (matthew.pocock@newcastle.ac.uk), Morgan Taschuk (mtaschuk@gmail.com)
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Team Members:
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''Megan''
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Nina Nielsen (nina.nielsen-dzumhur@newcastle.ac.uk), Mark Wappett (mark.wappett@newcastle.ac.uk), Megan Aylward (megan.aylward@newcastle.ac.uk)
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• Continue coding up part models
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Agenda 1
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• Work on database and JDBC
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Discussing the GA Homework
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Nina describes her Java code on the screen (eclipse).
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• Present Thesis writing at first group writing meeting on Thursday
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Mark describes his Java code on the screen (intelliJ).
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Both only took about 10 seconds to run. Agree that these programmes are much better than BlueJay!
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Run out of time so decide Megan can describe her code later.
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Agenda 2
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'''Mark'''
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Discussing more application ideas. HAVE TO KNOCK ONE OUT TODAY!
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Mark describes another idea based on MRSA
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• Continue developing EA – adding multiple Mapping functionality and separate hidden layer node promoter scoring
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Based on a potential vaccine developed for Malaria parasite.
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Works by priming the T cells to EDA175 conserved\to parasite.
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As soon as it gets into body should trigger an immune response.
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Presence of proteins on MRSA surface are quite conserved too (Isda and isdb).
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Utilize the same theory. Use Bacillus because harmless, to alter the surface.
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Jan mentions a lot of work has been carried out to use spores of Bacillus as oral vaccines. The spores are easy to probe, harvest and are very stable.
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However Jan also says although this is a good idea and would make a good biobrick, it is already relatively simple to make and you wouldn’t need to implement a GA. Also not sexy enough!?
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Anil asks if Mark has identified a particular protein on MRSA
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Marks mentions there are potentially 4..could use them all?
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But Matt asks if these proteins are specific to MRSA or all SA and it turns out they are not specific to MRSA. This is dangerous as SA exists non-pathogenically on our hands and other places and triggering an immune response to these bacteria wouldn’t be great.
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Group discusses potential of a specific protein expressed extracellularly on MRSA.
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Morgan queries whether there is another way of detecting MRSA?
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Fall back to the problem of detection intracellularly?
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Idea last week didn’t work spatially.
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Nina talks about using two component systems and generating models to inhibit multiple signalling pathways in MRSA.
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• Print promoter strengths and add to tab-delimited files
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To maintain specificity to a type of resistance, the particular HK and RRs can be subjected. For example Vancomycin resistant superbugs with VanR and VanS proteins.
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But a problem with MRSA is that the proteins may not be well conserved.
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Matt mentions a need to find extracellular conserved proteins.
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• Look at CellML parsing and simulation – CellML needs to be added as fitness function.
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Megans draws a schematic/flow diagram on the board depicting how a Receptor on a bacillus plasmid, specific to proteins secreted extracellularly by MRSA, can cause a cascade of events in the Bacillus genome, including the expression of GFP (or/and othe fluorescent proteins).
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• E-mail Jan-Willem about Fridays in the lab over August
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This would provide a rapid diagnostic, which is missing in the market.
 
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Jan mentions that some kind of signal amplifier may be necessary to switch on the fluorescence protein effectively.
 
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A possibility of indicating the strength of the MRSA is also possible.
 
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Jen then suggests that the Bacillus (good bug) could maybe be used to detect the presence of many resistant bacteria (bad bugs) by detecting multiple proteins. Could have several colours for several types of “superbugs”.
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'''Time:'''
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Anil suggested the name “Police Bugs”
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14:30 – 15:30 (followed by discussion and drinks with Neil at the Northern Stage)
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Jen mentions that the amplification system links very nicely with an EA
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'''Attended by:'''
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Jan suggested that the one bug could be 50% MRSA sensitive and 50% another resistant bacteria (such as streptococcus) sensitive, as the interpretation could be easier that way.
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Anil Wipat - Supervisor
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Matt then suggested using combinations of colours so that the resistance is more specified and more types of bacteria can be defined and detected. For example, the presence of MRSA switching a red protein off, green on and yellow on but streptococcus switching red on, green on and yellow off. This would create a profile which would be more accurate too.
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Jen Hallinan – Supervisor
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Matthew Pocock – Supervisor
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Mark Wappett – Project 3
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Agenda 3
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Megan Aylward – Project 1
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Editing Wiki
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• Morgan went through how to add documents and edit the wiki page. A series of buttons that work like a very simple HTML.
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'''Not Attended by:'''
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Action Plan.
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Morgan Taschuk
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• Organize meeting for artificial neural networks for week starting 06/04/08
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• Research and read about specific extracellular proteins secreted from MRSA, possible receptors or RR that could be expressed on Bacillus to receive an input when the MRSA protein is secreted.
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• Put appropriate papers on wiki
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AOB
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Nina Neilson-Dzumhur
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• Matt will be talking about EA on Friday 04/04/08
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• Anil is away next week.
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Jan-Willem
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Meeting Content:
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Jen starts with the Edinburgh trip and Meeting.  Brings up the e-mail discussing the itinery of the stay.
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Accommodation will be provided free in student Dorms, and we will be setting off by Train on the morning of the 15th of July.
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Need to put some though into what to tell them – essentially now everything as we have nothing left to hide. 
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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.
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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
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Altering miscellaneous features would be a good idea.
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Action Plan
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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.
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Next Meeting: 03/04/08 at 15.30 CT 701.
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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. 
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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.
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Start with the Introduction, background or even the methods section as this may still be fresh in everyones minds.
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Point made that we really need to be all coded up over the next four weeks so this is really crunch time.
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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. 
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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. 
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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.
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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. 
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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.
 +
 
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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.
 +
 
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The normal iGEM meeting will be moved to 3:30 directly after the Writing group meeting from now on.
 +
 
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2:30 Meeting concludes and group moves down to Northern Stage to meet with Neil.
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AOB – Discussed at Northern Stage
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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.
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Still £1,000 up for grabs for another person to come on board in the lab with Rea.
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Mark suggests his friend Jess.

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.

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