Newcastle University/5 June 2008

From 2008.igem.org

(Difference between revisions)
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'''Minutes'''
'''Minutes'''
 +
 +
Minute Taker: Nina Nielson
Action Plan for next week
Action Plan for next week
-
Group
+
'''Group'''
 +
 
• Design a flyer/poster.
• Design a flyer/poster.
 +
• Look at which parts have been identified already. If some of the parts that we are using haven’t been added to the repository yet, the group should put them on.
• Look at which parts have been identified already. If some of the parts that we are using haven’t been added to the repository yet, the group should put them on.
 +
• Add iGem calendar of events to our calendar on our wiki.
• Add iGem calendar of events to our calendar on our wiki.
 +
• We need to research safety of our application. Do we understand the implications? Ask Jan for some tips, cosh form etc..
• We need to research safety of our application. Do we understand the implications? Ask Jan for some tips, cosh form etc..
 +
• We also need to ask Jan if he actually has the strains of bacteria we are going to be using. Thus we need to define the strains that we have been looking at for him.
• We also need to ask Jan if he actually has the strains of bacteria we are going to be using. Thus we need to define the strains that we have been looking at for him.
 +
• Look at cell-cell signalling article on iGem page.  
• Look at cell-cell signalling article on iGem page.  
-
• Do Hibernet tutorial
+
 
 +
• Do Hibernet tutorial]
 +
 
• Do cellML tutorial and start modelling parts.
• Do cellML tutorial and start modelling parts.
 +
• Compare interfaces with User stories.
• Compare interfaces with User stories.
-
Megan
+
'''Megan'''
 +
 
• Research the comC rather than vncR/S TCS in S. pneumoniae (or another suitable two component system).
• Research the comC rather than vncR/S TCS in S. pneumoniae (or another suitable two component system).
 +
• Continue adding to Java.doc.
• Continue adding to Java.doc.
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• Investigate more parts for the chosen peptides.
• Investigate more parts for the chosen peptides.
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• Finish designing the architecture for her database.
+
 +
• Finish designing the architecture for her database.                            
 +
 
• Practise using JBDC
• Practise using JBDC
   
   
-
Nina
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'''Nina'''
 +
 
• Find all associated parts for PlcR/PapR (Blast the peptide).
• Find all associated parts for PlcR/PapR (Blast the peptide).
-
• Email Jan about making sensor-fluorescent protein biobricks, strains of bacteria, and safety information.
+
 
 +
• Email Jan about making sensor-fluorescent protein biobricks, strains of bacteria, and safety information
 +
.
• Investigate potential for using Bacillus anthracis as well as Bacillus cereus. Find associate parts for this species too.
• Investigate potential for using Bacillus anthracis as well as Bacillus cereus. Find associate parts for this species too.
 +
• Practise using JBDC
• Practise using JBDC
-
Mark
+
'''Mark'''
 +
 
• Finish registering to iGem 2008
• Finish registering to iGem 2008
 +
• Meeting with Jen to discuss EA on Tuesday – develop his own action points for EA.
• Meeting with Jen to discuss EA on Tuesday – develop his own action points for EA.
 +
• Construct architecture
• Construct architecture
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Attended by:
Attended by:
 +
Neil Wipat – Supervisor
Neil Wipat – Supervisor
 +
Jen Hallinan – Supervisor
Jen Hallinan – Supervisor
-
Matthew Pocock - Supervisor
+
 
 +
Matthew Pocock - Supervisor
 +
Morgan Taschuk – Project 5
Morgan Taschuk – Project 5
-
Mark Wappett – Project 3
+
 
 +
Mark Wappett – Project 3
 +
Megan Aylward – Project 1
Megan Aylward – Project 1
 +
Nina Nielsen – Project 2
Nina Nielsen – Project 2
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Matt gave some general comments
Matt gave some general comments
• When introducing the bug, give some interesting facts about it. Such as what infections it is responsible for etc…
• When introducing the bug, give some interesting facts about it. Such as what infections it is responsible for etc…
 +
• Show alignments of the cleaved peptides to show they are unique. Only Mark did this.  
• Show alignments of the cleaved peptides to show they are unique. Only Mark did this.  
 +
• Nina stop leaning on chairs and tables and standing on one leg. Try to stand still and sound believable.
• Nina stop leaning on chairs and tables and standing on one leg. Try to stand still and sound believable.
 +
• Mark stop saying like and er and um. Try and replace this with taking a breath.
• Mark stop saying like and er and um. Try and replace this with taking a breath.
 +
• All of the students should also try and point at the screen.
• All of the students should also try and point at the screen.
 +
• Jen said in general, the talks are much better than the proposal presentations 
• Jen said in general, the talks are much better than the proposal presentations 
 +
• Neil says try and sound enthusiastic and happy. Be American!
• Neil says try and sound enthusiastic and happy. Be American!
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Nina draws the layout of the package (guided by Matt).
Nina draws the layout of the package (guided by Matt).
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Matt suggests to look at Hibernet – object relational mapping, for an example of JDBC. Megan and Nina should definitely look at the Hibernet tutorial with access (on windows).
Matt suggests to look at Hibernet – object relational mapping, for an example of JDBC. Megan and Nina should definitely look at the Hibernet tutorial with access (on windows).
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PartR
PartR
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getTypes();
getTypes();
 +
getAllPartsID()
getAllPartsID()
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getPartTypeID(partType)
getPartTypeID(partType)
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getModel(partID)
getModel(partID)
-
 
+
List <Part types>
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                      List <Part types>
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List<All Parts>
-
                      List<All Parts>
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List<Part types>
-
                      List<Part types>
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cellML
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                      cellML
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-
 
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Both Nina and Mark should attempt this exercise.
Both Nina and Mark should attempt this exercise.
The team should then compare the interfaces with user stories.
The team should then compare the interfaces with user stories.
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-
 
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This week
 
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Month May June July August
 
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Week 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
 
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Task Parts defined,
 
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Design docs.  finished Programme
 
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design (pseudocode) Basic
 
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programme
 
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finished
 
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Coding final
 
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programme Finish
 
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Coding Integration DNA sequence
 
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synthesis WRITE UP
 
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(possibly half hour labs too)
 
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Line 208: Line 201:
• Neil and Jen are away next week
• Neil and Jen are away next week
 +
• Neil emphasises importance of finishing a week earlier since DNA synthesis takes approx. 3 weeks, not 2 weeks.
• Neil emphasises importance of finishing a week earlier since DNA synthesis takes approx. 3 weeks, not 2 weeks.
• Edinburgh rendez vous is on the 15/16th July not June.
• Edinburgh rendez vous is on the 15/16th July not June.
 +
• CellML tutorial talk 06/06/08 9.30 am by Neil.
• CellML tutorial talk 06/06/08 9.30 am by Neil.
 +
• A writing group should be set up – group references shared since a lot of overlap.
• A writing group should be set up – group references shared since a lot of overlap.
-
 
-
 
-
.
 

Revision as of 14:38, 11 July 2008

Back to Calendar


Minutes

Minute Taker: Nina Nielson


Action Plan for next week

Group

• Design a flyer/poster.

• Look at which parts have been identified already. If some of the parts that we are using haven’t been added to the repository yet, the group should put them on.

• Add iGem calendar of events to our calendar on our wiki.

• We need to research safety of our application. Do we understand the implications? Ask Jan for some tips, cosh form etc..

• We also need to ask Jan if he actually has the strains of bacteria we are going to be using. Thus we need to define the strains that we have been looking at for him.

• Look at cell-cell signalling article on iGem page.

• Do Hibernet tutorial]

• Do cellML tutorial and start modelling parts.

• Compare interfaces with User stories.

Megan

• Research the comC rather than vncR/S TCS in S. pneumoniae (or another suitable two component system).

• Continue adding to Java.doc.

• Investigate more parts for the chosen peptides.

• Finish designing the architecture for her database.

• Practise using JBDC


Nina

• Find all associated parts for PlcR/PapR (Blast the peptide).

• Email Jan about making sensor-fluorescent protein biobricks, strains of bacteria, and safety information . • Investigate potential for using Bacillus anthracis as well as Bacillus cereus. Find associate parts for this species too.

• Practise using JBDC

Mark

• Finish registering to iGem 2008

• Meeting with Jen to discuss EA on Tuesday – develop his own action points for EA.

• Construct architecture





The meeting

Time: 14:30 – 17:20

Attended by:

Neil Wipat – Supervisor

Jen Hallinan – Supervisor

Matthew Pocock - Supervisor

Morgan Taschuk – Project 5

Mark Wappett – Project 3

Megan Aylward – Project 1

Nina Nielsen – Project 2


Meeting Content

Agenda 1: Update on Biosensor

Students briefly discuss the bioinformatic analyses for S. aureus, S. pneumoniae, B. cereus, L. monocytogene that they have carried out this week.

Mark explains that the autoinducer peptide released by S. aureus is unique to the species.

Megan mentions that she has had difficulties locating the repressor of the vncR/S two component system (TCS). It is then suggested that an alternative TCS is exploited (since there are 12 others to choose from in S. pneumoniae). Megan suggests the comC two component system. This was ruled out earlier since it was thought to be too similar to other species.

Nina explains that she has found a promoter (pxylA), repressor (Spo0A) and other components of the PlcR/PapR TCS and that the pentapeptide released by B. cereus is unique to the species.

Mark comments on difficulties he has faced with L. monocytogene. The lisK/R system has no autoinducer system discovered. He is concerned that the common arg system is too similar although it has a unique HK. Neil approved that this feature was suitable enough to use.

Neil suggests using other Bacillus species such as Bacillus anthracis. Mark previously searched for a unique two component system and peptide but struggled. The group decides another attempt could be useful.

Neil then also suggests producing sensor BioBricks linked directly to fluorescent proteins to show that the system works. This can be done with each of the species. Jan should be emailed to help design these.

Nina offered to email Jan and research this. She should also inquire the combination of fluorescent protein outputs that are distinguishable to allow more sensors to be sensed.

Making the biobricks would also qualify the team for the awards.


Agenda 2: Teacher’s Meeting in Paris

Jen attended the iGem teachers’ meeting in Paris last weekend and summarized it. Talks were given by Randy Rettberg and Tom Knight. Jen showed us an example of an exercise.

Once a basic part has been added, the process is similarly repeated to add a composite part. (run of basic parts)


Adding parts exercise example (pt53) >add a part >add a basic part now //use the next number available (easier than assigning ranges of numbers each). >Write a short description of the part: pt53 >Write a long description of the part: tumour protein p53 – Guardian of the genome. >Source: Genbank //write where you found the part in the source >Sequence: Paste the sequence in this box

An advantage of adding the sequence is that the repository annotates it, for example indicating restriction sites such as Xbal and Pst.

Jen also mentions that BioBricks are written in XML format which could be particularly useful for us since we will all be using cellML.


Agenda 3: Mini-talks

Students give 10 minute presentations on individual project progress for the supervisors to assess their presentation skills.

Matt gave some general comments • When introducing the bug, give some interesting facts about it. Such as what infections it is responsible for etc…

• Show alignments of the cleaved peptides to show they are unique. Only Mark did this.

• Nina stop leaning on chairs and tables and standing on one leg. Try to stand still and sound believable.

• Mark stop saying like and er and um. Try and replace this with taking a breath.

• All of the students should also try and point at the screen.

• Jen said in general, the talks are much better than the proposal presentations 

• Neil says try and sound enthusiastic and happy. Be American!


Agenda 4: Architecture

Nina expressed her problems with installing TortoiseSVN. Matt suggested uninstalling what she has installed and to shut down the system and reinstall with Morgan’s supervision.

Matt explained the architecture will consist of three top level directories (one each) which will be siblings with Morgan’s workbench.

The package will have a java.import function to import stuff to the URL. This ensures the same code isn’t written.


Within the package.

Nina draws the layout of the package (guided by Matt).

Matt suggests to look at Hibernet – object relational mapping, for an example of JDBC. Megan and Nina should definitely look at the Hibernet tutorial with access (on windows).

There is a link on the java exercises set by Morgan on the wiki.


Megan goes through some of the classes that she would incorporate


PartR

getTypes();

getAllPartsID()

getPartTypeID(partType)

getModel(partID)

List <Part types> List<All Parts> List<Part types> cellML

Both Nina and Mark should attempt this exercise. The team should then compare the interfaces with user stories.


AOB

• Neil and Jen are away next week

• Neil emphasises importance of finishing a week earlier since DNA synthesis takes approx. 3 weeks, not 2 weeks. • Edinburgh rendez vous is on the 15/16th July not June.

• CellML tutorial talk 06/06/08 9.30 am by Neil.

• A writing group should be set up – group references shared since a lot of overlap.

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