Newcastle University/29 May 2008

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  [[Team:Newcastle University/Notebook|Back to Calendar]]
  [[Team:Newcastle University/Notebook|Back to Calendar]]
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Attendance  14.30pm-16.15pm
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Morgan
 +
Matt
 +
Mark
 +
Megan
 +
 +
Absences
 +
Neil
 +
Jen
 +
Nina
 +
 +
Action points for following week
 +
 +
No specific individual points set
 +
 +
Group points
 +
• Carry out java practice on a daily basis
 +
• Meeting Moran 10.30 30/05 to go over java tutorial
 +
• Carry out bioinformatic analysis of every two-component operon that has been identified.
 +
• Spend 2 days next week going through the inputs and outputs for our systems. Come up with stories for every circumstance.
 +
• Brainstorm marketing ideas. Aim to produce a logo by next meeting.
 +
• Prepare for mini talks
 +
 +
Mini talks
 +
These will be carried out at the meeting next week 06/06/08. Each prepare a 10 minute presentation, approximately 5 slides each noting what we have achieved so far and how we see our project progressing.
 +
 +
Meeting
 +
 +
Go over the progress that we have made on the biological concept over the last few weeks so that Matt is up to date.
 +
Mark explains the agr system that we intend on using in S.aureas and that is present in L. monocytogene. 
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Then goes on to explain an alternative two-component system that is present in L. monocytogene.
 +
There are two potentially viable systems; cesRK, and lisRK.
 +
 +
The function of cesRK is not entirely clear so lisRK is probably favorable.
 +
LisRK has the receptor and histidine kinase and detects the truncated coding region of a peptide.
 +
 +
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Mention that we may not be able to use vnc system in S.pneumoniae because the repressor does not seem to be well characterised.
 +
Matt goes on to explain the bioinformatic analysis that should be carried out on every protein that we have found, and how this may enable us to discover all parts needed in the two-component system.
 +
Certain points include;
 +
Running all neighbouring open reading frames to the two-component systems in BLAST. This is particularly important in S.pneumoniae where it may uncover the repressor.
 +
 +
Run all proteins in BLAST
 +
Retrieve the amino acid sequence, using a repository such as UniProt or pfam.
 +
Run through interpro, discover any characterized domains/sequence motifs.
 +
Then input the sequences for all proteins into Clustal. This will highlight any conserved regions between the different proteins- this could highlight any potential problems with proteins that we did not expect to interact having interactions.
 +
Input sequences into SignalP (or other signaling tool) this should highlight any cleavage sites etc.
 +
 +
*These steps need to be carried out for every protein, working across the operon.
 +
 +
Review of what Megan and Mark have achieved computationally over the week.
 +
 +
Mark: Gone through the EA that is set up as a neural net.  Has managed to get it working.
 +
This has inputs and outputs and a certain number of hidden layers. Weights are randomly generated for each node.
 +
* it is mentioned that the weights should be set between 0 and 1 just while it is in this example stage.
 +
 +
Need to start thinking about fitness function and the mutate method. It doesn’t matter which fitness function is used at this stage.
 +
Just need put weighted values into a ‘black box’ then spit out outcome.
 +
Functions can be split into separate methods.
 +
Mutator can be used to add or remove from the threshold or weight.
 +
 +
 +
API
 +
2 components; the type of data that is taken in and the type that is given out.
 +
Work out what questions need to be ‘answered’
 +
What it needs to know?
 +
What it will be asked?
 +
What it will return?
 +
 +
Need to work out all changeable parameters that will be required.
 +
The EA will only need the unique ID and the type of each part.
 +
 +
Go over what user cases are. A storey of how the user interacts with the program, this will include:
 +
A set of minimum requests.
 +
Exact requirements for each ‘storey’
 +
 +
Morgan shows some examples of stories that she has created in the past to give an idea of the set up.
 +
 +
** All three students (Mark, Megan and Nina) must spend every week day in room 601, at least for a few hours. Generally between 12 and 3.
 +
 +
Marketing
 +
Probably best to have A4 size posters.
 +
 +
This should display in an eye catching and interesting way, The Name (BUG BUSTER), a LOGO, and the aim.
 +
 +
An iGEM specific website can be designed.
 +
 +
LOGO- this should be about the product being sold – the bugbuster. Look at clipart of bacteria, people/ things being “busted”. Fluorescent proteins/ colours.
 +
 +
 +
AOB
 +
 +
• Matt wishes to note that he is not happy with Ninas attendance to the meeting that had been organized between them for RDF. As he is very busy and does not have time to waste.
 +
• Arrange for Java tuition with Morgan. We will meet at 10.30 Friday morning 30/06. After the presentation meeting.
 +
• We should all continue/start to attend all Friday morning research group presentation meetings.

Revision as of 13:30, 11 July 2008

Back to Calendar


Attendance 14.30pm-16.15pm

Morgan Matt Mark Megan

Absences Neil Jen Nina

Action points for following week

No specific individual points set

Group points • Carry out java practice on a daily basis • Meeting Moran 10.30 30/05 to go over java tutorial • Carry out bioinformatic analysis of every two-component operon that has been identified. • Spend 2 days next week going through the inputs and outputs for our systems. Come up with stories for every circumstance. • Brainstorm marketing ideas. Aim to produce a logo by next meeting. • Prepare for mini talks

Mini talks These will be carried out at the meeting next week 06/06/08. Each prepare a 10 minute presentation, approximately 5 slides each noting what we have achieved so far and how we see our project progressing.

Meeting

Go over the progress that we have made on the biological concept over the last few weeks so that Matt is up to date. Mark explains the agr system that we intend on using in S.aureas and that is present in L. monocytogene. Then goes on to explain an alternative two-component system that is present in L. monocytogene. There are two potentially viable systems; cesRK, and lisRK.

The function of cesRK is not entirely clear so lisRK is probably favorable. LisRK has the receptor and histidine kinase and detects the truncated coding region of a peptide.


Mention that we may not be able to use vnc system in S.pneumoniae because the repressor does not seem to be well characterised. Matt goes on to explain the bioinformatic analysis that should be carried out on every protein that we have found, and how this may enable us to discover all parts needed in the two-component system. Certain points include; Running all neighbouring open reading frames to the two-component systems in BLAST. This is particularly important in S.pneumoniae where it may uncover the repressor.

Run all proteins in BLAST Retrieve the amino acid sequence, using a repository such as UniProt or pfam. Run through interpro, discover any characterized domains/sequence motifs. Then input the sequences for all proteins into Clustal. This will highlight any conserved regions between the different proteins- this could highlight any potential problems with proteins that we did not expect to interact having interactions. Input sequences into SignalP (or other signaling tool) this should highlight any cleavage sites etc.

  • These steps need to be carried out for every protein, working across the operon.

Review of what Megan and Mark have achieved computationally over the week.

Mark: Gone through the EA that is set up as a neural net. Has managed to get it working. This has inputs and outputs and a certain number of hidden layers. Weights are randomly generated for each node.

  • it is mentioned that the weights should be set between 0 and 1 just while it is in this example stage.

Need to start thinking about fitness function and the mutate method. It doesn’t matter which fitness function is used at this stage. Just need put weighted values into a ‘black box’ then spit out outcome. Functions can be split into separate methods. Mutator can be used to add or remove from the threshold or weight.


API 2 components; the type of data that is taken in and the type that is given out. Work out what questions need to be ‘answered’ What it needs to know? What it will be asked? What it will return?

Need to work out all changeable parameters that will be required. The EA will only need the unique ID and the type of each part.

Go over what user cases are. A storey of how the user interacts with the program, this will include: A set of minimum requests. Exact requirements for each ‘storey’

Morgan shows some examples of stories that she has created in the past to give an idea of the set up.

    • All three students (Mark, Megan and Nina) must spend every week day in room 601, at least for a few hours. Generally between 12 and 3.

Marketing Probably best to have A4 size posters.

This should display in an eye catching and interesting way, The Name (BUG BUSTER), a LOGO, and the aim.

An iGEM specific website can be designed.

LOGO- this should be about the product being sold – the bugbuster. Look at clipart of bacteria, people/ things being “busted”. Fluorescent proteins/ colours.


AOB

• Matt wishes to note that he is not happy with Ninas attendance to the meeting that had been organized between them for RDF. As he is very busy and does not have time to waste. • Arrange for Java tuition with Morgan. We will meet at 10.30 Friday morning 30/06. After the presentation meeting. • We should all continue/start to attend all Friday morning research group presentation meetings.

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