Team:Cambridge-JIC/Notebook/CL W4 Monday

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<strong>Trang-Anh</strong> Talked to people about various things such as time planning. Discussed the strategy for codon optimisation and for promoter identification. Wrote C++ code to extract the sequences corresponding to the matching proteins between Mpoly and Athal, from their positions in the blast output table. All relevant files are in the Dropbox under Data_mining/Codon_optimisation.
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<strong>Angelina</strong>
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- Had some further considerations on the promoter-finding project and background reading, which raised a few questions on how best to proceed… so I organised a discussion with team to see what other ideas people had, which also highlighted a general enthusiasm for running an enhancer trap scheme.<br>
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- I spoke to Jim H who gave some really useful pointers, clearing up how the datasets on the marchantia genome were put together and how best I could work with them. <br>
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- Now excited to have a clear plan going forward: we’ll do some research on well characterised plants (e.g. Arabidopsis) in the context of cool/useful/ interesting applications that we would like to find promoters for, and use this to generate a gene list from which we can identify candidate promoters to test in our chassis. <br>
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Latest revision as of 11:27, 30 July 2014

Home Team Official Team Profile TimeLine Project Outreach Marchantia Informatics Parts Modeling Notebook Protocols Safety Dry Work Technology Attributions

Hugh worked on wiki; reading - biology and html; group meeting

Ginny -finished day with some Wet Lab fun: Ecoli Colony amplification
-started day having realized objectively the risk with GUS enzyme
-rise and down fall of UNagggeee (sni snif) focus on new chassis for Unag
-psychological reinvestment of energy onto new project
-worked on Safety Wiki Page: outline completed and filling in details
-started on Attributions (still debating outline)
-joined in random discussions

Will Gel extraction and increase of DNA concentration in preparation for Gibson of construct #1; continued development of HTML

Trang-Anh Talked to people about various things such as time planning. Discussed the strategy for codon optimisation and for promoter identification. Wrote C++ code to extract the sequences corresponding to the matching proteins between Mpoly and Athal, from their positions in the blast output table. All relevant files are in the Dropbox under Data_mining/Codon_optimisation.

Angelina - Had some further considerations on the promoter-finding project and background reading, which raised a few questions on how best to proceed… so I organised a discussion with team to see what other ideas people had, which also highlighted a general enthusiasm for running an enhancer trap scheme.
- I spoke to Jim H who gave some really useful pointers, clearing up how the datasets on the marchantia genome were put together and how best I could work with them.
- Now excited to have a clear plan going forward: we’ll do some research on well characterised plants (e.g. Arabidopsis) in the context of cool/useful/ interesting applications that we would like to find promoters for, and use this to generate a gene list from which we can identify candidate promoters to test in our chassis.


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