Team:Berkeley Software/NinaNotebook

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Revision as of 23:22, 5 June 2009 by NinaRevko (Talk | contribs)

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Nina 2 June 2009

Today is the second day of iGEM. Yesterday I spent time looking at java tutorials.

New Tasks Given are to look at tutorials for wiki that will be working or not -- media wiki embedded html for complicated stuff keep clean, so no need to clean up later think of a plug-in 1 wiki entry per week

Nina 3 June 2009

Nina Revko - on UCB campus

My 1st official entry

I am a member of computational team, majoring in bioengineering in fall 2009.

On Monday my team met, and everyone got acquainted with each other. We are still missing one member Lesie, who will join the team on Monday. After meeting with members of computational team, everyone went for a lab safety training and lunch social, where we met other members and leaders including the participants of the wet lab. Instructors were surprised with the size of this year's iGEM team.

Even though, we started working only on Monday, today is Wednesday, and everyone is overwhelmed with tasks and information. I think that we will adjust very soon and will produce effective results.

We got acquainted with Clotho, NetBeans, some Clotho code and CVS already.

This week short-term goals:
  1. search for bugs in Clotho
  2. edit Notebook
  3. modify .html help files
  • MainToolBar
  • MySQLlogin
Longer short-term goals:
  1. proof-read and become familiar with the rough draft of paper for assembly of biological parts(implementation of dynamic programming - hash tables in Java - and determining the minimum cost for assembly)
  2. together with Bing, meet with Chris Anderson and Jenn and learn how the robot works in the wet lab + their protocols (.csv file)
Long term goal for the 1st part of iGEM:
Robot/Automation project (brief structure):
  1. select parts (basic and compound)
    • do it through Part Manager - 1 click
    • put in Algorithm Manager
  2. run Assembly Algorithm w/Algorithm Manager Plug-in => record wells and physical locations of the each part
  3. create 2 protocols (.csv)
    1. human
    2. robot
  • both protocols should take into account actions that user should perform (grab samples from freezer with appropriate bar code - talk to wet lab members); the way dilution will be performed; the way plates will be managed before the complete assembly takes place (Plate Manager)


--NinaRevko 23:05, 3 June 2009 (UTC)


Nina 5 June 2009

After meeting with J.Christopher Anderson... The questions raised:

  • how to delete theoretical parts from the database (with no associated physical part?
  • requirements that will be tried to be implemented with the following assumptions:
    • start with a single plate where the basic parts are located - are all in 1 plate put there by user
    • cell stocks are not taken into account initially
    • bring parts in/out - allow for flexibility and playing around with parts
    • export assembly tree into a .csv file for robot with taking into account of "left-y", "right-y" and different antibiotics compatibility (AC, CA, AK, KA, CK, KC) - "lefty"/"righty" are currently not specified in db
    • after the robot is done and parts were made, display what parts were successful -- allow for user's input (in form of a tree?!)
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