Team:Berkeley Software/JoannaNotebook

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* Talk to Richard about plugins
* Talk to Richard about plugins
* First assess what is already available with regard to Java and GUIs
* First assess what is already available with regard to Java and GUIs
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** NetBeans Visual Library?
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** [http://platform.netbeans.org/tutorials/nbm-visual_library.html NetBeans Visual Library]?
** Take a look at BioJADE and ProMoT source code
** Take a look at BioJADE and ProMoT source code

Revision as of 23:04, 5 June 2009

Back to Berkeley Software notebook index

Joanna's iGEM 2009 Notebook

Joanna starting to make a snowman in Tahoe

Hi there, my name is Joanna Chen. Welcome to my notebook for iGEM 2009. I am on the UC Berkeley Computational Tools team. This summer we will be working on improving and adding to Clotho, a tool last year's team started making. I'm excited to be working on this project, and hope the team will have plenty to show by the end of iGEM. When school starts in the fall, I will be a senior majoring in Bioengineering at UC Berkeley.


Week of June 1, 2009

Monday was the first day of iGEM. We met as a team at 9am. Then, we went to a lab safety training, so we can go into the wet lab to work with the Berkeley experimental iGEM team when necessary. Following that, we had a pizza lunch with (almost) everyone at Berkeley involved with iGEM this summer. There, the computational and wetlab teams got to meet each other and hear both team leaders talk briefly about plans for the upcoming weeks. In the afternoon, Doug gave the computational team a brief overview of EDA (Electronic Design Automation) - his area of research - before showing us two webpages about Clotho and having each of us get an account on Bugzilla, the bug tracking tool we will be using. He then gave an overview of projects we could work on this summer to improve Clotho. We ended the day by setting up CVS with Netbeans so we could download the current source code for Clotho.

Tuesday morning, we had a long team meeting where Doug introduced us to editing this wiki, gave us a Clotho tutorial, and briefly discussed the Ptolemy coding standards which we will be using. Doug also assigned each of us a Clotho help file or two to be in charge of and edit by the end of the week. Mine was the Features Library. I spent the afternoon playing with Clotho, finding bugs in Clotho, and improving the help file.

Wednesday Doug gave us a tutorial on the Clotho Data Model. Later, I had my meeting with Doug to talk about my project area for the summer. I will be working on Visualization with Richard. We also decided my short term project would be to make a plugin with drag and drop functionality for icons (more on these shortly). Afterward, I spent a little more time playing with Clotho and looking for bugs.

Project description: Visualization

3 Areas we could work on:

  • Design
    • Several levels of abstraction, from DNA sequence to icons of features (which ideally can be dragged and dropped in the window) to parts and even systems(??)
  • Data Management
    • Be able to visually represent the relationships between data
  • Simulation

Some existing visualization tools to look at:

Tool Location Area
[http://gcat.davidson.edu/VizABrick/ Viz-a-brick] Davidson Data Management
[http://web.mit.edu/jagoler/www/biojade/ BioJADE] MIT Design
[http://www.tinkercell.com/Home TinkerCell] UW Simulation/Design
GeneDesigner DNA 2.0 Design
[http://www.genocad.org/genocad/ GenoCAD] VA Tech Design
[http://endy.openwetware.org/Notebook/BioBrick_Open_Graphical_Language.html BOGL] OpenWetWare Icons

Short-Term Task - 1st Plugin: Drag and Drop Icons

  • Create a new plugin in Views menu of Clotho's Main Toolbar
  • Have some icons and some connectors
  • Allow user to drag icons around and connect them
  • Talk to Richard about plugins
  • First assess what is already available with regard to Java and GUIs
    • [http://platform.netbeans.org/tutorials/nbm-visual_library.html NetBeans Visual Library]?
    • Take a look at BioJADE and ProMoT source code

Thursday

  • More playing with Clotho and bug-finding, including testing the Parts Manager by adding random (and malformed) information for parts
  • Committed the changes I made in the Features Library help file
  • Looked into BioJADE (haven't found much that was useful)
  • Group meeting
    • Decided on meeting times for each of the project areas
    • Everyone reported the bugs they found to Doug

Friday

  • Adding more content to this page

Week of June 8, 2009

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