Team:Berkeley Software/DougNotebook

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= [[User:Densmore|Densmore]] 01:33, 7 June 2009 (UTC) =
= [[User:Densmore|Densmore]] 01:33, 7 June 2009 (UTC) =
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Today (Saturday), Bing, Nade, Richard, and I came into the DOP Center. With the exception of Richard, everyone was here to close as many bugs as possible before the next beta build on Monday. Richard was here to work on the plug-in tutorial and materials.
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In general it was a pretty successful day. We closed all the "easy" bugs and got to most of the critical other ones. In general I think it is a pretty solid version for the wet lab to start with. The major missing piece right now is a way for someone to delete entries in the database. This is an issue since you need to decide what to do with all parts that refer to the newly deleted item. Should you fill those pointers to "null"? If so, we need to make sure none of the tools will "break" if they read a null value (this should be done anyway). Another option is for a more elaborate delete. For example if I delete a biobrick, perhaps I should delete all samples which refer to it as well?
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Anyway, those issues will be taken care of next time:)
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Here is the list of bugs we found on Thursday. It is now broken down into those that are "fixed" and those that are "open". While the open list looks large, really most of these are not bugs bug just comments from the group. I kept these around so we would have a record of them.

Revision as of 01:46, 7 June 2009

Densmore 16:00, 2 June 2009 (UTC)

Douglas Densmore - Out of the lab (Peru salt pools)

Yesterday was the first official day for Berkeley's 2009 iGEM computational team. In the morning we had an introductory meeting and the students filled out forms so that they had key access to Cory Hall, the DOP Center, and their office space. It was great that we were able to get this taken care of so quickly!

After the short time together in the morning, they went to safety training from 10-noon. This was followed by a meeting of both teams over pizza lunch in Stanley Hall. This was a good chance to meet everyone and get some logistics out of the way (stipends, photo release forms, etc).


In the afternoon we did the following:

  • Watched a short video on EDA
  • I gave an overview of the two web pages related to Clotho
  • Everyone signed up for Bugzilla and got a quick little overview
    • http://biocad-server.eecs.berkeley.edu/bugzilla
  • I gave an overview of the 6 different project areas available for this summer
    • Visualization tools
    • Language development
    • Plug-in and community development
    • Workflow development (Kepler)
    • Data Model revamp
    • Robot/Automation
  • Everyone configured Netbeans and set up CVS so that they could download Clotho


At the end of the meeting the students were given tasks for the week. The first tasks for the team are as follows:

  1. Think about which project(s) you would like to be involved in.
  2. Add an entry to your notebook with the following:
    • Introductory paragraph
    • Picture
    • Short description of their first short project
    • Short description of their first long project (with a bulleted list of tasks they are going to need to take)
  3. Play with Clotho
    • Take notes on all the bugs they find
      • Prize for the most/best bugs found
  4. Give feedback on the help files
  5. Meet with Doug before the week is out to talk about their role on the team



Today we:

  1. Discussed how to edit the wiki
  2. Went through a quick Clotho tutorial
  3. Talked about the coding standards for the project
    • http://ptolemy.eecs.berkeley.edu/ptolemyII/ptIIlatest/ptII/doc/coding/style.htm
  4. Decided on the owners for the help files. They are:

Richard

  • SequenceView

Nina

  • Main Toolbar
  • Clotho mySQL Connection

Joanna

  • Features Library

Adam

  • Info View
  • Enzyme Library
  • Notepad

Bing

  • Database Manager
  • mySQL Pobol Connection

Thien

  • Parts Navigator

Doug

  • Plate Manager
  • Algorithm Manager

Nade

  • Parts Manager



Densmore 19:47, 3 June 2009 (UTC)

Today I met with Nina, Joanna, and Adam (or at least I will by the end of the day) to assign them each to projects and to explain to them more about what they are doing. Here are the project assignments so far:

Project Assignments
Project PI One PI Two
Data Model Bing Evan
Visualization Richard Joanna
Robot Automation Nina Bing
Workflows (Kepler) Thien ?
Language Dev. Adam Lesia
Plug-In/Community Lesia Richard

The projects have both a PI One (Principle Investigator One) and a PI Two (yes I understand that it is strange to have two "principle" investigators). On Thursday each project will be assigned a day of the week for the weekly meeting. These meetings will be between 2-3 hours long each



Densmore 01:33, 7 June 2009 (UTC)

Today (Saturday), Bing, Nade, Richard, and I came into the DOP Center. With the exception of Richard, everyone was here to close as many bugs as possible before the next beta build on Monday. Richard was here to work on the plug-in tutorial and materials.

In general it was a pretty successful day. We closed all the "easy" bugs and got to most of the critical other ones. In general I think it is a pretty solid version for the wet lab to start with. The major missing piece right now is a way for someone to delete entries in the database. This is an issue since you need to decide what to do with all parts that refer to the newly deleted item. Should you fill those pointers to "null"? If so, we need to make sure none of the tools will "break" if they read a null value (this should be done anyway). Another option is for a more elaborate delete. For example if I delete a biobrick, perhaps I should delete all samples which refer to it as well?

Anyway, those issues will be taken care of next time:)


Here is the list of bugs we found on Thursday. It is now broken down into those that are "fixed" and those that are "open". While the open list looks large, really most of these are not bugs bug just comments from the group. I kept these around so we would have a record of them.

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