January 2004 Newsletter

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January 2004 Newsletter

This newsletter is coming out after only a short break, since we wanted to notify people about the first planned SEED Tech-Developers Meeting. It will be held in San Diego at the Burnham Institute on February 22-24. We realize that this is terribly short notice, but plans were not final until today.

The meeting will be for people actually writing code for the SEED; we intend to hold these meetings to help finalize what goes into the next release. The topics now on the agenda are as follows:

  1. We have made a beta release (0.0.0) available to a few people, and comments/criticisms are coming in. These will be reviewed.
  2. It has become essential that we immediately address the issue of adding genomes to the SEED, since we now have 20-40 that need to be added as soon as possible. This will include
    1. construction of a server to call genes in prokaryotes,
    2. reformatting data from several key sources (i.e., building tools to simplify additions from these major sources),
    3. how much effort to put into initial automated annotations (and what is wrong with the existing tool), and
    4. dividing up the work and responsibilities.
  3. We need to finalize the additions to the SEED needed to support the annotation of subsystems. Ross wants to launch the subsystem annotation effort in March, so it is critical that these tools be finalized and blessed at the meeting (they will be reviedwed and corrected in response to criticisms from the annotators, but we need an initial tool that is basically adequate to get things moving).
  4. We will begin discussions on the following two topics (the actual coding/integration will begin after the Feb meeting and, hopefully, will move to center stage for the April or June meetings):
    1. The SEED does not handle processing DNA well. We need facilities for displaying/aligning/editing regions of DNA. Several users have pointed towards capbilities offered by Artemis as an example. Bielefeld's system has addressed these issues. We need to talk about what capabilities are needed and how to best introduce them.
    2. It is clear that the SEED will be used heavily in interpretation of expression data (ESTs, microarrays, and proteomic data). The plans on how this topic will be handled will be talked about over beers.

Other topics can be added, but these should consume most of the three days. We recommend that those who come spend all three full days, but it is not essential. Let us know what your plans/restrictions are, and we will try to work things out. Again, this is a working meeting for groups/individuals who intend to actively participate in SEED development. We are going to schedule another series of meetings targeted towards SEED users and annotators. These should start by March; we will keep you posted.

If you have questions or need help, please contact Ross, Veronika, or Andrei.

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