February 2004 Newsletter

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February 2004 Newsletter

We are writing this short newsletter to make some comments on the upcoming SEED Developers Meeting in San Diego (Feb 22-24) and to cover a small number of miscellaneous items.

For those coming to the meeting, it is critical that you establish contact with Andrei Osterman or Ross Overbeek. Their email addresses are as follows:

Ross Overbeek  Andrei Osterman
Ross@TheFIG.info   Andrei@TheFIG.info

The meeting will start at the North Campus of Burnham Institute at 10am on Sunday, Feb 24. The address is

The Burnham Institute
10901 North Torrey Pines Road
La Jolla, California, 92037
858-646-3100

However, we strongly recommend that you link up a bit before that. There is nothing worse than being somewhat disoriented in a strange town. The recommended list of hotels is as follows:

Best Western Stratford Inn
710 Camino Del Mar
Del Mar, California 92014
Tel.: 858-755-1501, x.121 (Dana Hill, Director of
Sales
Fax: 858-755-4704
Toll: 1-800-446-7229
Web: www.pacificahost.com
E-mail: dana@pacificahost.com
Rate: $79 up
 
Del Mar Inn
720 Camino Del Mar
Del Mar, California 92037
Tel.: 858-755-9765
Fax: 858-792-8196
Toll: 1-800-451-4515
Web: www.delmarinn.com
Rate: $99 up
 
Hampton Inn
11920 El Camino Real
San Diego, California 92130
Tel.: 858-792-5557 (Mike Macklosky, Sales Manager)
Fax: 858-792-7263
Web: www.hamptoninndelmar.com
Rate: $94

There is a free shuttle service to the Burnham Institute from these hotels, which is what makes them particularly attractive (the prices are pretty good, as well). Ross is planning on staying at the Best Western Stratford Inn and suggests that anyone who wishes meet him for breakfast on Sunday morning at 8am.

This will be a fairly unstructured meeting. The basic rules will be as follows:

  1. Participants should come with specific objectives (things they want done or data they want to walk away with). It is their responsibility to formulate a strategy to meet those objectives. For example, Ross has roughly these goals:
    1. He will try to set up a collaboration to call genes (including starts) accurately for prokaryotes. The initial emphasis will probably be for organisms in which some objective (e.g., proteomic) data exists.
    2. The SEED is weak on DNA-related issues. The team at Bielefeld University has built an open source annotation system that is quite strong in these areas. A major topic will be the issue of what it would take to merge systems, exchange tools, or whatever. No serious discussions have yet taken place, but we hope to have some at the meeting.
    3. Ross will arrive with the pre-release version of the SEED that will be modified for an official release about mid March. He will offer copies to those who wish them.
    4. He will demonstrate the new annotation tools/strategy and wishes to seriously discuss how to launch the major annotation effort in March.
    These goals may not match very closely with what other participants want. That is ok.
  • We will occasionally have large discussions covering topics of general interest, but it is expected that smaller groups focusing on specific issues will emerge.
  • If there is a key topic that you wish to speak on (for, say, up to 30 minutes), feel free to prepare a talk. However, we will not be scheduling talks, and our view is that they should happen spontaneously and may be for limited groups.
  • For those people with wireless cards (airports), if you plan on using them at the Burnham, you must send your ID to Andrei Osterman. On a Mac, you can get this from the System preferences/Network settings display. This is critical if you plan to use the airport on Sunday. Andrei needs to get his system support people to help set this up the week before (i.e., next week).
  • Ross has tried this unstructured approach in the past, and it has worked well. Some of the rest of us are a bit nervous, but we shall see.

    A Separate Matter

    FIG was recently asked (by a granting agency) to justify efforts to build integrations. The precise request was as follows:

    Please describe the usefulness of KEGG, WIT, ECOCYC, and ERGO to the microbiology community

    We have already written about what advantages such systems provide, but we believe that the thrust was more "what have they actually done to help the community?" To answer this, we need microbiologists who have actually benefited in some way from one or more of these systems. If any such person would like to write 2-3 sentences, we would be grateful. Please note that we are not asking for comparisons of the systems, just general support for the view that integrations to support comparative analysis will become increasingly significant.

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