In-Between Fall 2004 Newsletter

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In-Between Fall 2004 Newsletter

We are writing this short newsletter to update people on a number of issues, most notably the upcoming SEED Developers Meeting. The important topic that we need to point out is this: it appears that somewhat more people than expected will be coming, it would be a strain to fit them into the facilities at the University of Chicago during the part of the week we were going to run there (Oct. 27-29), and so we are going to run the WHOLE meeting at Argonne National Lab.

The reason we had not originally planned on doing the whole thing at ANL was based on worries about being able to get people into the lab (we must get people cleared by ANL security). We have checked, and it appears that everyone (that we know about) coming to the second half can easily be cleared. So, it is critical that, if you have not discussed your attendance with us, but you would like to come, please contact us immediately. If it emerges that there are people who would like to come, but cannot get clearance, we will run a small parallel version at the University of Chicago (or, we will help them get set up for a second tutorial that we will be holding at MIT in Boston on Nov 1-2).

So, that is the important message: PLEASE MAKE SURE THAT WE KNOW IF YOU ARE COMING AND MAKE SURE THAT WE HAVE GOTTEN CLEARANCE FOR YOU.

Agenda for the Developers Meeting (Oct 25-26)

The SEED Developers Meeting will be held at Argonne National Lab on Oct 25-26. There are good cheap hotels available (on site for about $65/night; contact Veronika or Cheryl Zidel).

These meetings are intended to be largely free format with intense exchanges between individuals extending the SEED. Inevitably small subgroups will form and work on specific technical issues. However, we will consider the following to be a draft agenda:

October 25

Building 221, room A216, Mathematics and Computer Science Division, Argonne National Lab (wireless connections are available, so bring your laptops)

9:30 - 10:30

Summary of the Key Topic: Preparing a DVD Distribution that Contains Communicating Versions of GenDB and SEED.

One group of individuals will spend much of the entire week attempting to prepare this release.

11:00 - 12:00

Overall Development Plans for The SEED (Where We Will Be Going Over the Next 6 Months)

12:00 - 1:30

Lunch, walks around the grounds, getting to know one another

1:30 - 2:30

What it takes to install and maintain a version of the SEED. This discussion, like many of the discussions that will take place over the two days, will include a discussion of the same topic as it relates to GenDB. Our joint goal with the group at the University of Bielefeld is to produce easily installed versions of our open source software.

2:30 - 3:00

Coffee, discussions

3:00 - 5:00

Adding new genomes to the SEED

We must stress that not everyone will be attending these discussions. One group will organize itself to focus on the development of the distribution DVDs. Members will come and go. It will (intensionally) be a somewhat unstructured, hopefully intensly productive, exchange.

October 26

9:30 - 10:30

Issues Relating to Preparing Genomes for Entry to the SEED

10:30 - 11:00

Coffee

11:30 - 12:30

Improving Gene Calls (both protein encoding and RNA encoding genes)

12:30 - 2:00

Lunch

2:00 - 5:00

Status of the Subsystem Support Components of the SEED. This discussion will focus on what support now exists for developing subsystems, what is planned, and some obvious uses of the developed subsystems.

The three days that follow (Oct 27-29) are intended to be less technical, more tutorial, but also somewhat unstructured. We anticipate that many users will come only for these three days.

October 27: What Can One Do With the SEED?

9:30 - 11:00

An Introduction to Annotation/Subsystem Construction

11:00 - 11:30

Coffee

11:30 - 12:30

Some Examples

This tutorial session will include numerous points where we simply hand out IDs of genes we consider interesting and ask people to figure out whatever they can about them in 15-20 minutes. Then, we will discuss some approaches to answering such questions using the SEED. These short "challenge questions" are designed to be fun exercises which allow people to play with the system.

12:30 - 2:00

Lunch

2:00 - 3:00

Starting a Subsystem

3:00 - 3:30

Coffee

3:30 - 5:00

Users Will Either Start or Extend Subsystems of their Choice.

We are going to try to help people learn to work on development/annotation of subsystems. People with experience will help beginners get started.

October 28

9:30 - 10:30

Challenge Problems

10:30 - 11:00

Coffee

11:30 - 12:30

Looking at Some Detailed Problems/Inconsistencies in Existing Subsystems

12:30 - 2:00

Lunch

2:00 - 4: 00

Working on Subsystems

4:00 - 4:30

Coffee

4:30 - 5:00

Challenge problems

October 29

9:30 - 11:00

Extending Subsystems

Once a subsystem has been carefully constructed to include 10-20 diverse entries, how can one extend it to 200 organisms?

11:00 - 11:30

Coffee

11:30 - 12:00

Challenge Problems

12:00 - 2:00

Lunch

2:00 - 5:00

Work on subsystems, discuss the status of the subsystems effort, and what uses can be made of subsystems

That is approximately what we plan to do.

Hope you can make it.

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