August 2003 Newsletter

Comments on technical progress

by Ross

July was a good month in many, many respects. We made substantial progress in getting our basic tools and environment in order. Let me list just a few of the most significant developments:

1. As I count it, about 13 new genomes reached the "complete or near complete" status that means we should add them to the FIG collection. I am working with Natalia Maltsev and Niels Larsen to get the additions going smoothly.
2. TIGR made many of their tools freely available. This was a wonderful gesture, since a substantial amount of effort and resources went into the construction of some of them. FIG will probably use glimmer (their gene calling tool) in calling prokaryotic genes (it will post-process the glimmer calls to arrive at a working set of genes in most cases).
3. I wrote a new "automated annotation" tool for making initial assignments of function to protein-encoding genes. Early tests indicate that it works quite well, but we clearly need to do far more comprehensive benchmarks to see where we stand.
4. We started analyzing a few complete genomes with these initial tools, and the results look good so far. This is a big step towards being able to provide high-throughput, accurate annotations.
5. I am within about 1-2 weeks of being able to finally deliver the initial version of the "resolution center" for analyzing differences in gene calls to Ralph Butler. I had to recode all of the graphical routines (I made yet another version of the old "GenoGraphics" functionality, and I'm pretty pleased with it), and I have been going through the FIG collection of genomes to document which have distribution restrictions. When all of this is completed properly, I will give Ralph a system which he can use to study the gene calls for the widely distributed genomes.

A lot more is now starting to happen based on these developments, but I think that I should avoid saying annything until the next newsletter -- better to discuss advances after they have occurred.

Goals for August

It is always difficult to set reasonable goals. One the one hand, we are very close now to being able to offer some of the critically needed capabilities that people are asking for. On the other hand, we must set priorities and some important steps will have to be delayed.

I think that the right way to summarize the main goals for August is "this will be the month in which we distribute initial releases to 2-3 of the FIG collaborators". These will go only to people working on critical support of FIG services, but it will be a big step.

In addition, the critical step of establishing a FIG web server will occur in late August or September (I hope). We are waiting to get one of the new Apple servers. I am very pleased with my Mac, and using that platform for development and web service seems reasonable to me (given our limitations in terms of systems administration and support).

This will lay the foundations for major advances in September and October. During these months I will be travelling more, but I do plan on initiating web-based access to the FIG collection of genomes and some really interesting new tools that we are working on.

On the More General Front

1. Personnel?
2. Overbeek/Osterman web-based course
3. Financial Strategy?

well, that's it for this month.

good luck,

The FIG Gang