Notes from the Biomass

The three major DNA sequence repositories (Genbank, EMBL, and DDBJ) decided to include for a location identifier in 2005. You can now access EMBL via a map of the world.

Not that I think that it is highly useful as of now but it gives a birds eye view of things to come.

The market for most specialized science software is rather small, consequently the software is usually expensive. Many scientists even expect scientific software to be transparent (or downright free the younger they are) but how would one sustain a company in a niche market?
Dan Gezelter from the OpenScience project is facing the dilemma and summarizes the points that may have been made before but have never been solved.
Giving the software away for free and try to live off consulting is an approach that has been tried by the people involved in MySQL or WordPress with Automattic.com. However, the small market size will make it a very risky business - after all, grad students are always cheaper than any outside consultant, even if they would work for food and lodging.

Yesterday night I strolled over to the newthinking store in Mitte to attended the Webmontag, a platform for networking and presentations of web applications. Three applications and a Web2.0 map that were presented might be of interest to the usual suspects here. Besides, I want to bookmark them anyway.

DeepaMeetha is a ... hmm ... tool for the creation of topic maps and ontologies, similar to mind maps. The interface is quite unusual though usable and integrates web sites (and a browsing element), email and other information sources. While I can't see an immediate application for me, the concepts and the design of the software is definitely worth checking out.

Tim Pritlove presented Pentabarf, an open source web application to organize conferences. It was used in the planning of the recent 22C3 with 3000 participants over four days with four parallel tracks and several other larger conferences. It worked smoothly and seems ideally suited for conferences, workshops or summer schools in academic environments.

If you want to play buzzword bingo2.0, this illustration of the Web2.0 mind cloud map, presented by kosmar, its creator is ideal. You could also make use of it to explain what Web2.0 is about. I admit that the explanations around the mind mind somewhat shifted my personal views of Web2.0 from overly hyped buzz to actual progress on concepts on how to use the web.

One example of how these technologies could be put in place was provided by Plazes.com, a fresh Berlin start up that provides an application for geo-localization by computer networks. The developers presented the site in a rather low tone, open to suggestions and rather critical, even though it smelt a little like the old New Economy. I've already signed up of course.

These three hours, two hours longer than planned, standing in a crowd of smoking people were three hours well spent. Some pictures can be found on Netzpolitik.org.

Gene prediction in prokayote genomes might not be the most taxing question in current bioinformatics research. However, after a dealing with genome comparisons recently, I realized that many differences between the genomes exist solely in the annotation procedure and not in their sequence. This seems to be pronounced for the genomes that were sequenced several years ago, when gene prediction was more difficult due to lack of reference strains.

Nielsen and Krogh developed Easygene 1.2 (described in Bioinformatics a month ago) that homogenizes the gene predictions for prokaryotic genomes using a fully automated procedure. They discover discrepancies between their methods and the deposited annotation that convincingly hint at errors in the original annotation for many genomes. Typical errors result in many genomes being overannotated: too many small ORFs are considered real genes.

A web server of their results is provided but as new genomes appear in the dozens each month, I wish they would provide the code for a stand alone installation too. Anyway, good to know that they take care of such seemingly dull but important work.

You don't see it, but it's there: StatCounter is a somewhat lesser known, free service to the analyze the traffic on you blog, similar but superior to SiteMeter (and others). Recommended.

[via micropersuasion and performancing.com]

Other Mac users wondered that I ran Firefox on my Powerbook instead of using Safari - it was slow and not the great experience that you got from Firefox on Windows boxes. I only realized how "bad" it really was until I installed the Firefox 1.5 Release Candidate 1 yesterday. Now, surfing the internet is pure bliss again.

[N.B. I was this close to include a smiley in this post]

Greg Wilson, author of Data Crunching is offering a course on coding practices in scientific software development. There is also a quick survey to determine whether the course is for you. However, I guess this is recommended reading for the many bioinformatics scientists who are struggling with day to day problems as programming is only one of their activities.
The course is written for people with basic understanding of Python.

Well, not that this would be big big news - but I played with the 2.1 version of Cytoscape, a tool for network layout and analysis and I am impressed about the changes.

I thought the old interface was hard to use and not very userfriendly - but the new release from February 2005 def. has changed things to the better and did not undergo feature bloat.

Check it out - particularly if you were disappointed with the 2.0 release.