Politics, Information Technology, and Genomics


In a previous post, I discussed the sequence read format (SRF), the implementation of the SRF specification for Illumina/Solexa data, and potential implementations for Roche/454 and AB SOLiD data. Well, the potential AB SOLiD implementation has become an actual implementation with the release of solid2srf version 0.6.6. The software is released under the Applied Biosystems SOLiD™ Tools Software License (Unsupported) license [pdf], which appears to be an open source license. Quoting from the license: You... Full Post

Renewable energy from bacteria?

There has been a lot of research in recent years, largely funded by the Department of Energy, into microorganisms that can produce fuels or other usable, renewable forms of energy. Recently, The Genome Center, working with Prof. Himadri B. Pakrasi, sequenced the very interesting Cyanothece sp. ATCC 51142 genome. The Cyanothece 51142 genome has both a circular chromosome (standard for cyanobacteria) and a linear chromosome (unique among cyanobacteria). Cyanobacteria are the only known bacteria to... Full Post

Open access under attack

Since Congress voted to encourage NIH to adopt an open access policy for scholarly publications that resulted from research it funded, the journal publishers have lobbied Congress to reverse it. It seems the efforts of publishing companies are beginning to pay off with the introduction of the bill HR 6845. The bill would shift rights away from the article authors, the researchers, and back to large publishing houses. In an age of internet publishing and... Full Post

Just the facts

Well, it seems the campaign season is in full swing, you can tell by the smell of bs in the air. How can you distinguish the truth from the lies? Well, if you are like many people, the truth is everything that reinforces your world view and the lies are things that contradict your world view. If you desire a more objective definition of truth, I strongly suggest frequent visits to FactCheck.org. They have had... Full Post

No one defies artificial life

There is interesting story in Wired about an alternative approach to creating artificial life, Biologists on the Verge of Creating New Form of Life. While some are trying to create artificial bacteria, the Szostak lab's protocellular work is trying to create a form of life that does not currently exist, but may be similar to the earliest forms of life on Earth. Thus, they not only have to face the controversy of creating artificial life,... Full Post