tag:blogger.com,1999:blog-85986852011-08-02T16:17:01.092-07:00Information BiologyInformaton consists of differences that make a difference. To be alive is to draw distinctions and act (or not) accordingly.rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.comBlogger91100tag:blogger.com,1999:blog-8598685.post-1097524208274658502004-10-11T13:41:00.000-07:002004-10-21T07:40:40.863-07:00Systems biologyIt's the new new thing.
It's news in Wired
There's an Institute for Systems Biology
Nature Biotechnology features Systems Biology in a recent issue. The article on commercialization links to players. See the figures from the original article for details (subscription required).
Public companies with research programs on systems
Eli Lilly
Johnson & Johnson
Novartis
Novo Nordisk
Systems rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com2tag:blogger.com,1999:blog-8598685.post-1097517025678051272004-10-11T10:48:00.000-07:002004-10-20T07:53:54.703-07:00The microbiomeGreetings "highly complex conglomerations of human, fungal, bacterial and viral cells"!
The concept of the superorganism is not new. The most familiar, and perhaps comfortable examples from classical biology are social insects like the honey bee and colonial protozoa like volvox. In both these cases, the superorganism is composed of multiple individuals of the same species, although for bees rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0tag:blogger.com,1999:blog-8598685.post-1097510034232092902004-10-11T08:41:00.000-07:002004-10-11T10:48:43.286-07:00Technology making a differenceA Macarthur fellowship to MIT instructor Amy Smith, who provides engineering solutions to third world problems that are cheap, simple, maintainable and effective. All the trees are being cut down in Haiti to cook food? Provide a way to to turn abundant agricultural waste into charcoal. Is it taking all day to grind grain for daily bread? Provide a cheaper non motor driven mill that does therghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0tag:blogger.com,1999:blog-8598685.post-1097358579937846332004-10-09T14:48:00.000-07:002004-10-09T14:50:12.773-07:00Protecting Bioinformatics ValuePDF by a patent lawyer on bioinformatics IP.rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0tag:blogger.com,1999:blog-8598685.post-1097166070296334912004-10-07T08:49:00.000-07:002004-10-08T11:11:26.600-07:00Fruitflies really do like bananasThe nobel prize for medicine went this year to Richard Axel and Linda B. Buck who described the genes and cells of the olfactory system.
Interestingly, expression of functional olfactory receptors, an important subclass of G-protein coupled receptors in tissue culture has proven difficult.
As a result, the premier genetic model organism, Drosophila melanogaster, is now gaining acceptance in rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0tag:blogger.com,1999:blog-8598685.post-1097011200681315562004-10-05T14:13:00.000-07:002004-10-05T14:20:00.680-07:00podcastingOkay, I've had a chance to listen to a bit of those 720 Mb of downloaded mp3s that came in by default with installation of pyPodder. It is painful to listen to, and I couldn't find anything in there worth keeping.
Take my word, you won't be missing anything by skipping it all. I'm still interested in the concept as a way to update the compute farm, but as far as personal use is concerned, I'm rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0tag:blogger.com,1999:blog-8598685.post-1097009486684585092004-10-05T13:41:00.000-07:002004-10-05T13:57:51.186-07:00File distribution methodsA problem faced by all large scale compute farms is distribution and maintenance of large amounts of data. For bioinformatic compute farms, this is the sequence data that underlies all other analyses.
Do methods of distributing mp3 encoded audio such as RSS 2.0 enclosures, BitTorrent and scripted clients used in podcasting offer an alternative method for distribution?
I'm currently rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0tag:blogger.com,1999:blog-8598685.post-1097008710987185912004-10-05T13:24:00.000-07:002004-10-05T13:41:06.483-07:00network analysis using tools from bioinformaticsSlashdot follows up on a previous article describing use of sequence analysis methods taken from bioinformatics to enable network protocol analysis.
The actual source code is now available at Protocol Informatics. They seem to be taking C++/python approach, and have a rather fresh look at bioinformatics, with a few interesting links.
I've signed up for the mailing list and downloaded the code.rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0tag:blogger.com,1999:blog-8598685.post-1097004834118414282004-10-05T11:11:00.000-07:002004-10-24T12:35:16.640-07:00Why Information Biology?Why not bioinformatics, or computational biology, or systems biology? Information Biology is the phrase that best fits my own particular slant on computation and living systems. I was captured at an early age by the realization that DNA and proteins can be beautifully summarized as strings of alphabetic characters. This now common place representation still amazes me.
Bateson defined rghammondshttp://www.blogger.com/profile/16534007359744554034noreply@blogger.com0