Slashdot Mirror
Domain: bioinformatics.org
Stories and comments across the archive that link to bioinformatics.org.
Stories · 6
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Sixth Bioinformatics Open Source Conference
Shipud writes "The sixth Bioinformatics Open Source Conference will take place this June in Detroit, MI. Open source licensed software has proven to be the most popular and useful for bioinformatics research. This includes the EMBOSS suite for sequence analysis, the Biopython; Bioperl, and Biojava collaborativelty constructed toolboxes; the ubiquitous RasMol and PyMol molecular visualization tools, and more, much more. Here is one opinion as to why open source and collaborative development have been such a raging success even at big pharma, despite the apparent IP hurdles." -
Mathematica vs. Matlab?
Ninnux asks: "I wanted to find out from the community which was the better mathametics modeling package: Mathematica or Matlab. The cancer center I research and program for is considering purchasing a license set. I'll be working with Bayesian machine learning and other bioinformatic approaches for hormone pathway modeling. I know Matlab has various toolboxes that would be rather useful, but I'd like to hear what people think." While I'm sure direct comparisons will be made, I think focusing on the specific niche will help Ninnux the most; so, how well does each piece of software handle Bayesian functions and other bioinformatic computations? -
Who Owns Science?
immerrath writes "The New York Times has an article [Sorry, tomorrow's article, no Google link yet] on a movement that is rapidly gaining support in the scientific community: the Public Library of Science(PLoS). The founders, Nobel Laureate Harold Varmus, Stanford biologist Pat Brown and Berkeley Lab scientist Michael Eisen, argue that scientific literature cannot be privately controlled or owned by the publishers of scientific journals, and must instead be available in public archives freely accessible by anyone and everyone. This has very important implications for the fundamental principle that Science must transcend all economic, national and other barriers. For a while now, PLoS has been trying to get scientific journals to release the rights to scientific papers; many major journals have not complied -- in response, PLoS is starting PLoS-standard-compliant journals (for which they received a $9 million grant from the Gordon and Betty Moore Foundation), to demonstrate the validity of the idea and persuade academic publishers to adopt the free access model. They even have a GPL-like open access Licence, and their journals have some very prominent scientists on the editorial board. Here is the text of an earlier Newsweek article about PLoS, and here is a Nature Public Debate explaining the issues. Michael Eisen received the 2002 Benjamin Franklin award for his work on PLoS. Don't forget to sign the PLoS open letter!" -
Open Source Bioinformatics Report
An unnamed reader writes: " Bioinformatics.org has a story outlining recent activity in open source software development within the discipline of bioinformatics. The report covers a recent meeting in Copenhagen, Denmark called the Bioinformatics Open Source Conference, and describes a large number of projects and groups important to bioinformatics open source development. Most interesting was the appendix describing important online biological data sources. A student at Stanford University wrote the full report." -
Open Source Bioinformatics Report
An unnamed reader writes: " Bioinformatics.org has a story outlining recent activity in open source software development within the discipline of bioinformatics. The report covers a recent meeting in Copenhagen, Denmark called the Bioinformatics Open Source Conference, and describes a large number of projects and groups important to bioinformatics open source development. Most interesting was the appendix describing important online biological data sources. A student at Stanford University wrote the full report." -
Pipes In GUI? (Redeux)
jw3 revives an old question: "Unix wouldn't have 10% of its functionality without pipes, which allow gluing together smaller utilities and that way accomplish more complicated tasks. Fancy GUI's, however, while being nice and user-friendly and all are a totally different philosophy (see interview with David Korn, answer to question 6, which I rather fancied). Now I have found an ingenious project, called Piper, which tries to create a pipelike mechanism for a GUI interface. Interestingly enough, it is being written by biologists, who just lack the flexibility of the Unix piping mechanism, but, on the other hand, need lots of GUI for their work. What do you think about this project, fellow Slashdotters?" Based on the last conversation we've had on this topic, do you think the Piper project is a step in the right direction?