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Wednesday, October 04, 2006

Bioinformatics: Open Source or Open Access??

I have heard that bioinformatics is ahead of chemoinformatics. However, I discoverd that this is not necessarily the case, while preparing for a homology modeling course I gave this week at the CUBIC. Open Access is really no issue there, with open access journals and many open access databases. But it is different when it comes down to open source software.

Below is a list of bioinformatics programs which are free for academic use, but not open: And this not even includes the many websites which do not offer the software behind them. And these programs cover several steps in the whole homology modeling process. Open source homology modeling is not possible at this moment :(

But, on the bright side, there are already some open source programs involved too: And protein structure viewers is hardly a problem at all; several open source viewers are available, among which Rasmol, PyMOL and Jmol.

In other words: we might not want to look at bioinformatics too much.

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6 comments:

  1. Unknown10:54 AM, October 05, 2006

    Egon,
    I would those call those applications rather modelling applications than bioinformatics applications. And especially this connection is IMHO still not really bridged with good open source software, because people like to sell every little tool to the pharmaceutical industry ... I just say missing bond orders in PDBs.

    And nice overview, good direction!

    Kind regards, Joerg

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  2. Anonymous8:34 PM, October 05, 2006

    I would disagree. The software that's widely used by bioinformaticians (it might be different for structural biology...PROCHECK, etc.) is 95% open source. Here are some examples:
    - BLAST (by NCBI)
    - fasta (by Bill Pearson)
    - clustalw (by Des Higgins)
    - hmmer (by Sean Eddy)
    - phylip (by Joe Felsenstein)
    - emboss package
    - bioperl perl library
    - genewise (by Ewan Birney)
    These are some of the most used programs in bioinformatics, but almost every bioinformatics program published nowadays is open source. This underlines the importance of creating a similar variety of open source tools for cheminformatics, until 95% of cheminformatics software is also open source!

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  3. Egon Willighagen4:16 PM, October 25, 2006

    Hi Avril,

    thanx for your comment. the tendency was maybe a bit too generic, but we chemoinformaticians are trained to say everything in bioinfo is opensource and in chemistry not.

    Lot's of areas of bioinformatics this is indeed true, but not for homology modeling. That's what I tried to say.

    Some other open source bioinfo bits outside homology modeling:
    - BioJava
    - BioConductor

    Lot's of good things happening, but it is annoying that, as opensource software developer, the course you are giving only contains closed source software :(

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  4. Anonymous8:45 PM, November 15, 2006

    This comment has been removed by a blog administrator.

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  5. Anonymous10:11 AM, December 19, 2006

    This comment has been removed by a blog administrator.

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  6. Egon Willighagen12:31 PM, December 19, 2006

    There were two comments on bioinformatics books, which actually pointed to a file sharing website which, I think, illegally shares books. Lot's of books really. But it is illegal, and I disapprove of it. Please don't advertise illegal activities in my blog.

    ReplyDelete