When Biology meets the Penguin
July 8, 2006
Due to its flexible license several versions of Linux Operating System has been developed.
Some of this variants, properly called distributions or distros, are address to desktop users ( e.g. Ubuntu ), some as web-servers and some other has been developed to make a powerful O.S. for scientific tasks.
Obiviously open source!
Obiviously free of charge!
The most widely used bioinformatic distros are:
“…Debian-Med is a “Custom Debian Distribution” with the aim to develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research. The goal of Debian-Med is a complete system for all tasks in medical care which is built completely on free software…”
For a full featured discussion read here.
This “Custom Debian Distribution” comes with several molecular biology and medical genetics softwares. For a complete software list read here.
One benefit of this distro is that it is based on Debian, a stable and widely known Linux distro. One disadvantage is that Debian is not a total user-friendly and you need some linux skills to use it proprerly.
“…Bioknoppix is a customized distribution of Knoppix Linux Live CD. With this distrubution you just boot from the CD and you have a fully functional Linux OS distribution with open source applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesn’t touch the host computer, being ideal for demonstrations, molecular biology students, workshops, etc…”.
One of the big benefit of this distro is that it comes as a LiveCD that mean you do not need to install anything on your pc. Simply boot your computer directly from the bioKnoppix cd to use it.
You can find a ( very ) short Bioknoppix on-line tutorial here.
The Bioknoppix distro comes with several bioinformatic softwares. The complete list is here.
“…Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software. VigyaanCD v1.0 is based on KNOPPIX…”
For a list of software included read here. For a ( very ) short tutorial read here and here.
“…DNALinux is a Linux distribution with bioinformatics software pre-installed…”
DNALinux is still in beta, that means it still not finished but it is usable enought for most needs. As BioKnoppix and VigyaanCD it is a LiveCD but DNALinux distro is based on SLAX. Here you can find a list of softwares included in DNALinux.
BSML
June 29, 2006
Bioinformatic Sequence Markup Language ( BSML ) is an extensible markup language ( XML ) derived standard that “encodes biological sequence information and includes graphical representations of biologically meaningful objects such as sequences, genes, electrophoresis gels, and multiple alignments”.
A detailed BSML overwiev is available here whereas the FAQ page is here.
The last BSML DTD release ( 3.1 ), the BSML reference manual and tutorial are available here. A BSML presentation is also avaible ( pdf, ppt ).
You can manage BSML file with LabBook Java Genomic XML Viewer, that is freely available, or you can purchase LabBook Genomic Workspace.
BioBar, a bioinformatic firefox plug-in
June 29, 2006
FireFox, the well known open source web browser, now is useful also for bioinformatic web surfers. Biobar is a new plug-in that provides rapid and easy access to several bioinformatic databases, directly whitin firefox.
"The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases".
Biobar also has several links to the major bioinformatics sites including European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ) and other important databases for nucleotide, protein, 3D-structure data, sequence, structure alignment and analysis tools.
The complete list of resources currently accessible through biobar is listed here.
You can install the latest biobar release ( 1.4 ) from here.
