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:

debianlogo.png

“…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.

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“…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.

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“…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.

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“…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.

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Chimera is a free and multiplatform molecular visualization program with extensible capabilities and several interesting features.

With Chimera you can use several render modes such as: stick, ball-and-stick, CPK, ribbon, a special nucleotide representations and molecular surfaces. Other interesting graphics features are the ability to translation, scaling, and rotation and stereo viewing. You can use standard color modes ( RGB, CMYK, transparency, etc ) to colour yout model.

With Chimera you can easily add hydrogen atoms and its comes with a powerful high-quality hydrogen bond identification algorithm. Interactive bond rotation, distance and angle measurements is also possible.
Chimera can display 3D data acquired via electron and light microscope, x-ray density maps, electrostatic potential and other more. You can also sclice and segment your model. Morover, with the Multiscale extension, you can display molecular complexes and quaternary structure.
It is also possible to display molecular dynamics trajectories simulation with the Amber8 Sander module.

Docking analisys is possible via the ViewDock module that allows to view molecules in binding site and that permit to screen ligand candidates by hydrogen bonds.

Chimera also comes with the powerful Multalign Viewer extension that permit multiple sequence alignments and calculates consensus sequence and conservation histogram. You can also superimpose a structure based on the sequence alignment.

Using Collaboratory extension, Chimera can also work in a distributed computing environment that allows to conduct a shared molecular modelling session over a standard network connection.

Finally, Chimera has powerful and extensible programmable core. You can interact with all Chimera functions through Python script and so you can implement your own algorithms and extensions.

Screenshots and Animation gallery is aveible here and here.
Here you can find a Command Quick Reference Sheet ( pdf ).
Two Chimera tutorial is aveible here and here.
A guide to Volume Data Display here.
Here you can find the Chimera Programmer’s Guide with python extension examples.

The latest Chimera version is 1.2199 and it is aveible here for Linux, SGI IRIX, HP Tru64 Unix, Mac OS X and Windows.

BSML

June 29, 2006

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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.

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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.

Events and Courses

June 28, 2006

Several interesting events and courses are listed below.

Today is the early registration deadline for the two-day 3Dsig Structural Bioinformatics and Computational Biophysics Satellite Meeting within the Annual meeting of the International Society for Computational Biology ( ISMB ) ( with the same link ) in Fortaleza, Brasil, August 6-10.

At Inst. Gulbenkian de Ci\u00eancia in Oeiras, Portugal, there is course titled “A Primer on Molecular Evolution, Phylogenetics and Phylogenomics” ( July 24th – 28th, 2006 ).

Kerala University invites applications for 3rd batch of MPhil Bioinformatics (To start in January 2007). Application forms and bochures are available from here and the last date for application is 30 Sept 2006. The programme admits postgraduate students from engineering, computing and life sciences or allied streams.

At the Pasteur Institute a course will be offered in “Informatics in Biology“. The next session will take place from the 8th of January to the 27th of April 2007.

A second level international master in “COMPUTATIONAL AND SYSTEMS BIOLOGY” is aveible at the Università di Trento in cooperation by The Microsoft Research. The Course will start in November 2006 anf the deadline for application is August 14, 2006. Applicants will receive notification by September 18, 2006. More information on the Master Course and how to apply can be found here.

BioRuby

June 27, 2006

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Four months ago BioRuby 1.0.0 has been released. You can download the tar.gz file here and here you can view changelog list.

BioRuby is one of the newest bioinformatic programming languages and this project aims to implement an integrated environment for bioinformatics with a Ruby language library and with a powerful interactive shell.

BioRuby currently allows you to work with sequences for several task as traslation, splicing, similarity search, multiple alignment and sorting and also more. You can also connect with several databases as GenBank, RefSeq, EMBL, TrEMBL, SwissProt, MEDLINE, PROSITE, TRANSFAC, KEGG, FANTOM and PDB.

A first BioRuby on-line tutorial can be found here and here. A comprensive BioRuby shell documentation is also here.

Enjoy programming.

Wellcome to bioTAG

June 27, 2006

 

bioTAG is the new Italian Bioinformatic Weblog whose aims is to inform about bioinformatic trends in softwares, researches and tecnologies, for scientists and students.The posts will fall in several categories :

bioTAG news: news about bioTAG blog
bioprogramming : news about bioinformatic programming languages
webtools : news about bioinformatic web-based tools
molecular modeling : news about molecular modeling softwares
sequence analisys : news about sequences analisys softwares
biostatistics : news about biostatistics softwares
biosoftwares : news about other kind of bioinformatic software
papers : news about papers, researchs and books about bioinformatic
events : news about bioinformatic events
instruments : news about scientific instruments

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