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.
A mythological molecular modeller
July 2, 2006
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.
