LECTURE #3

Software and tools

Software tools for bioinformatics range from simple command- line tools, to more complex graphical programs and standalone web-services available from

various bioinformatics companies or public institutions.

Types

Linux OS distributions for bioinformaticsOpen source bioinformatics softwareWeb services in bioinformatics

Bioinformatics workflow management systems

Linux OS distributions for bioinformatics

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.

http://bioknoppix.hpcf.upr.edu/

Linux OS distributions for bioinformatics

BioPuppy is an minimal Linux OS and electronic workbench for bio-informatics and computational biology. It has been designed to meet the needs of beginners, learners, students, staffs and Research scholars.

It provides both standard and cutting edge bioinformatics software tools on a Linux base. It is powerful, configurable and easy to maintain. It has been customized for ease of use and provides an ideal system for scientists handling and analyzing biological data.

http://biopuppy.org/

Linux OS distributions for bioinformatics

Bio-Linux 6.0 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux 10.04 base. There is a graphical menu for bioinformatics programs, as well as easy access to theBio-Linux bioinformatics documentation system and sample data useful for testing programs.

http://nebc.nerc.ac.uk/tools/bio-linux

Linux OS distributions for bioinformatics

BioSLAX is a new live CD/DVD suite of bioinformatics tools that has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD/DVD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX.

SLAX is becoming the live CD/DVD of choice because of its ability to modularize almost any application and plug it into the system on the fly.

http://www.bioslax.com/

Open source bioinformatics software

Many free and open source software tools have existed and continued to grow since the 1980s.

The combination of a continued need for

new algorithms for the analysis of emerging types of biological readouts, the potential for innovative in

silico experiments, and freely available open code bases have helped to create opportunities for all research groups to contribute to both bioinformatics and the range of open source software available, regardless of their funding arrangements.

The open source tools often act as incubators of ideas, or community-supported plug-ins in commercial applications.

http://en.wikipedia.org/wiki/List_of_open-source_bioinfo rmatics_software

Open source bioinformatics software

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

http://biojava.org/wiki/Main_Page

Open source bioinformatics software

BioPerl is a thriving open source project, with nearly all of the founding developers still involved.

BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.

http://www.bioperl.org/wiki/Main_Page

Open source bioinformatics software

Biopython is a set of freely available tools for biological computation written

in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world.

http://biopython.org/wiki/Main_Page