Category: Bioinformatics Platform

Cell Illustrator 5.0 – Platform for Systems Biology

Cell Illustrator 5.0

:: DESCRIPTION

Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.

DEVELOPER

Human Genome Center, Institute of Medical Science, The University of Tokyo

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac / Linux
  • Java

:: DOWNLOAD

 Cell Illustrator

:: MORE INFORMATION

Citation

Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S,
Cell Illustrator 4.0: A computational platform for systems biology,
In Silico Biol, 2010; 10:0002

Darwin 2.1 – Programming Environment for Bioinformatics

Darwin 2.1

:: DESCRIPTION

Darwin (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences) is a programming environment with its own, modern language and a growing library of functions for sequence management and analysis, statistics, numerics, graphics, parallel execution and more.

::DEVELOPER

CBRG – Computational Biochemistry Research Group ,Institut für Wissenschaftliches Rechnen at the ETH Zurich.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  Darwin

:: MORE INFORMATION

Citation

G. H. Gonnet, M. T. Hallett, C. Korostensky, and L. Bernardin
Darwin v. 2.0: an interpreted computer language for the biosciences
Bioinformatics 2000 16: 101-103.

CARGO 2.0 – Web Portal to Integrate Biological Information

CARGO 2.0

:: DESCRIPTION

CARGO (Cancer And Related Genes Online) is a configurable biological web portal designed as a tool to facilitate, integrate and visualize results from Internet resources, independently of their native format or access method. The tool is designed to be used by experimental biologists with no training in bioinformatics. In the current state, the system presents a list of human cancer genes.

::DEVELOPER

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CARGO

:: MORE INFORMATION

Citation:

Cases I, Pisano DG, Andres E, Carro A, Fernández JM, Gómez-López G, Rodriguez JM, Vera JF, Valencia A, Rojas AM.
CARGO: a web portal to integrate customized biological information.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W16-20. Epub 2007 May 5.

BioSLAX 7.5 – BioInformatics LiveCD Suite

BioSLAX 7.5

:: DESCRIPTION

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.

::DEVELOPER

the BioInformatics Center (BIC), National University of Singapore

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable CD-ROM drive

:: DOWNLOAD

 BioSLAX

:: MORE INFORMATION

VLinux 2.0 alpha 2 – Linux Workbench for Bioinformatics

VLinux 2.0 alpha 2

:: DESCRIPTION

VLinux is a Linux distribution and appliance for students and researchers in Bioinformatics. It is based on the well known openSUSE Linux distribution and is built using Novell’s Suse Studio.

::DEVELOPER

Vimalkumar Velayudhan

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable CD-ROM drive

:: DOWNLOAD

 VLinux

:: MORE INFORMATION

bioknoppix 0.2.1 – Knoppix Linux Live CD for Molecular Biologist

bioknoppix 0.2.1

:: DESCRIPTION

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.

::DEVELOPER

Carlos M Rodriguez (carlos@hpcf.upr.edu), High Performance Computing Facility ,University of Puerto Rico

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable CD-ROM drive

:: DOWNLOAD

 bioknoppix

:: MORE INFORMATION

Quantian 0.7.9.2 – Knoppix / Debian Variant Tailored to Numerical and Quantitative Analysis

Quantian 0.7.9.2

:: DESCRIPTION

Quantian (Quantian Scientific Computing Environment) is a remastering of Knoppix, the self-configuring and directly bootable cdrom/dvd that turns any pc or laptop (provided it can boot from cdrom/dvd) into a full-featured Linux workstation. Quantian also incorporates clusterKnoppix and adds support for openMosix, including remote booting of light clients in an openMosix terminal server context. Earlier releases are still available; see below for URLs for downloads as well as ordering information.

::DEVELOPER

Dirk Eddelbuettel

:: SCREENSHOTS

:: REQUIREMENTS

  • live Linux DVD ROM

:: DOWNLOAD

 Quantian

:: MORE INFORMATION

Citation:

Christopher N. Lawrence , Dirk Eddelbuettel
Quantian: A Comprehensive Statistical Computing Environment
The Political Methodologist, Volume 13, Number 2, Fall 2005

VigyaanCD 1.0 – Workbench for Bioinformatics

VigyaanCD 1.0

:: DESCRIPTION

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.

At present the following ready to use software comes on VigyaanCD: Arka/GP, Artemis, Bioperl, BLAST (NCBI-tools), ClustalW/ClustalX, Cn3D, EMBOSS tools, Garlic, Glimmer, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, MUMer, NJPlot, Open Babel, Octave, PSI3, PyMOL, Ramachandran plot viewer, Rasmol, Raster3D, Seaview, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available.

::DEVELOPER

Pratul K. Agarwal

:: SCREENSHOTS

:: REQUIREMENTS

  • live Linux CD

:: DOWNLOAD

 VigyaanCD

:: MORE INFORMATION

BioSeqAnalyzer 1.0 – Analyze DNA and Protein Sequences

 BioSeqAnalyzer 1.0

:: DESCRIPTION

BioSeqAnalyzer is a bioinformatics software tool for analyzing DNA and protein sequences.

::DEVELOPER

Arun Jagota (biobay@comcast.net) and Jim Serwer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  BioSeqAnalyzer

:: MORE INFORMATION

Register

ISYS 1.35 – Platform for Integrating Heterogeneous Bioinformatic Resources

ISYS 1.35

:: DESCRIPTION

ISYS (Integrated SYStem) is a Java-based plugin framework for loosely-coupled integration of independently developed components. It provides both service-oriented and event-based communication whose semantics may be contributed by component developers.

::DEVELOPER

Andrew Farmer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • java

:: DOWNLOAD

ISYS

:: MORE INFORMATION

Citation

Siepel A, Farmer A, Tolopko A, Zhuang M, Mendes P, Beavis W, Sobral B.
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources.
Bioinformatics. 2001 Jan;17(1):83–94