SBW 2.12.2 – Systems Biology Workbench

SBW 2.12.2

:: DESCRIPTION

SBW ( Systems Biology Workbench), is an open source framework connecting heterogeneous software applications.

Researchers in quantitative systems biology make use of a large number of different software packages for modeling, analysis, visualization, and general data manipulation. The Systems Biology Workbench (SBW), is a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms-to communicate and use each others’ capabilities via a fast binary encoded-message system.

SBW goal was to create a simple, high performance, open-source software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages.

::DEVELOPER

Sauro Lab at University of Washington

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX/Linux

:: DOWNLOAD

SBW

:: MORE INFORMATION

Citation

Sauro, Hucka, Finney, Wellock, Bolouri, Doyle, Kitano.
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.”
OMICS. 2003 Winter;7(4):355-72.

AIBench 2.5.4 – Artificial Intelligence WorkBench

AIBench 2.5.4

:: DESCRIPTION

AIBench is a lightweight, non-intrusive, MVC-based Java application framework that eases the connection, execution and integration of operations with well defined input/output.

::DEVELOPER

SING Group.

:: SCREENSHOTS

AIBench

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE

:: DOWNLOAD

 AIBench

:: MORE INFORMATION

Citation

AIBench: a rapid application development framework for translational research in biomedicine.
Glez-Peña D, Reboiro-Jato M, Maia P, Rocha M, Díaz F, Fdez-Riverola F.
Comput Methods Programs Biomed. 2010 May;98(2):191-203. doi: 10.1016/j.cmpb.2009.12.003

BEW 2.1.0 – Biofilms Experiment Workbench

BEW 2.1.0

:: DESCRIPTION

BEW is a novel software workbench for the operation and analysis of Biofilms experimental data.

::DEVELOPER

SING Group.

:: SCREENSHOTS

bew

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE
  • R

:: DOWNLOAD

 BEW

:: MORE INFORMATION

Citation

Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench.
Pérez-Rodríguez G, Glez-Peña D, Azevedo NF, Pereira MO, Fdez-Riverola F, Lourenço A.
Comput Methods Programs Biomed. 2015 Mar;118(3):309-21. doi: 10.1016/j.cmpb.2014.12.005.

CLC Main Workbench 7.6.4 – Bioinformatics Workbench

CLC Main Workbench 7.6.4

:: DESCRIPTION

CLC Main Workbench is a bioinformatics workbench.CLC Main Workbench aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.

CLC Main Workbench creates a software environment enabling users to make a large number of advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.

::DEVELOPER

CLC bio

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  MacOsX / Window

:: DOWNLOAD

CLC Main Workbench

:: MORE INFORMATION

Bio-ULanix Beta2R3 – Linux Workbench for Bioinformatics

Bio-ULanix Beta2R3

:: DESCRIPTION

Bio-ULAnix comtains more than 220 Bioinformatic programs installed and ready to work.Bio-ULAnix will allow the academic and research community to take advantage of the great amount of computational applications in Bioinformatics that have been specifically developed for the GNU/Linux Free Operating System. This, without the users having to worry about installing and tuning their own Linux. Bio-ULAnix becomes, thus, an easily transportable Biocomputing Laboratory.

::DEVELOPER

National Center for Scientific Calculations

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DVD-ROM drive

:: DOWNLOAD

 Bio-ULanix

:: MORE INFORMATION

G-InforBIO 1.90 – E-Workbench for Comparative Genome Analysis

G-InforBIO 1.90

:: DESCRIPTION

G-InforBIO is an e-Workbench for “databasing”, comparative genome analysis. The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses.

::DEVELOPER

WFCC-MIRCEN World Data Centre for Microorganisms

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 G-InforBIO

:: MORE INFORMATION

Citation

Naoto Tanaka, Takashi Abe, Satoru Miyazaki and Hideaki Sugawara,
G-InforBIO: Integrated system for microbial genomics“,
BMC Bioinformatics, 7, 368, (2006).

InforBIO 5.28 – E-Workbench for Databasing, Classification & Identification of Microbes

InforBIO 5.28

:: DESCRIPTION

InforBIO is an e-Workbench for databasing, classification and identification of microbes. InforBIO can identify the phenotypic characteristics that discriminate and are associated with the clusters of a phylogenetic tree.

::DEVELOPER

WFCC-MIRCEN World Data Centre for Microorganisms

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 InforBIO

:: MORE INFORMATION

Citation

Hideaki Sugawara, Naoto Tanaka, and Satoru Miyazaki (2003)
An e-Workbench for the study of microbial diversity,
The system design and basic functions. Microbial. Cult. Coll., 19, 59-67 (InforBIO.pdf)

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

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