JABAWS 2.2 – JAva Bioinformatics Analysis Web Services

JABAWS 2.2

:: DESCRIPTION

JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview. JABAWS is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. Analysis services allow prediction of protein disorder with DisEMBL, IUPred, Ronn and GlobPlot; and calculation of amino acid alignment conservation with AACon.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX/ Amazon EC2
  • Java

:: DOWNLOAD

 JABAWS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2001-2. doi: 10.1093/bioinformatics/btr304. Epub 2011 May 18.
Java bioinformatics analysis web services for multiple sequence alignment–JABAWS:MSA.
Troshin PV, Procter JB, Barton GJ.

jORCA 201404 – Easily integrating bioinformatics web services

jORCA 201404

:: DESCRIPTION

jORCA is a desktop client able to efficiently integrate different type of web-services repositories mapping metadata over a general definition to support scalable service discovery and to achieve flexible inter-communication between tools. jORCA manages repositories heterogeneity supported by the Modular-API that provides a uniform view of metadata (e.g. GRID-based, WSDL–services, BioMoby and others), making the integration of bioinformatics Web-Services easier.

::DEVELOPER

Bioinformatics and Information Technologies LaboratoryUniversity of Malaga

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 jORCA

:: MORE INFORMATION

Citation

Victoria Martín-Requena, Javier Ríos, Maximiliano García, Sergio Ramírez and Oswaldo Trelles
jORCA: easily integrating bioinformatics Web Services.
Bioinformatics (2010) 26 (4): 553-559.

CopasiWS / CopasiWSCient 0.9 – Basic Simulation Web Services for Biochemical Systems

CopasiWS / CopasiWSCient 0.9

:: DESCRIPTION

CopasiWS provides web service interfaces to the numerical simulation and optimization methods of COPASI. It consists of a suite of basic services for simulation and analysis of biochemical reaction networks.

CopasiWSClient: A Command Line Application for Running CopasiWS

::DEVELOPER

Mendes Research Group

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java
  • Apache Tomcat
  • COPASI

:: DOWNLOAD

 CopasiWSCopasiWSClient

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Nov 29;11:582. doi: 10.1186/1471-2105-11-582.
Systematic integration of experimental data and models in systems biology.
Li P1, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW.

Tav4SB 0.2.2 – Web service operations for analysis of the Kinetic models of Biological Systems

Tav4SB 0.2.2

:: DESCRIPTION

The Tav4SB (Taverna services for Systems Biology) project is a simple grid environment providing a set of Web service (WS) operations, together with bundling them workflows, prepared for the Taverna Workbench. Target application area is the System Biology field, in particular, analysis of kinetic models of biological systems.

::DEVELOPER

CompBio@MIMUW

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • Taverna

:: DOWNLOAD

 Tav4SB

:: MORE INFORMATION

Citation

BMC Syst Biol. 2012 Apr 5;6:25. doi: 10.1186/1752-0509-6-25.
Tav4SB: integrating tools for analysis of kinetic models of biological systems.
Rybiński M, Lula M, Banasik P, Lasota S, Gambin A.

CARMAweb 1.3 – R- and Bioconductor-based web service for Microarray Data Analysis

CARMAweb 1.3

:: DESCRIPTION

CARMAweb (Comprehensive R-based Microarray Analysis web service) is a web application designed for the analysis of microarray data. CARMAweb performs data preprocessing (background correction, quality control and normalization), detection of differentially expressed genes, cluster analysis, dimension reduction and visualization, classification, and Gene Ontology-term analysis. This web application accepts raw data from a variety of imaging software tools for the most widely used microarray platforms: Affymetrix GeneChips, spotted two-color microarrays and Applied Biosystems (ABI) microarrays.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CARMAweb

:: MORE INFORMATION

Citation

Rainer J., Sanchez-Cabo F., Stocker G., Sturn A. and Trajanoski Z.
CARMAweb: comprehensive R- and Bioconductor-based web service for microarray data analysis
Nucleic Acids Research, 2006 vol 34(Web Server Issue):W498-503.