Tag: Integration

Pathview 1.24.0 – R package for Pathway based Data Integration and Visualization

Pathview 1.24.0

:: DESCRIPTION

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.

::DEVELOPER

Weijun Luo <luo_weijun at yahoo dot com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 Pathview

:: MORE INFORMATION

Citation

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.
Luo W, Brouwer C.
Bioinformatics. 2013 Jul 15;29(14):1830-1. doi: 10.1093/bioinformatics/btt285.

MOWServ 2 – Web platform for Bioinformatics tools Integration

MOWServ 2

:: DESCRIPTION

 MOWServ2 is the new version of the current platform offered by the Spanish National Institute of Bioinformatics (INB), provides an integrated access to databases and analytical tools.

::DEVELOPER

Bioinformatics and Information Technologies LaboratoryUniversity of Malaga

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

MOWServ: a web client for integration of bioinformatic resources.
Ramírez S, Muñoz-Mérida A, Karlsson J, García M, Pérez-Pulido AJ, Claros MG, Trelles O.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W671-6. Epub 2010 Jun 4.

miRMaid 1.0 – microRNAs data structured for easier access and integration

miRMaid 1.0

:: DESCRIPTION

miRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRMaid

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Jan 14;11:29. doi: 10.1186/1471-2105-11-29.
miRMaid: a unified programming interface for microRNA data resources.
Jacobsen A, Krogh A, Kauppinen S, Lindow M.

Judi 1.0 – Data and Model Integration for Biology

Judi 1.0

:: DESCRIPTION

Judi ( Java platform for unsupervised data and model integration ) is a software written in Java, with an aim to provide a user-friendly tool for general unsupervised data and model integration. For many problems in biology, such as gene function prediction and differentially expressed gene identification, and general feature selection problems, there are often multiple data sources available and/or multiple models/tools have been developed to solve the problem. The combination of evidences from multiple data sources and the integration of the output from different models will probably enhance our ability to solve the problem. Judi implements several algorithms and also provides a user-friendly interface to facilitate this process.

::DEVELOPER

Xuebing Wu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

  Judi

:: MORE INFORMATION

Citation

Xuebing Wu, Feng Zeng, Rui Jiang (2008)
Integrative inference of gene networks from expression data.
Poster at RECOMB Regulatory Genomics/Systems Biology/DREAM3, Oct 29-Nov 2, 2008. MA, USA

BioWarehouse 4.6 – Database Integration for Bioinformatics

BioWarehouse 4.6

:: DESCRIPTION

BioWarehouse is a database interoperation environment that supports data mining and integration of multiple databases including the UniProt, BioCyc, NCBI Taxonomy, Genbank, CMR, ENZYME, Gene Ontology, and KEGG databases.

::DEVELOPER

BioWarehouse Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • MySQL

:: DOWNLOAD

 BioWarehouse

:: MORE INFORMATION

Citation

Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David WJ Stringer-Calvert, Jessica D Tenenbaum3 and Peter D Karp
BioWarehouse: a bioinformatics database warehouse toolkit
BMC Bioinformatics 2006, 7:170

GAZE 0.1 – Integration of Gene Prediction data

GAZE 0.1

:: DESCRIPTION

GAZE is a tool for the integration of gene prediction signal and content sensor information into complete gene structures.

::DEVELOPER

Kevin Howe,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GAZE

:: MORE INFORMATION

Citation

GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.
Howe KL, Chothia T and Durbin R
Genome research2002;12;9;1418-27

M-BISON 1.0 – Microarray-Based Integration of data SOurces using Networks

M-BISON 1.0

:: DESCRIPTION

M-BISON is a software to implement an efficient method for the integration of biological knowledge with microarray gene expression data to enhance identification of differentially expressed genes

::DEVELOPER

M-BISON Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 M-BISON

:: MORE INFORMATION

Citation

Bernie J Daigle Jr and Russ B Altman
M-BISON: Microarray-based integration of data sources using networks
BMC Bioinformatics 2008, 9:214