Bio2RDF r3 – Largest network of Linked Data for the Life Sciences

Bio2RDF r3

:: DESCRIPTION

Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.

::DEVELOPER

Bio2RDF team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Bio2RDF

:: MORE INFORMATION

Citation

Alison Callahan, Jose Cruz-Toledo, Peter Ansell, Michel Dumontier:
Bio2RDF Release 2: Improved Coverage, Interoperability and Provenance of Life Science Linked Data.
ESWC 2013: 200-212.

Anni 2.1 – Text-mining tool for the Life Sciences

Anni 2.1

:: DESCRIPTION

Anni provides an ontology-based interface to Medline and retrieves documents and associations for several classes of biomedical concepts, including genes, drugs and diseases, with proven text-mining technology.

::DEVELOPER

the Biosemantics Group.

:: SCREENSHOTS

Anni

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

Anni

:: MORE INFORMATION

Citation

Anni 2.0: a multipurpose text-mining tool for the life sciences.
Jelier R, Schuemie MJ, Veldhoven A, Dorssers LC, Jenster G, Kors JA
Genome Biology 2008 Jun 12, 9(6):R96

NAIL 1.01 – Network Analysis in the Life Sciences

NAIL 1.01

:: DESCRIPTION

The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results.

::DEVELOPER

NAIL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MaxLab

:: DOWNLOAD

  NAIL

:: MORE INFORMATION

Citation

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks.
Hurley DG, Cursons J, Wang YK, Budden DM, Print CG, Crampin EJ.
Bioinformatics. 2014 Sep 21. pii: btu612.

Segminator II 0.1.1 – Analysis of viral data generated using the 454 Life Sciences Sequencing Platform

Segminator II 0.1.1

:: DESCRIPTION

 Segminatoris a tool for extracting data from reads generated using the 454 Life Science sequencing platform

::DEVELOPER

John Archer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Segminator

:: MORE INFORMATION

Citation

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.
Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A, Robertson DL.
BMC Bioinformatics. 2012 Mar 23;13:47.

PhpLabWare 0.63 – Web-driven Life Sciences Lab Database Management System

PhpLabWare 0.63

:: DESCRIPTION

Phplabware is a web-driven database management system. Phplabware runs on a server and is accessed through a web browser. Databases can be designed within a web-interface. Data-entry takes place in forms, which can be altered using phplabware’s plugin mechanism. Search results can be output in reports, which are generated based on simple HTML templates. Phplabware supports file and image uploads and allows for full-text searches in uploaded materials. A UNIX-like user and group access control mechanism allows for fine-grained read and write control at both the level of a complete database as well as individual records. The (php-based) plugin mechanism allows for easy and fast adaptation of phplabware to any specific needs.

Phplabware was developed at a number of Molecular Biology labs, and therefore ships with predefined databases targeted to the needs of Life Sciences labs. Currently, modules are available for antibodies, protocols, pdfs, pdbs, and files.

::DEVELOPER

Nico StuurmanVale Lab, UCSF

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PhpLabWare

:: MORE INFORMATION

Demo Database : Symbiodinium Culture Database