Tag: Biological Database

BioSemantic – Integration of Biological Databases

BioSemantic

:: DESCRIPTION

BioSemantic is a framework developed to automate the integration of biological databases. Data are distributed across many different biological databases, in constant evolution, dispersed across different laboratories, with different data models.

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
  • Java

:: DOWNLOAD

  BioSemantic

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Apr 15;14:126. doi: 10.1186/1471-2105-14-126.
Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.
Wollbrett J, Larmande P, de Lamotte F, Ruiz M.

Biobar 2.0.9 – Firefox Toolbar for Browsing Biological Data and Databases

Biobar 2.0.9

:: DESCRIPTION

Biobar is a bioinformatics oriented browsing toolbar for Firefox that provides access to major biological data resources directly from your browser.The main advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structure, Plant and Animal-specific databases. The latest release of Biobar provides access to over 40 biological data collections.In addition to the browsing features, Biobar also provides links to important bioinformatics sites and services including those at the European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ).

::DEVELOPER

Protein DataBank Europe

:: SCREENSHOTS

:: REQUIREMENTS

  • Firefox

:: DOWNLOAD

 Biobar

:: MORE INFORMATION

Synergizer – Provide Translations of Biological Database Identifiers

Synergizer

:: DESCRIPTION

The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a “namespace”) to another.

::DEVELOPER

Roth Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Synergizer for Perl , for Java

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Oct 1;24(19):2272-3. Epub 2008 Aug 12.
The Synergizer service for translating gene, protein and other biological identifiers.
Berriz GF, Roth FP.

ANDY 0.2 – Large Biological Database Searching on Computer Clusters

ANDY 0.2

:: DESCRIPTION

ANDY  (seArch coordination aND analYsis)  is a set of Perl programs and modules for easily running large biological database searches, and similar applications, over the nodes of a Linux/Unix computer cluster in order to achieve speedup through parallelization. Users specify their cluster runs through a straightforward XML configuration file, in which they specify a template for the pipeline or sequence of commands they want to run on the nodes, as well as the locations and types of data sources for the command lines and other information.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

  ANDY

:: MORE INFORMATION

Citation:

Andrew Smith,John-Marc Chandonia,Steven E. Brenner
ANDY: a general, fault-tolerant tool for database searching on computer cluster
Bioinformatics (2006) 22 (5): 618-620