PyPDB 2.0 – a Python API for the Protein Data Bank

PyPDB 2.0

:: DESCRIPTION

PyPDB is a Python 3 toolkit for performing searches with the RCSB Protein Data Bank (PDB) using its XML-based API.

::DEVELOPER

William Gilpin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

 PyPDB

:: MORE INFORMATION

Citation

PyPDB: a Python API for the Protein Data Bank.
Gilpin W.
Bioinformatics. 2015 Sep 14. pii: btv543

PathwaysWeb 2.0 – Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning

PathwaysWeb 2.0

:: DESCRIPTION

PathwaysWeb provides publicly available information on genes, biological pathways, Gene Ontology terms, gene gene interaction networks with interaction directionality, and links to related PubMed documents.

::DEVELOPER

PathwaysWeb team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PathwaysWeb: A Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning.
Melott JM, Weinstein JN, Broom BM.
Bioinformatics. 2015 Sep 23. pii: btv554.

BioBlend 0.16.0 – Python library for interacting with CloudMan and Galaxy‘s API

BioBlend 0.16.0

:: DESCRIPTION

BioBlend is a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs.

::DEVELOPER

Enis Afgan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Python

:: DOWNLOAD

 BioBlend

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1685-6. doi: 10.1093/bioinformatics/btt199. Epub 2013 Apr 28.
BioBlend: automating pipeline analyses within Galaxy and CloudMan.
Sloggett C1, Goonasekera N, Afgan E.

QMLGalaxyPortal 1.2.5 – A mobile QML app for interfacing with the Galaxy API

QMLGalaxyPortal 1.2.5

:: DESCRIPTION

QMLGalaxyPortal is quick and easy way to check the status of biomedical research on Galaxy and review your history.

::DEVELOPER

QMLGalaxyPortal team

:: SCREENSHOTS

:: REQUIREMENTS

  • iOS/ Android

:: DOWNLOAD

 QMLGalaxyPortal

:: MORE INFORMATION

Citation:

Galaxy Portal: Interacting with the Galaxy platform through mobile devices.
Børnich C, Grytten I, Hovig E, Paulsen J, Čech M, Sandve GK.
Bioinformatics. 2016 Jan 27. pii: btw042

BECAS – Biomedical Concept Annotation Tool, API and Widget

BECAS

:: DESCRIPTION

becas is a web application, API and widget for biomedical concept identification. It helps researchers, healthcare professionals and developers in the identification of over 1,200,000 biomedical concepts in text and PubMed abstracts.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Python

:: DOWNLOAD

 BECAS API

 :: MORE INFORMATION

Citation

BeCAS: biomedical concept recognition services and visualization.
Nunes T, Campos D, Matos S, Oliveira JL.
Bioinformatics. 2013 Aug 1;29(15):1915-6. doi: 10.1093/bioinformatics/btt317

HAL 2.1 – Hierarchical Alignment Format API

HAL 2.1

:: DESCRIPTION

HAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. HAL is a graph-based representation which provides several advantages over matrix/block-based formats such as MAF, such as improved scalability and the ability to perform queries with respect to an arbitrary reference or subtree.

::DEVELOPER

Glenn Hickey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • Python

:: DOWNLOAD

 HAL

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 15;29(10):1341-2. doi: 10.1093/bioinformatics/btt128. Epub 2013 Mar 16.
HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Hickey G, Paten B, Earl D, Zerbino D, Haussler D.

GO4J 1.1 – A Set of API used to Manipulate Gene Ontology Vocabulary

GO4J 1.1

:: DESCRIPTION

GO4J is a set of Java API to manipulate local GO (Gene Ontology) vocabulary. It has four features: parsing four kinds of GO defintion; organize all GO ids with directed graph; evaluating semantic similarity between any two GO ids; visualizing relations between any ids.

::DEVELOPER

 Guoqing Zhang

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 GO4J

:: MORE INFORMATION

Ruby UCSC API 0.6.2 – An API for the UCSC Genome Database

Ruby UCSC API 0.6.2

:: DESCRIPTION

Ruby UCSC API, a library to access the UCSC genome database using Ruby.It will facilitate biologists to query the UCSC genome database programmatically.

::DEVELOPER

Mishima, Hiroyuki (hmishima at nagasaki-u.ac.jp)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Ruby

:: DOWNLOAD

  Ruby UCSC API

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 21;13:240. doi: 10.1186/1471-2105-13-240.
The Ruby UCSC API: accessing the UCSC genome database using Ruby.
Mishima H, Aerts J, Katayama T, Bonnal RJ, Yoshiura K.