SEQ v0.9.4 – Language for Bioinformatics

SEQ v0.9.4

:: DESCRIPTION

SEQ is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

SEQ

:: MORE INFORMATION

Citation:

Ariya Shajii et al.
Seq: a high-performance language for bioinformatics
Proceedings of the ACM on Programming LanguagesOctober 2019 Article No.: 125 https://doi.org/10.1145/3360551

BioPAX level 3 – Biological Pathway Exchange Language

BioPAX level 3

:: DESCRIPTION

BioPAX (Biological Pathway Exchange) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.

::DEVELOPER

BioPAX Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 BioPAX

:: MORE INFORMATION

Citation:

Demir et al.
The BioPAX community standard for pathway data sharing
Nature Biotechnology 28 , 935–942 (2010) doi:10.1038/nbt.1666

Rust-Bio 0.4.0 – Bioinformatics Library for the Rust language

Rust-Bio 0.4.0

:: DESCRIPTION

Rust-Bio makes many algorithms and data structures that are useful for bioinformatics available for the Rust language.

::DEVELOPER

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Rust

:: DOWNLOAD

  Rust-Bio

:: MORE INFORMATION

Citation

Rust-Bio: a fast and safe bioinformatics library.
Köster J.
Bioinformatics. 2015 Oct 6. pii: btv573.

GMQL 1.0.1 – GenoMetric Query Language

GMQL 1.0.1

:: DESCRIPTION

GMQL provides a next-generation query language for querying NGS data.

::DEVELOPER

Genomic Computing group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GMQL

:: MORE INFORMATION

Citation

GenoMetric Query Language: A novel approach to large-scale genomic data management.
Masseroli M, Pinoli P, Venco F, Kaitoua A, Jalili V, Palluzzi F, Muller H, Ceri S.
Bioinformatics. 2015 Feb 3. pii: btv048.

Logol – Pattern matching language and tools

Logol

:: DESCRIPTION

Logol is a language used to describe some patterns in a DNA/RNA/Protein sequence

::DEVELOPER

GenOuest

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Logol

:: MORE INFORMATION

Citation

Catherine Belleannée, Olivier Sallou, Jacques Nicolas.
Expressive Pattern Matching with Logol.
Application to the Modelling of -1 Ribosomal Frameshift events. JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp. 5-14.