Tag: Bioinformatics

BioShaDock – A Curated BioInformatics Container Registry

BioShaDock

:: DESCRIPTION

BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images.

::DEVELOPER

BioShaDock team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BioShaDock

:: MORE INFORMATION

Citation

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.
Moreews F, Sallou O, Ménager H, Le Bras Y, Monjeaud C, Blanchet C, Collin O.
F1000Res. 2015 Dec 14;4:1443. doi: 10.12688/f1000research.7536.1. eCollection 2015.

Snakemake 6.4.1 – Scalable Bioinformatics Workflow Engine

Snakemake 6.4.1

:: DESCRIPTION

Snakemake is a workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.

::DEVELOPER

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Snakemake

:: MORE INFORMATION

Citation

Snakemake–a scalable bioinformatics workflow engine.
Köster J, Rahmann S.
Bioinformatics. 2012 Oct 1;28(19):2520-2.

KNOB 4.1 – CD-bootable Linux for bioinformatics

KNOB 4.1

:: DESCRIPTION

KNOB (KNOPPIX for Bio) is one CD-bootable Linux for bioinformatics based on KNOPPIX-JP. KNOB has many bioinformatics tools like BioRuby, BioPerl, Biopython, EMBOSS, ClustalW, BLAST, FASTA, G-language, R, Bioconductor etc…

::DEVELOPER

Itoshi NIKAIDO

:: SCREENSHOTS

:: REQUIREMENTS

  • live Linux DVD ROM

:: DOWNLOAD

 KNOB

:: MORE INFORMATION

WebLab 1.2 – Multifunctional Bioinformatics Analysis Platform

WebLab 1.2

:: DESCRIPTION

WebLab is a multifunctional bioinformatics analysis platform integrating diversified tools with unified, user-friendly web interface. However, WebLab is not a mere bioinformatics toolbox, we also offer powerful data management function, group strategy and knowledge sharing mechanism, which will bring considerable advance of efficiency for both wet bench and in silico scientists working in biomedicine community.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 WebLab

:: MORE INFORMATION

Citation

Liu, X., Wu, J., Wang, J., Liu, X., Zhao, S., Li, Z., Kong, L., Gu, X., Luo, J. and Gao, G. (2009)
WebLab: a data-centric, knowledge-sharing bioinformatic platform.
Nucleic Acids Res.2009) doi: 10.1093/nar/gkp428

Orange-Bioinformatics 3.28.0 – Orange Bioinformatics add-on for Orange data mining software package

Orange-Bioinformatics 3.28.0

:: DESCRIPTION

Orange Bioinformatics is an add-on for Orange data mining software package. It extends Orange by providing common functionality for basic tasks in bioinformatics. It also provides widgets for Orange Canvas, which enable users who are not programmers to manage microarray and genomic data flow and to customize their analysis by combining common data analysis tools to fit their needs.

::DEVELOPER

BioLab , University of Ljubljana

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Orange-Bioinformatics

:: MORE INFORMATION

Citation:

Tomaž Curk, Janez Demšar, Qikai Xu, Gregor Leban, Uroš Petrovič, Ivan Bratko, Gad Shaulsky, Blaž Zupan.
Microarray data mining with visual programming.
Bioinformatics. 2005 Feb 1;21(3):396-8.

EMBOSS 6.6.0 / Jemboss 1.5 – Suite of Bioinformatics Tools

EMBOSS 6.6.0 / Jemboss 1.5

:: DESCRIPTION

EMBOSS (European Molecular Biology Open Software Suite) is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Jemboss is a graphical user interface to EMBOSS.

EMBOSS Online Version

::DEVELOPER

EMBOSS team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux
  • JAVA

:: DOWNLOAD

EMBOSS ; Jemboss

:: MORE INFORMATION

Citation:

EMBOSS: The European Molecular Biology Open Software Suite (2000)
Rice,P. Longden,I. and Bleasby,A.
Trends in Genetics 16, (6) pp276–277

NCBI C++ Toolkit 22.0 – Collection of C++ Modules for Bioinformatics

NCBI C++ Toolkit 22.0

:: DESCRIPTION

NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications. NCBI C++ Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.

::DEVELOPER

NCBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

NCBI C++ Toolkit

:: MORE INFORMATION

Citation

The NCBI C++ Toolkit Book [Internet].
Vakatov D, editor.

Bio++ 2.4.1 – C++ Libraries for Bioinformatics

Bio++ 2.4.1

:: DESCRIPTION

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is fully Object Oriented and is designed to be both easy to use and computer efficient.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bio++

:: MORE INFORMATION

Citation:

Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K.
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.
BMC Bioinformatics. 2006 Apr 4;7:188.

BioDWH 0.2 – Bioinformatics Data Warehouse

BioDWH 0.2

:: DESCRIPTION

BioDWH is a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system. It stands out from other approaches by providing up-to-date integrated knowledge, platform and database independence as well as high usability and customization.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java
  • Oracle or MySQL

:: DOWNLOAD

 BioDWH

:: MORE INFORMATION

Citation

BioDWH: a data warehouse kit for life science data integration.
Töpel T, Kormeier B, Klassen A, Hofestädt R.
J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-93.

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