Tag: Biological Data

BioCircos.js v1.1.1 – Circos JavaScript Library for Biological Data Visualization on Web Applications

BioCircos.js v1.1.1

:: DESCRIPTION

BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web.

::DEVELOPER

CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
  • Java

:: DOWNLOAD

 BioCircos.js

:: MORE INFORMATION

Citation:

BioCircos.js: an Interactive Circos JavaScript Library for Biological Data Visualization on Web Applications.
Cui Y, Chen X, Luo H, Fan Z, Luo J, He S, Yue H, Zhang P, Chen R.
Bioinformatics. 2016 Jan 27. pii: btw041.

NGSANE 0.5.2.0 – Analysis Framework for Biological Data from High Throughput Experiments

NGSANE 0.5.2.0

:: DESCRIPTION

NGSANE (Next Generation Sequencing ANalysis for Enterprises ) is a framework for advanced production informatics of Next Generation Sequencing libraries.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NGSANE

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1471-2. doi: 10.1093/bioinformatics/btu036. Epub 2014 Jan 26.
NGSANE: a lightweight production informatics framework for high-throughput data analysis.
Buske FA1, French HJ, Smith MA, Clark SJ, Bauer DC.

Seqcrawler 0.6.2 – Biological Data Indexing and Browsing Platform

Seqcrawler 0.6.2

:: DESCRIPTION

Seqcrawler provides a complete open source search and store solution for labs or platforms needing to manage large amount of data/meta-data with a flexible and customizable web interface.

::DEVELOPER

Seqcrawler team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Seqcrawler

:: MORE INFORMATION

Citation

Seqcrawler: biological data indexing and browsing platform.
Sallou O, Bretaudeau A, Roult A.
BMC Bioinformatics. 2012 Jul 24;13:175. doi: 10.1186/1471-2105-13-175.

Genatomy – Visualizing Tool for Biological Data

Genatomy

:: DESCRIPTION

Genatomy is a visualizing tool for biological data, such as gene expression, genotypes, growth curves, copy number variation and more. It can be used to analyze the data mathematically and to study the biological aspects of the data and the results.

::DEVELOPER

Dana Pe’er Lab

:: SCREENSHOTS

Genatomy

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 Genatomy

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6441-6. doi: 10.1073/pnas.0810208106.
Modularity and interactions in the genetics of gene expression.
Litvin O, Causton HC, Chen BJ, Pe’er D.

JustClust – Analysing Biological Data with Cluster Analysis

JustClust

:: DESCRIPTION

JustClust is a tool for analysing biological data with cluster analysis. JustClust can handle many formats of data and cluster the data with many state-of-the-art techniques. The aim of JustClust is to provide an easy-to-use application which can perform any analysis on any data.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

JustClust

::REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 JustClust

:: MORE INFORMATION

GEMS – Entropy-scaling Search of massive Biological data

GEMS

:: DESCRIPTION

GEMS is a suit of softweares for entropy-scaling searching of massive biological data.

Ammolite is production-quality software designed to do a Tanimoto distance similarity search over chemical graphs for small molecules.

MICA (Metagenomic Inquiry Compressive Acceleration) is a full drop-in replacement for BLASTX and DIAMOND supporting all command-line options that is 3.5x faster than DIAMOND (and over 3000x faster than BLASTX) with no loss in specificity and less than 5% loss in sensitivity.

esFragBag (entropy-scaling FragBag) is prototype software that applies entropy-scaling to accelerate only the all r-nearest neighbor search functionality of FragBag by a factor of ~10 with no loss in specificity and less than 0.2% loss in sensitivity.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Ammolite, MICA, esFragBag

:: MORE INFORMATION

Citation

Entropy-scaling search of massive biological data.
Yu YW, Daniels NM, Danko DC, Berger B.
Cell Syst. 2015 Aug 26;1(2):130-140.

NYoSh Analysis Workbench 2.0 – Biological data analysis based on Meta Programming System

NYoSh Analysis Workbench 2.0

:: DESCRIPTION

NYoSh (Not your ordinary Shell) Analysis Workbench is a data analysis workbench built on top of MPS. Takes advantage of composable languages to create a platform intermediate between command line flexibility and user-friendly custom interfaces.

::DEVELOPER

Campagne Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • Active MQ

:: DOWNLOAD

NYoSh Analysis Workbench

:: MORE INFORMATION

Citation

PeerJ. 2014 Jan 2;2:e241. doi: 10.7717/peerj.241. eCollection 2014.
Composable languages for bioinformatics: the NYoSh experiment.
Simi M, Campagne F.

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