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

::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

 AmmoliteMICAesFragBag

:: 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.

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.

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

BauerLab

:: 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.

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.

BioJava 4.1.0 – Java Framework for Processing Biological Data

BioJava 4.1.0

:: DESCRIPTION

BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.

::DEVELOPER

BioJava Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BioJava

:: MORE INFORMATION

Citation:

BioJava: an open-source framework for bioinformatics in 2012.
Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.
Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494.

BioJava: an Open-Source Framework for Bioinformatics ,
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.
Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397.

MOBY 1.16 / BioMoby – Interoperability between Biological Data Hosts and Analytical Services

MOBY 1.16 / BioMoby

:: DESCRIPTION

MOBY (Model Organism Bring Your) system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach.

::DEVELOPER

The BioMoby Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 MOBY

:: MORE INFORMATION

Citation

The BioMoby Consortium (2008)
Interoperability with Moby 1.0 — It’s better than sharing your toothbrush!
Briefings in Bioinformatics, 9 (3), pp. 220-231.