cb2bib 2.0.1 – Manage Bibliographic data in BibTeX Format

cb2bib 2.0.1

:: DESCRIPTION

The cb2Bib is a free, open source, and multiplatform application for rapidly extracting unformatted, or unstandardized bibliographic references from email alerts, journal Web pages, and PDF files.

::DEVELOPER

Pere Constans

:: SCREENSHOTS

cb2bib

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

  cb2bib

:: MORE INFORMATION

Fizzy v1.4 – Feature Selection for Biological Data Formats

Fizzy v1.4

:: DESCRIPTION

Fizzy is a feature subset selection tool that uses FEAST in the background to run feature selection on biological data formats.

::DEVELOPER

Drexel’s EESI Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Python

:: DOWNLOAD

 Fizzy

:: MORE INFORMATION

Citation

Fizzy: feature subset selection for metagenomics.
Ditzler G, Morrison JC, Lan Y, Rosen GL.
BMC Bioinformatics. 2015 Nov 4;16:358. doi: 10.1186/s12859-015-0793-8.

CellH5 / CellH5Browser 1.1 – Format for Data Exchange in High-content screening / Image Browser

CellH5 / CellH5Browser 1.1

:: DESCRIPTION

CellH5 is an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs

CellH5Browser is an interactive gallery image browser based on the CellH5 data format. For testing download a CellH5 example data set for the CellH5Browser from a time-lapse microscopy dataset.

::DEVELOPER

CellH5 team

:: SCREENSHOTS

CellH5Browser

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R pacakge/ MatLab / Python

:: DOWNLOAD

  CellH5 / CellH5Browser

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jun 15;29(12):1580-2. doi: 10.1093/bioinformatics/btt175. Epub 2013 Apr 16.
CellH5: a format for data exchange in high-content screening.
Sommer C1, Held M, Fischer B, Huber W, Gerlich DW.

SVGenes 0.4.1 -SVG Format Genome Browser Style Pictures

SVGenes 0.4.1

:: DESCRIPTION

SVGenes (bio-svgenes) is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface.

::DEVELOPER

Team MacLean – Bioinformatics @ The Sainsbury Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Ruby
  • BioRuby

:: DOWNLOAD

 SVGenes

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1890-2. doi: 10.1093/bioinformatics/btt294. Epub 2013 Jun 6.
SVGenes: a library for rendering genomic features in scalable vector graphic format.
Etherington GJ1, MacLean D.

Unrooted – Draw Binary Tree Expressed in the standard Phylogenetic Tree Format

Unrooted

:: DESCRIPTION

Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). Trees are drawn in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.

::DEVELOPER

Unrooted team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows

:: DOWNLOAD

 Unrooted

:: MORE INFORMATION

MetNetMaker 1.6.2 – Creation of Novel Metabolic Networks in SBML format

MetNetMaker 1.6.2

:: DESCRIPTION

MetNetMaker is the only free software designed solely to create metabolic networks based on the KEGG LIGAND database ready for Flux-Balance Analysis in the COBRA toolbox.MetNetMaker helps with creating a Metabolic Network by keeping track of the details, like naming conventions, cellular compartments and network subdivisions so that FBA-ready networks in SBML format can be created by anyone familiar basic concepts of metabolism.

::DEVELOPER

Tom Forth.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MetNetMaker

:: MORE INFORMATION

Citation

Forth,T. et al. (2010)
MetNetMaker: A free and open-source tool for the creation of novel metabolic networks in SBML format.
Bioinformatics (2010) 26 (18): 2352-2353.

EmblEx 20121203 – Parse and Extract data from EMBL entries to various formats

EmblEx 20121203

:: DESCRIPTION

EmblEx (EMBL Extractor) is a software for molecular biologists and bioinformaticians. It consists of a series of perl scripts and makes use of a MySQL database. Using EmblEx is through a graphical interface within a web browser or through the command line under linux or windows.

::DEVELOPER

Virtual Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 EmblEx

:: MORE INFORMATION

iConvert.pl – Convert Tree Files and Sequence Files between common Formats

iConvert.pl

:: DESCRIPTION

iConvert.pl: Perl script converting tree files and sequence files between common formats . This program supports FASTA, PIR, Clustal and Nexus sequence files and Phylip, Nexus, Clustal tree files.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

  iConvert.pl

:: MORE INFORMATION