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