PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.
The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.
KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, BioPAX, SIF, SBGN, SBML-qual, GML, GraphML, JPG, GIF, LaTeX, etc.
Checker is a Microsoft Windows-based software application for checking biotechnology Sequence Listings for compliance with 37 Code of Federal Regulations (CFR) 1.821 – 1.825 for both ‘old rules’ (October 1990) and ‘new rules’ (July 1998).
Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. See the table below for a complete list (click the headers to sort, and format names to see all information).
Bio-Formats’s primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.