OIO is a Web-based metadata/data management front-end which is built using Zope and works with Postgresql. No programming is required to build and manage Web-forms or to perform data mining/analysis on the collected data. It is in production at the Harbor/UCLA Medical Center for clinical outcomes management and research data. Forms created with OIO and hosted on any OIO server can be downloaded as XML files. Once downloaded from the "Forms library" and imported into an OIO server, the necessary database tables are automatically recreated and the imported forms become immediately available to the users of that OIO server.
The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.
Renal Growth is a tool for radiologists and paediatricians to plot renal length and volume measurements against nomograms for age and weight. It allows for multiple observations from birth to 13 years. Individual patient data files can be stored and reused. Length and volume charts can be exported as JPEG files for importing into a PACS system or other clinical record.
Visualization of Protein Ligand Graphs (VPLG) uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, usually alpha helices and beta strands) or ligand molecules, while the edges model contacts and relative orientations between them. The graphs can be visualized, written to a database, and saved in a text-based file format.
Fqutils provides a basic set of bioinformatics command line tools for working with sequence data in FASTQ format. It complements Greg Hannon's fine Fastx Toolkit suite. One characteristic of Fqutils is that it correctly handles the full FASTQ format as described by the published standard, which specifically allows multi-line sequence and quality score information per record. Fqutils is intended to be useful as part of the early portions of post-sequencing pipelines and quality assessment processes.