Wandora is a general purpose data extraction, management, and publishing application based on Topic Maps and Java. Wandora has a graphical user interface, layered presentation of knowledge, several data storage options, rich data extraction, import and export capabilities, and an embedded HTTP server that enables dynamic publication of Topic Maps. Wandora is well suited for rapid ontology construction and knowledge mashups.
Wunderbar is a program which is able to identify mislabeled samples in genotype data when a few extra independent genotypes are available ("genetic barcoding"). Wunderbar calculates the likelihood that genotype mismatches have occurred by chance. It is capable of reliable and sensitive detection of sample mismatches and swaps even in the presence of numerous genotyping errors and in the presence of linkage disequibrilium between the individual genotypes. It only requires a few SNPs to work well.
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.
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.
Virtual Token Descriptor for eXtensible Markup Language (VTD-XML) refers to a collection of efficient XML processing technologies centered around a non-extractive XML parsing technique called Virtual Token Descriptor (VTD). Depending on the perspective, VTD-XML can be viewed as either an XML parser, a native XML indexer or a file format that uses binary data to enhance the text XML, an incremental XML content modifier, an XML slicer/splitter/assembler, or an XML editor/eraser.
Emergent is a neural network simulator with a built-in scripting language which allows for the creation and analysis of complex, sophisticated models of the brain in the world. Networks and all of their state variables are visually inspected in 3D, allowing quick "visual regression" of network dynamics and robot behavior. Emergent is a direct descendant of the PDP and PDP++ neural network packages.