Software Map

BLAST is a set of similarity search programs
designed to explore all of the available sequence
databases regardless of whether the query is
protein or DNA. It uses a heuristic algorithm
which seeks local as opposed to global alignments,
and is therefore able to detect relationships
among sequences which share only isolated regions
of similarity. It can be run locally as a full
executable, and can be used to run BLAST searches
against private, local databases, or downloaded
copies of the NCBI databases. It runs on Mac OS,
Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF,
and HP- UX systems.

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.

SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses, and patients.

LabKey Server is open source software that helps scientists manage, analyze, and share complex datasets. It supports tandem mass spectrometry, flow cytometry, assays for neutralizing antibodies, Luminex, observational studies, and secure, Web-based collaboration. The software is modular, configurable, and customizable. It can be installed in your institution on any modern hardware and operating system. It is designed to integrate with your existing systems, instruments, and work flows, and to be readily adapted by skilled programmers to novel methods of inquiry. The project is under active development by a team of professional software engineers and a community of active contributors. New versions are released about four times per year.

Pathomx is a workflow-based tool for the analysis of metabolomic and other omics datasets. It is interactive, visual, extensible, intelligent, and free for any use. It lets you dynamically build analysis workflows using the interactive editor. Drag and drop connections between plugin tools to create a complete workflow through which to run your analysis. Data can be loaded and processed automatically, and new approaches tested simply by connecting tools.

AntFlow builds upon Apache Ant to provide a new
approach to simplifying system automation that
uses pipelines of hot folders chained together to
perform a given task. Using XML, it associates an
automated task such as data transfer, encryption,
or XML processing with a directory on the local
system. Whenever a file is copied or written into
the hot folder, the associated task is executed
and the file is moved to the next hot folder in
the pipeline for further processing.

PCP (Pattern Classification Program) is a machine learning
program for supervised classification of
patterns. It runs in interactive and batch modes, and
implements the following machine learning algorithms and
methods: k-means clustering, Fisher's linear discriminant,
dimension reduction using Singular Value Decomposition,
Principal Component Analysis, feature subset selection,
Bayes error estimation, parametric classifiers (linear and
quadratic), pseudo-inverse linear discriminant, k-Nearest
Neighbor method, neural networks, Support Vector
Machine algorithm (SVM), model selection for SVM, cross-validation, and bagging
(committee)
classification.

PhpLabware is a database system with features similar to Filemaker and Access, but is completely Web-based. Relational
databases can be defined through the Web interface and extended with PHP plugin code. User and group access is regulated at the record level. It was written by and for life sciences research scientists, but should be generally useful as a Web-based front end to SQL databases.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, and conversion of different chemical file formats. It is written in 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.