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S3DB - Simple Sloppy Semantic Database - is a PHP / mySQL,postgreSQL implementation of a local database infrastructure with a semantic architecture. The philosophy of its development is data driven.
GTdb - Modular genotype database for all markers. The
database has core which captures information common to different
variation measurements and extensions to method and instrument
specific data.
The metabolomics standards initiative (msi) will develop a Core Information for Metabolomics Reporting (CIMR) recommendation and a more formal and semantically defined corresponding ontology (msi-ontology).
Trauma registry suite; Data collection application and server scripts to build trauma data warehouse and perform web-based analysis reporting. Cross-platform compatible for Windows, Apple, Unix, or Linux.
The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.
HyPhy is a comprehensive environment for maximum likelihood statistical analysis of genetic sequence data. It includes a large collection of out of the box analyses, a feature-rich graphical user interface for custom data analysis and a scripting languag
ProteinFinder - a C language parallel computing engine for tandem protein mass spectrometry database search. ProteinFinder is interfaced with MySQL relational database MassSpec that hosts the experimental data, predicted databases, and search results.
The CHIP Cluster Generator attempts to create spatio-temporal cluster data in an automated fashion to help evaluate epidemic detection software. The spatio-temporal data will then be used to determine robustness of spatial detection algorithms.
PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.
TAS (Transcription Analysis System) is a multi-tier framework for running parameterized SQL queries. Users can analyze new data or new combinations of data with a few clicks in a GUI. Potentially complex/repetitive database interaction is all automated
Biological research groups need to store and analyze large amounts of diverse data. LISA (LabInfoSystem:) stores this information in an easily accessible customizable web-based database. LISA requires PHP4 and MySQL. Keywords: Structural Biology, Genomics
The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.
PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management.Statistical validation, , visualization, and converters from raw MS data open mzXML mzData format