Projects

BioMart

BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL). The system can be used with any type of data and comes with a range of query interfaces and administration tools, including 'out of the ... [More] box' website that can be installed, configured and customised according to requirements. The system simplifies the task of creation and maintenance of advanced query interfaces backed by a relational database and it is particularly suited for providing the 'data mining' like searches of complex descriptive (e.g. biological) data. BioMart can work with existing data repositories by converting them to a required BioMart format as well as newly created databases. [Less]

GNAT NER

GNAT is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers. GNAT is available both for local download (suitable for large-scale processing) and as a web ... [More] service (suitable for more limited processing or testing). A combination of local and remote processing is also available, where CPU-heavy operations are performed locally and memory-intensive operations are performed remotely (this is suitable for large-scale processing where a large amount of memory is not available). GNAT uses LINNAEUS (Gerner et al., 2010) for species detection and BANNER (Leaman et al., 2008) in one part of its false positive filtering process. [Less]

FlyGATE

FlyGATE is a knowledge database dedicated to the transposable element (TEs) sequences of the Drosophila melanogaster genome.

MOLGENIS model-driven database platform

MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.

PPI Benchmark

A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature.

cistrome

The python modules hosted here are the core of Cistrome Database, developed by Shirley's Lab in Dana-Farber Cancer Institute. The Cistrome Database aims to provide a data storage framework and common analysis tools for ChIP-chip/ChIP-seq data.

rnavirusdb

A web site supporting access to a database of RNA viruses, with tools for query and alignment.

microbial-phenotype-database

The Microbial Phenotype Ontology and Database is an effort to bring a well-defined controlled vocabulary to the assignment of properties to various microbes (predominantly Bacteria & Archaea). Aside from a formal ontology of terms, software and human curation of term-specie associations are being developed.

neark

Will type later.

vardbdev

A web database and bioinformatics analysis tool for gene families involved in antigenic variation and immune system evasion in pathogens.