Java

BioResource Index

The BioResource Index is an database of commonly used bioinformatics and systems biology software tools and databases. The index covers resources for the analysis of high-throughput genetic, transcriptional, sequence analysis and proteomic profiling. BioResource Index was developed as part of the StemDB database project, funded by the EU FP7 project Eurosystem.

StemDB

The Stem Cell Database (StemDB) aims to be a comprehensive resource for information relevant to stem cell research. In addition to storing information about publications, experiments, cell lines, etc. relevant to stem cell research, StemDB offers a range of project management tools that have been used throughout its history in a number of  EU projects (EuroStemCell, EuroSyStem). 

GeneProf

GeneProf is a web-based data analysis suite for high-throughput sequencing data (RNA-seq and ChIP-seq) coupled with a rich database of ready-analysed sequencing experiments. GeneProf aims to simplify and streamline workflow creation in order to make functional genomics data more widely accessible to computational and experimental researchers. 

JEnsembl

We have implemented (and continue to develop) a version-aware Java API to Ensembl genome annotation datasources (both vertebrate genomes at ensembl.org and other taxa at ensemblgenomes.org).