BioConductor
Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
Bioconductor is primarily based on the R programming language but we do accept contributions in any programming language. Although initial efforts focused primarily on DNA microarray data analysis, many of the software tools are general and can be used broadly for the analysis of genomic data, such as SAGE, sequence, or SNP data.
The broad goals of the projects are to
- provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data;
- facilitate the integration of biological metadata in the analysis of experimental data: e.g. literature data from PubMed, annotation data from LocusLink;
- allow the rapid development of extensible, scalable, and interoperable software;
- promote high-quality documentation and reproducible research;
- provide training in computational and statistical methods for the analysis of genomic data.
Gene Ontology
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The GO project has developed three structured controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. There are three separate aspects to this effort: first, the development and maintenance of the ontologies themselves; second, the annotation of gene products, which entails making associations between the ontologies and the genes and gene products in the collaborating databases; and third, development of tools that facilitate the creation, maintenance and use of ontologies.
The use of GO terms by collaborating databases facilitates uniform queries across them. The controlled vocabularies are structured so that they can be queried at different levels: for example, you can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or you can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to genes or gene products at different levels, depending on the depth of knowledge about that entity.
International HapMap ProjectThe HapMap is a catalog of common genetic variants that occur in human beings. It describes what these variants are, where they occur in our DNA, and how they are distributed among people within populations and among populations in different parts of the world. The International HapMap Project is not using the information in the HapMap to establish connections between particular genetic variants and diseases. Rather, the Project is designed to provide information that other researchers can use to link genetic variants to the risk for specific illnesses, which will lead to new methods of preventing, diagnosing, and treating diseases.
Microarray Gene Expression Data Society - MGED SocietyThe Microarray Gene Expression Data (MGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments. The current focus is on establishing standards for microarray data annotation and exchange, facilitating the creation of microarray databases and related software implementing these standards, and promoting the sharing of high quality, well annotated data within the life sciences community. A long-term goal for the future is to extend the mission to other functional genomics and proteomics high throughput technologies
The MolTools consortium
The MolTools consortium started on January 1st 2004, as a joint research programme bringing together 12 leading European academic groups, four biotech SMEs and one US laboratory working in the area of postgenomic technology development. The partners have pioneered a series of important molecular techniques and will now work together to establish next-generation tools for molecular analysis. Its scientific aims are to establish genome analysis technologies set to monitor extensive molecular repertoires, and with the capacity to investigate even single molecules. Its current research projects include:
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