Britain and China have formed a bioinformatics partnership to equip scientists with the computational skills to share data and analyses in metabolomics – the study of metabolites in living cells whose abundances can provide an indication of an organism’s cellular condition and health.
The partnership will work with four international networks dedicated to building computational and bioinformatics skills capacity: Software Carpentry; Data Carpentry; ELIXIR; and the Galaxy Project.
Funding from the UK’s Biotechnology and Biological Research Council (BBSRC) has allowed the European Bioinformatics Institute (EMBL-EBI), the Universities of Birmingham, Manchester and Oxford, The UK’s Sainsbury Laboratory and The Genome Analysis Centre (TGAC) to join with the Chinese organisation, BGI, and its open-access journal, GigaScience, to promote the sharing of data and analyses.
Although metabolic data has been stored and shared through public databases such as MetaboLights, which launched in 2012, the data sharing effort is yet keeping pace with the publication of scientific papers in metabolomics. The award from the BBSRC will enable the consortium to host training workshops to develop the skills of scientists in the UK and China in managing and sharing their metabolomics data and analyses.
Dr Peter Li, data organisation manager at GigaScience, said: ‘This funding will enable a synergistic exchange of our experience in data curation and publication with the expertise in metabolomics teaching provided by our UK-based partners.’ He continued, ‘Bioinformatics education is of great interest to BGI as a channel of communicating how science can be performed in an open manner which we are promoting in GigaScience.’
BGI, formerly known as the Beijing Genomics Institute but now headquartered in Shenzhen in the Guangdong province of China, was founded in 1999 and is one of the world’s foremost gene sequencing centres. It includes both private non-profit genomic research institutes and sequencing application commercial units. Its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies.
According to Dr Christoph Steinbeck of EMBL-EBI, there is already a lot of commitment in the metabolomics research community to sharing and reuse of data: ‘Our main challenge is simply in training people how best to incorporate this into their regular working practices. The BBSRC has recognised that this area of molecular biology is growing more quickly than any other, and that we need to do everything we can to train and support scientists in sharing data. That will lead to better quality data, more efficient research and shorter time to discovery.’
GigaScience is co-published by BGI and BioMed Central, the open-access publisher. It covers research that uses or produces ‘big data’ across the life sciences. It also offers a forum for discussing the difficulties of handling large-scale data. Its publication format integrates manuscript publication with complete data hosting, and incorporates analyses tools. It is a requirement of manuscript submission to GigaScience that all supporting data and source code be made available in the GigaScience database, GigaDB, as well as in their publicly available repositories. GigaScience will provide users access to associated online tools and workflows, and has integrated a data analysis platform.