A partnership between the University of Birmingham, BGI and its open-access journal, GigaScience, has received funding from the UK's Natural Environment Research Council (NERC) to develop a software platform for the analysis of large-scale environmental metabolomics data.
Metabolomics involves the detection and quantification of small molecules (metabolites) in living organisms and can provide an indication of their cellular condition and health. The toxicological responses of organisms to pollutants can be studied using environmental metabolomics, enabling researchers to discover diagnostic markers for monitoring and risk assessment of our environment. Research at Birmingham focuses extensively on the metabolic responses of the freshwater model organism, Daphnia, to both pollutants and engineered nanomaterials.
Sophisticated computational analyses must be performed on metabolomics data in order to measure the abundances of the metabolites. However, this typically requires expert knowledge in computer programming and biostatistics, restricting the usefulness of metabolomics to specialised laboratories. This project will develop a new software platform to make it much easier for non-specialist scientists to analyse their metabolomics datasets.
As the first metabolomics project in the recently announced Joint BGI-University of Birmingham Environment & Health Centre, the funding will enable a developer from the University's School of Biosciences, to travel to Hong Kong and work with GigaScience in developing the popular Galaxy workflow system for use in metabolomics data analyses.
Dr. Peter Li, Data Organisation Manager at GigaScience, commented, "This funding from NERC will enable a synergistic exchange of skills in the curation and automated analysis of large-scale data that we have in GigaScience with the University of Birmingham's expertise in metabolomics". He continued "This is an area of the life sciences that is of great interest to BGI as they move and broaden their expertise from being a major genomics organization into more integrative research in the life sciences".
Professor Mark Viant from the University of Birmingham added, "This collaboration with BGI aligns perfectly with one of our major goals at Birmingham, to develop tools and resources to facilitate the wider use of metabolomics by environmental scientists, and subsequently to provide training in these tools".
The project is funded by the UK NERC under the Mathematics & Informatics for Environmental Omic Data Synthesis programme.
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GigaScience is co-published by BGI, the world's largest genomics organization, and BioMed Central, the world's largest open-access publisher. The journal covers research that uses or produces 'big data' from the full spectrum of the life sciences. It also serves as a forum for discussing the difficulties of and unique needs for handling large-scale data from all areas of the life sciences. The journal has a completely novel publication format -- one that integrates manuscript publication with complete data hosting, and analyses tool incorporation. To encourage transparent reporting of scientific research as well as enable future access and analyses, 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, maximizing the potential utility and re-use of data. (Follow us on twitter @GigaScience; sina-weibo http://weibo.
BGI was founded in 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and 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, supporting a variety of disease, agricultural, environmental, and related applications. BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 250 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, have sequenced the human Gut metagenome, and a significant proportion of the genomes for the 1,000 genomes project. For more information about BGI please visit http://www.
A leading UK research-intensive university, the University of Birmingham is a vibrant, global community and an internationally-renowned institution, in the top 100 globally. With approximately 28,000 students and 6,000 members of staff, its work brings people from more than 150 countries to Birmingham. The University has a bold strategy to develop its global reputation by enhancing its international presence and collaborations. In addition to China, Birmingham has strategic partnerships in the USA, India, Brazil and Australia.
NERC is the UK's main agency for funding and managing world-class research, training and knowledge exchange in the environmental sciences. It coordinates some of the world's most exciting research projects, tackling major issues such as climate change, food security, environmental influences on human health, the genetic make-up of life on earth, and much more. NERC receives around £300m a year from the government's science budget, which it uses to fund research and training in universities and its own research centres.