EMBnet.journal

The South African EMBnet Node: AGM 2010 report

Winston Hide, Alan Christoffels

The South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville

The South African National Bioinformatics Institute[1] (SANBI) conducts high-quality scientific research focused upon delivery of translatable biomedical discoveries, primarily through local and international collaboration with partner organisations. SANBI is part of the University of the Western Cape, situated outside Bellville near Cape Town. The Institute is headed by a Director, who reports through the Faculty of Natural Sciences, and provides overall leadership to the organization. The Institute consists of a group of faculty supported by technical and administration staff, guiding research of a group of Masters and PhD students and Post-Doctoral scientists.

SANBI became a member of the European Molecular Biology Network[2] in 1997. It developed close relationships with faculty at the University of Witwatersrand and University of Pretoria, supporting training and research there and at other sites around the country.

SANBI is well recognised in the areas of gene expression and host-pathogen disease research, including HIV, Trypanosomes and Malaria; and in the provision of bioinformatics and biomedical informatics training. This recognised expertise and proven capacity development has enabled the Institute to secure additional funding from a number of high-profile international agencies, e.g., National Institutes of Health, to expand its training programmes with the aim of developing faculty capable of producing NIH-funded research.

The Institute provides long-term skilling to impact on diseases prevalent in Africa, in particular the discovery of genetic factors that contribute to disease resistance in hosts, e.g., HIV and Man, and the genetic relationship contributing to cancers. SANBI’s first major scientific breakthrough was in 1999, in collaboration with US investigators, and resulted in the discovery of a genetic cause for a type of blindness in humans called retinitis pigmentosa. SANBI became the bioinformatics research centre for the Centre for AIDS Programme in South Africa in 2003, and for the South African AIDS Vaccine Initiative in 2005, and has been integral to HIV research in South African vaccine development. The Institute has recently delivered high-impact publications in the area of mammalian gene regulation, with a resulting expansion in knowledge of how genes deregulate in cancers. The Institute has had a strong influence on the development of health biotechnology locally, and internationally, through development and deployment of software tools for genetic research, adopted by international biotechnology companies, such as Affymetrix, and by over 400 research institutions worldwide.

Staffing

SANBI recently went through a change in management as a result of the resignation of the founding Director, Winston Hide, who moved to Harvard School of Public Health, and now holds a visiting professorship at SANBI. In addition, owing to the creation of the King Abdullah University of Science and Technology, a group of faculty and staff also moved from SANBI, in 2009, to establish bioinformatics in Saudi Arabia.

New Faculty have subsequently been appointed, including a National Bioinformatics Research Chair holder, the interim director, Alan Christoffels, and Simon Travis (HIV Specialist). Owing to the change in management, and movement of several members of the institution to new positions both internally and elsewhere, continuity with EMBnet has had to be renewed. SANBI has completed the process of hiring three additional research staff members, one of which will become our new EMBnet Node manager.

Impact of EMBnet on South Africa and SANBI

The EMBnet node and management model has been of great impact in Africa. First, EMBnet actively supported the establishment of SANBI and provided training to our staff and subsequently to several of our institutions. Second, the model of management and node structure was adopted by SANBI in its drafting of a successful proposal to establish the South African National Bioinformatics Network. Although the network took up an aggressive 3-year training programme, it has subsequently been disbanded, as government priorities have changed. Now, more than ever, SANBI and African sites need continuity with European programmes such as EMBnet, in particular in terms of training opportunities and co-development. SANBI is currently a development site for the Galaxy system, providing a development nexus for annotation systems, in addition to being a site for deployment of EMBOSS.

Service

Since becoming a member of EMBnet, SANBI has provided online and remote support for bioinformatics activities throughout South Africa. It provides online specialized tools through its website, and complements these with specialised training and databasing services, such as those for HIV, and focused support of national and local research efforts in trypanasomes, tsetse fly genomics, cancer, food safety, and related biotechnology projects. Faculty and staff at SANBI have provided onsite trainings for other institutions, and a staff member also has been seconded to the national health laboratory service, to provide expertise and training remotely over longer periods of time.

Training

SANBI hosts bioinformatics training workshops for African scientists funded through the WHO, the UK Welcome Trust, the SA National Research Foundation, the US National Institutes of Health and the Centres for Disease Control. With the disbanding of the National Bioinformatics Network, SANBI continues to fill the gap in national training, by coordinating 6-week introductory bioinformatics courses across the country. In February 2010, the national course was attended by 30 delegates, representing 5 universities. Annually, SANBI hosts a regional Ensembl training course for 25 delegates, which is presented by an EBI trainer. Most recently, SANBI hosted a national workshop, for 45 attendees, on genomics data interpretation, with presenters from South Africa, Harvard and Stanford. In addition, SANBI offers formal degrees at PhD and Masters level. SANBI is a founding member of the African Society for Bioinformatics and Computational Biology, and will be a host organisation for the 2011 regional meeting of the International Society for Computational Biology in Cape Town.

Facilities

The Institute has adequate scientific computer infrastructure, and is the site for a pair of high performance 32 CPU IBM P-690 servers and, in the next month, an 8 CPU Xserve cluster, which provide a significant proportion of the research compute infrastructure for bioinformatics in Africa. SANBI scientists have workstations and Internet access, as well as backup and disk storage. In late 2010, SANBI will move its premises to a new building, offering extensive training facilities, a visiting scientist facility and meeting rooms, in addition to the research and service provision currently performed.

Research

• Delivery of an African driven analysis and annotation of Glossina, the vector for the tsetse fly.
• Through capacity developed from genome annotation, we apply expertise and technologies developed to other relevant organisms to African health, with a particular emphasis upon integration of HIV clinical, immune and sequence diversity outcomes, and pathways analysis in Malaria.
• We integrate comparison of vector, host and pathogen genomes to deliver unique African knowledge of HIV and Malaria.
• Develop and apply understanding of normal and diseased human gene expression to diseases relevant to South Africans.
• Develop capacity of scientists through tightly defined research projects that have high impact on health in South Africa.

EU Collaborative projects

SANBI faculty and post docs have enjoyed funded collaborations through the EU FP funding programmes and currently we serve on the SYSCO programme, together with Institut Pasteur Tunis and Paris, and Max Planck Berlin.