ELIXIR talk – session: ELIXIR National collaborations, international standards.
Abstract
When SIB Swiss Institute of Bioinformatics was founded in 1998, bioinformatics was still in its infancy. Today, SIB is an independent, non-profit organization recognized of public utility. SIB acts as the Swiss node of ELIXIR and is the biggest national node within the consortium. SIB includes 60 research and service groups, which bring together 750 scientists in the fields of genomics, transcriptomics, proteomics, evolution, population genetics, systems biology, structural biology, biophysics and clinical bioinformatics. SIB leads and coordinates the field of bioinformatics in Switzerland. Its data science experts join forces to advance biological and medical research and enhance health by providing the national and international life science community with a state-of-the-art bioinformatics infrastructure, including resources, expertise and services. The Institute federates world-class researchers and delivers training in bioinformatics. Core bioinformatics databases, software and services SIB’s 60 research and service groups develop, maintain and provide a large portfolio of core bioinformatics resources that are essential to the worldwide life science community. The SIB portal ExPASy – the first website in the biomedical field set up in 1993 – gives access to over 150 high-quality databases and software tools. SIB’s impact is illustrated by the fact that practically each life scientist worldwide is relying on resources to which SIB is contributing. Within ELIXIR, the Swiss node is the provider of various renowned bioinformatics resources. UniProtKB/Swiss-Prot, the expert-curated part of the UniProt Knowledgebase, is developed and maintained by the UniProt consortium which includes SIB, the EMBL-EBI, European Bioinformatics Institute, and PIR, the Protein Information resource. UniProtKB/Swiss-Prot brings together experimental results, computed features and scientific conclusions. The UniProt website counts on a monthly basis over 800,000 requests. The hallmark of the Swiss-Prot group is manual biocuration, with more than 60% of its staff fully dedicated to this task. The time and labour-intensive expert curation of proteins function is essential to provide the scientific community with high quality reference datasets. The datasets in this expert-annotated and non-redundant protein sequence database are not only reliable but also computationally usable thanks to the use of various ontologies and structured knowledge developed by the group and international collaborators. SWISS-MODEL, another example of an ELIXIR Service offered by the Swiss node, is worldwide one of the most widely used, automated protein structure homology-modelling servers for generating 3D models of a protein. Comparative approaches are currently the most accurate and reliable computational methods to derive 3D models of proteins, for which experimental structures are not available. SWISS-MODEL automates the complex process of model building on an easy to use web-based system, making model information also available for non-specialists. SIB is offering its expertise to different capacity building initiatives that promote excellence in resource development and operation, bringing European bioinformatics service provision to the next level. The Swiss node is strongly involved in ELIXIR’s activities that support the long-term sustainability of core data resources, notably within the data platform, both through the work on the key indicators for data resources as well as through the long term sustainability working group. Offering key competencies and research support Through eleven core facilities and high-performance computing (HPC) centres, as well as embedded bioinformaticians, SIB groups provide expert data analysis services and computing power to life scientists in academia and industry, thus enabling them to perform world-class biomedical research. The services provided include analysis of high-throughput data (genome/exome sequence, RNA sequencing, proteomics), scientific support of (bio)medical projects, development of algorithms, biostatistics training, as well as access to computational space, helpdesk and support. In addition to its bioinformatics core facilities and HPC centres, SIB provides competencies to the Swiss universities and research institutes by embedding bioinformaticians in laboratories. The presence of these embedded bioinformaticians in the research groups is a real advantage, as they can provide direct guidance on how to manage and analyse data for optimized use of the various bioinformatics tools. Federating bioinformatics research groups from Swiss universities and research institutes Rather than centralizing expertise and capacity, SIB’s mission is to engage the bioinformatics community to collaborate. The decentralized, federating organizational structure of SIB was not only novel at its inception but it also is a model for countries setting up their bioinformatics infrastructure, as well as for ELIXIR, which has adopted the hub and nodes model. SIB has created a true bioinformatics culture in Switzerland, making universities and schools of higher education realize the importance of bioinformatics for the life sciences. As a result, an astonishing number of chairs of bioinformatics were created. SIB has put bioinformatics on the government’s roadmap for science, securing funding since 1997. Fostering collaboration and innovation at the highest level of scientific excellence Over time, a dense collaborative network has been established between the SIB groups from Swiss universities and research institutes located in the different cantons. SIB collaborates at the international level with many renowned institutions. As bioinformatics is an interdisciplinary area, most of SIB groups are involved in several fields of activity, ranging from genetic diseases, to the evolution of species, and bioinformatics infrastructure. Training first-rate researchers To ensure that the exceptional quality of bioinformatics is maintained over the coming years, it is of utmost importance to train the next generation of bioinformaticians and to ascertain that life scientists are trained to make the best of its resources. SIB provides continuing education in bioinformatics, organizes a PhD Training Network, and coordinates undergraduate education in bioinformatics. SIB also develops e-learning modules, which are freely accessible to all. Within ELIXIR, SIB is very active in the context of training, providing teaching activities to the international life science community and co-leading the training platform and the training work package in ELIXIR-EXCELERATE. Clinical bioinformatics Well aware that the wealth of data produced by modern technologies in medicine and the growing self-awareness of patients will change the way of considering medical data, SIB is proactive in the development of clinical bioinformatics. The Institute is embracing the challenge to strive for excellence in bioinformatics for personalized health, working towards a more global approach of the patient, and more targeted and effective therapies.
Authors
Ioannis Xenarios, SIB Swiss Institute of Bioinformatics, Switzerland
Christine Durinx, SIB Swiss Institute of Bioinformatics, Switzerland
Ron Appel, SIB Swiss Institute of Bioinformatics, Switzerland