UCL PLATFORM TECHNOLOGIES

UCL Computational and Systems Medicine

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Resources

This page describes resources which may be useful to people performing computational medicine research at UCL and elsewhere.

High-performance Computing

• UCL's Research Computing facility provides a large capacity computing cluster, Legion.
• HECToR (High-End Computing Terascale Resource) is the UK's high-end computing resource, available for researchers at UK universities. The HECToR support service run an ongoing programme of training courses covering topics ranging from good software development practises to optimisation of parallel codes. These training courses are provided free of charge to HECToR users, and also to UK academics funded by one of the participating research councils (EPSRC, NERC and BBSRC).
• The HPCx Consortium provide HPC services and associated support to the UK academic community. The Consortium also run a variety of training courses, primarily designed to support HPCx users but also of interest to other HPC users.  Registration is free for HPCx users and UK-based academics.
• The UK National Grid Service (NGS) aims to provide coherent electronic access for UK researchers to all computational and data based resources and facilities required to carry out their research, independent of resource or researcher location.

Computational Science

• The UCL Centre for Computational Science, headed by Prof. Peter Coveney, applies large scale computational methods to modelling of physical and biological systems from the nano- to the macro-scale. Peter Coveney is also co-PI of the EU Virtual Physiological Human Network of Excellence.
• CoMPLEX, the UCL Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, enables interdisciplinary research in the life sciences. It brings together life and medical scientists with mathematicians, physical scientists, computer scientists and engineers to tackle the challenges arising from complexity in biology and medicine. 

Translational Research

• The US National Institute of Health's "Roadmap for Translational Research" set out the first vision of a way to improve human health, by more effectively translating scientific discoveries into practical applications. Such discoveries typically begin at “the bench” with basic research — in which scientists study disease at a molecular or cellular level — then progress to the clinical level, or the patient's “bedside.”
• The UK MRC's Translational Research Strategy lays out the MRC's strategy for supporting such research in the UK. The MRC's Translational Research Group is responsible for implementing this strategy.

Computational and Systems Biology and Medicine

• The mission of the Johns Hopkins University Institute for Computational Medicine is to "develop quantitative approaches for understanding the mechanisms, diagnosis and treatment of human disease through applications of mathematics, engineering and computer science. Specific research areas include modeling of human disease processes, algorithms-based disease risk prediction, and biomedical image understanding."
• The Instititute of Systems Biology is a research institute that "tackles the multi-disciplinary challenges of systems biology, integrateing many sciences including biology, chemistry, physics, computation, mathematics and medicine."
• The Carnegie Mellon University/Microsoft Research Centre for Computational Thinking whose mission is “...to advance computing research and advocate for the widespread use of computational thinking to improve people's lives. The Center accomplishes this by seeding research activities, seminars, and symposia that lead to vivid demonstrations of the value of computational thinking in diverse areas of human life.”
• The Harvard Initiative in Innovative Computing, founded in 2005, is “an interdisciplinary research and development center dedicated to using innovative computing tools to accelerate discovery across all of the scientific disciplines.”
• The Oxford eScience Research Centre (OeRC) aims "to enable the use and development of innovative computational and information technology in multidisciplinary collaborations."
• The Oxford Centre for Integrative Systems Biology "aims to develop theoretical approaches which not only address problems at specific scales, but which bridge scales in a computationally efficient and mathematically tractable way."
• SystemsX.ch, the Swiss national initiative in systems biology, begun in 2007, is an umbrella for 14 research projects, integrating 1000 scientists in 200 groups at 11 Swiss universities and research institutions. The SyBIT project will supply tools and infrastructure for data management, data analysis and archiving for all SystemsX.ch projects; develop and promote standard interfaces for data access and establish processes and policies for quality and knowledge management.”
• The Microsoft Research/University of Trento Centre for Computational Biology (CoSBI) engages in the development of new tools and methodologies for “algorithmic systems biology” using modern computer science ideas (such as executable, rather than descriptive, models, process algebras).
• The Harvard/MGH SWAN project is developing an integrated, multi-disciplinary knowledge management platform for dementia research, making aggressive use of Semantic Web technologies.
• caBIG is “an information network enabling all constituencies in the cancer community – researchers, physicians, and patients – to share data and knowledge.”
• NCRI ONcology Information eXchange (ONIX) is a free-to-use portal that connects many of the main public sources of cancer research data. ONIX allows users to run searches simultaneously against multiple, selected resources. ONIX also holds a searchable catalogue of cancer-relevant resources which allows users to find new information and collaborative opportunities.
• The W3C Healthcare and Life Sciences Working Group aims to “develop, advocate for, and support the use of Semantic Web technologies for biological science, translational medicine and health care.”
• The University of Manchester eScience Projects (myGRID, myExperiment, http://www.biocatalogue.org) is an interrelated set of projects to use Web services to create a rich environment for workflow-based bioscience analysis.
• The Microsoft/British Library Research Information Centre is developing “a virtual research environment framework ... We view researchers as extreme information workers and the purpose of the RIC is to support researchers in managing the increasingly complex range of tasks involved in carrying out research.”
• The Microsoft Research/Johns Hopkins University: GrayWulf Petascale computing resource is a “Scalable Software Architecture for Data Intensive Computing.”
• The Microsoft/bioIT Alliance is a “group of organizations working together to realize the potential of personalized medicine... unites the pharmaceutical, biotech, hardware, and software industries to explore new ways to share complex biomedical data and collaborate among multi-disciplinary teams.”
• The IBM/Ecole Polytechnqiue Federal de Lausanne Blue Brain Project is the first comprehensive attempt to reverse engineer the mammalian brain using computational methods.

Information Management and Sharing

• The UK national Digital Curation Centre provides a national focus for research and development into curation issues and to promote expertise and good practice, both national and international, for the management of all research outputs in digital format.
• JISC is active in supporting and standardising Digital Repositories
• The biosharing blog has news and information about data policies and standards for information sharing in the biological domain.
  
• DataCite, is an international initiative to facilitate access to research data. The goal of this cooperation is to establish a not-for-profit agency that enables organisations to register research datasets and assign persistent identifiers to them, so that
  
• The International Society for BioCuration is a non-profit organisation for biocurators, developers, and researchers with an interest in biocuration. The society promotes the field of biocuration and provides a forum for information exchange through meetings and workshops.
• Database: The Journal of Biological Databases and Curation is a new journal which "provides a platform for the presentation of novel ideas in database research surrounding biological information, and aims to help strengthen the bridge between database developers and users."
• The Pistoia Alliance is "an initiative to provide an open foundation of data standards, ontologies and web-services to streamline the Pharmaceutical Drug Discovery workflow (Chemistry, Biological Screening, Logistics) through common business terms, relationships and processes."
• The W3C's Semantic Web Health Care and Life Sciences Interest Group, part of the Semantic Web Activity, is developing, advocating for, and supporting the use of Semantic Web technologies for biological science, translational medicine and health care. These domains stand to gain tremendous benefit by adoption of Semantic Web technologies, as they depend on the interoperability of information from many domains and processes for efficient decision support.
• The World Wide Web Consortium is developing a Linking Open Data platform which uses Semantic Web technology to support integration of data from many domains. The goal is to extend the Web with a "data commons "by publishing various open data sets as RDF on the Web and by setting RDF links between data items from different data sources. Here's a picture of the Linked Data universe:
  
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  Collectively, the LinkedData data sets currently consist of over 7.7 billion RDF triples, which are interlinked by around 142 million RDF links

• MIBBI: Minimum Information for Biological and Biomedical Investigations is an evolving set of standards for annotation of biomedical experiments across a wide variety of methodologies and domains
• The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification.
• The Genomic Standards Consortium aims to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data.
• The EBI's new Bioinvestigation Index is a new prototype infrastructure set to provide users with a common structured representation and storage mechanism for a variety of biological, biomedical and environmental studies. isaCreator is Java client used to edit experimental metadata; it produces output in ISA-Tab format. It supports tagging of data with OBO ontology terms accessed in real time via Ontology Lookup Service and BioPortal.