Unique Resources

1. Software and contents
Each partner brings unique expertise and software into the project: To underpin the three applications to be developed by Sealife London contributes the National electronic Library of Infection (NeLI) to the project, Scionics provides know-how on the high-throughput annotation pipeline Apart and access to high-throughput screening data on viral entry into the cell, and Edinburgh the Edinburgh Mouse Atlas, which links gene expression data to tissues and organs. These three contributions ensure the vertical integration from molecule and cell (Scionics) via tissue and organ (Edinburgh) to patient and population (London).
To implement the proposed applications, Dresden, Manchester, and Sophia-Antipolis provide a rich set of existing relevant software: Dresden has developed the GoPubMed system, which facilitates ontology-based literature search. Manchester has developed the Gohse system, which can provide GeneOntology annotations for free text. Manchester has also developed the myGrid system, which will ensure that the project has access to a large set of relevant Grid and Web Services. Sophia-Antipolis has developed Corese, the COnceptual REsource Search Engine, which allows one to reason over semantic web contents.

2. High-performance and grid computing:
To implement a semantic grid browser access to grid computing is required beyond the currently publicly available services. Dresden, Edinburgh, and Manchester provide such grid infrastructure.
Dresden's center for high-performance computing headed by Prof. Nagel has been setting up a EUR 15.000.000 computing infrastructure for data-intensive computing for biomedical applications. It consists of a high-performance computer with over 2 terabyte main memory, 50 terabyte disk space and petabyte archive and a Linux cluster with over 1000 nodes. The infrastructure is dedicated for biomedical applications. Additionally, Manchester is a regional eScience center in the UK and Edinburgh hosts the UK's national eScience center.

3. Reaching researchers:
Sealife members are well connected. Manchester, Dresden, Edinburgh, Sophia-Antipolis are members of the Networks of Excellence REWERSE and KnowledgeWeb, respectively. Manchester is member of the Life Science Network of Excellence Embrace, which will realize a Life Science Grid. Dresden is located within the Biotechnological Center (Biotec) with over 100 Biotec researchers as well as numerous companies. Dresden and Scionics are closely collaborating with the local Max Planck Institute for Molecular Cell Biology and Genetics with some 400 researchers. Manchester hosts some 150 Bioinformatics researchers and is part of the UK's Northwest Institute of Biohealth Informatics. Edinburgh is formally collaborating with the local Medical Research Council reaching some 200 researchers. Manchester and Edinburgh are regional centers and members of the UK's eScience programme.

Partners

• Dresden

  Prof. Dr. Michael Schroeder heads the 10 researcher strong bioinformatics group located in the Biotechnological Center (Biotec), TU Dresden. He is also a member of the Computer Science Department and the International Center in Computational Logic of TU Dresden.

  The bioinformatics group works on protein structure interactions and functional annotation with textmining, ontologies, and reasoning. They have developed the GoPubMed system for ontology-based literature mining, which will be central to the current proposal. Together with biologists and physicians, the group currently applies its work on protein interactions and on textmining to analyse gene expression data in the context of tumors and bone diseases.

  Michael Schroeder has published over 70 articles including a monograph, two patents and 13 journal articles in journals such as Bioinformatics, BMC Bioinformatics, Computers and Chemistry, and Nucleic Acid Research. He supervises 10 PhD students/research assistants and manages the nationally and EU-funded projects CODI, BioGrid, GeneStream, AgentLink, AgentCities, and the FP6 Network of Excellence REWERSE, Reasoning on the Web with Rules and Semantics. He is executive and steering committee member of REWERSE and leads the bioinformatics group of the network.

  The bioinformatics group at TU Dresden is located within the Biotechnological Center (Biotec). The Biotec is a unique interdisciplinary center hosting international research groups dedicated to genomics, proteomics, biophysics, cellular machines, tissue engineering and bioinformatics. Currently there are some 100 researchers from over ten different countries. Researchers have diverse backgrounds covering biology, medicine, physics, chemistry, computer science, and engineering. The academic groups are under one roof with biotec companies. The center hosts the fully accredited international masters programme in molecular bio-engineering, which brings classical biology and engineering together. The programme is running in its third year and has attracted 200 international applications of which ca. 30 are selected.

• Edinburgh

  Dr. Albert Burger is a Senior Lecturer in the Department of Computer Science, Heriot-Watt University and a Bioinformatics Research Scientist at the Medical Research Council Human Genetics Unit. He was recipient of a two-year Fulbright scholarship to the USA before coming to Edinburgh University for his PhD studies. He has over 15 years experience in databases and distributed systems working on bioinformatics issues for nearly ten years. He leads a group of 6 bioinformatics PhD students/research associates at Heriot-Watt and works with colleagues at the MRC and the university on interoperability problems in bioinformatics systems.

  At Heriot-Watt University, Albert Burger is head of BISEL , the Biomedical Informatics Systems Engineering Laboratory. BISEL focuses on issues that arise from bringing to bear the latest computer science developments in the context of biomedical research. The work concentrates on the next generation of distributed biomedical informatics systems and related human computer interaction (HCI) issues. For details on research done in BISEL, see here.

  At the Medical Research Council, Albert Burger is member of the Mouse Atlas group, which develops a digital atlas of mouse development, a resource for spatially mapped data such as in situ gene expression and cell lineage. The Mouse Atlas is an internationally recognised bioinformatics resource and the group collaborates with colleagues in the UK, US and EU. The Mouse Atlas is part of two currently funded EU life science projects, EuroGene and EurExpress. Albert Burger is working on integration and interoperability issues (including ontology and semantic web aspects) for the Mouse Atlas.

• London

  Dr. Patty Kostkova is a Research Fellow and the head of the City eHealth Research Center (CeRC), Institute of Health Sciences, The City University, London and a Consultant. She received her MSc in Computer Science from the Charles University, Prague, Czech Republic and her PhD in Computer Science from The City University, London, UK.

  She is interested in medical informatics and an application of digital libraries in health care. In particular, she is responsible for the National electronic Library of Infection (NeLI), the Antimicrobial Resistance Digital Library (AR DL) and the new Department of Health funded National Infection Control Manual project. In addition, she is looking at agent technologies, impact evaluation of Web sites and digital libraries, semantic Web, health care ontologies, agent-based personalisation. She has also worked as a consultant and temporary adviser for the World Health Organisation (WHO) Head Quarters, Geneva, when she has been involved in the design and the development of information systems and domain languages enabling a rapid development of applications for international surveillance and public health data management.

  Since 2000, City eHealth Research Center (CeRC) based at the Institute of Health Sciences, City University has been working on medical informatics and an application of digital libraries, Semantic Web and agent technologies in health care. The centre has been developing several National NHS-funded projects: National electronic Library of Infection (NeLI), The Antimicrobial Resistance Digital Library (AR DL), The Training in Infection Manual (TII) and the National Infection Control Manual (ICM), all available here. In addition to providing these services to the NHS professionals and public, we have been investigating digital libraries, quality of service, Semantic Web, health care ontologies, agent-mediated negotiation and personalization. In addition to IT research, CeRC has expertise in information science and social science in healthcare, in particular, evaluation and usability of digital libraries and Web sites and investigation of how healthcare information available on the Internet changes knowledge and attitude of health professionals and the public. They have a strong collaboration with health care professionals around infection in the UK and abroad and work closely with academic institutions, industrial partners and international agencies, such as WHO.

• Manchester

  Dr. Robert Stevens received an honours degree in biochemistry from Bristol; an M.Sc. in computational biology from York and a D.Phil. in computer science from York. He is currently a lecturer in bioinformatics within the BioHealth Informatics Group of the School of Computer Science at the University of Manchester. Principal research interests are in knowledge representation within biology and the use of Human Computer Interaction methods to improve the usability of bioinformatics tools. He is involved in projects such as Tambis, Gong, myGrid, which focus on the integration of distributed biomedical information using grid-technologies and ontologies.

  The Information management group conducts research into the design, development and use of data and knowledge management systems. IMG plays a leading role in standardisation and industrial forums, as leading members of the W3C Semantic Web activity and co-chairs of working groups of the pharmaceutical/biotech industrial forum I3C and the Global Grid Forum. Members of the group sit on a wide range of UK and international government and community funding and policy forming committees.

  Challenging applications motivate and validate IMG's research, in particular the Semantic Web and eScience. The group is split into four special interest groups that make up our portfolio of research interests: Augmentation of system to promote access by people with disabilities; Biological Information Management; Database and Knowledge Technologies Ontologies: Representation, reasoning and use. The Semantic Web and e-Science. Manchester is also host to the National centre for TextMining (NaCTeM), which has a remit to offer textmining services to UK.

• Scionics

  Scionics Computer Innovation GmbH was founded to supply database design, software creation, web interface design, hardware integration, and consulting to the international biomedical scientific research community. Scionics specializes in the organization, analysis, and presentation of research results including the integration of research hardware such as microscopes and image capturing systems. Scionics' customers comprise the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Newmark Laboratory, University of Illinois at Urbana Champaign, and Ludwig Institute of Cancer Research, San Diego. Scionics has also collaborated with EMBL, Heidelberg and the Harvard Medical School, Boston.

  Scionics was first founded as a partnership in Heidelberg, Germany and shortly thereafter began working with the forming Max Planck Institute for Molecular Cell Biology and Genetics. At the end of 2000, the company moved to Dresden, Germany and consistent with its growth incorporated and became Scionics Computer Innovation GmbH. The founding members of Scionics have spent several years doing database design, network infrastructure design, and integrating computer technology with current research methods.

  Dr. Bianca Habermann leads the bioinformatics service unit of Scionics comprising three researchers. She collaborates closely with researchers in the Max Planck Institute for Molecular Cell Biology and Genetics for whom she develops bioinformatics analysis tools. Together with one of the MPI groups she manages a nationally funded BMBF grant on systems biology. She has extensive experience in the high-throughput analysis of data using sequence- and structure-based methods with functional annotation from ontologies. Her group covers two topics: 1) functional prediction of proteins and 2) analysis of high-throughput data with the focus of pathway and network analysis.

• Sophia-Antipolis

  Dr. Olivier Corby is a Scientific Team Leader at INRIA Sophia-Antipolis and permanent responsible for the Edelweiss research team (previously known as Acacia, initiated by Rose Dieng-Kuntz). His research topics are Knowledge Engineering and Semantic Web. He works on mapping RDF/S, SPARQL and Conceptual Graphs (CG). He is the designer of the Corese Semantic Web Factory. He is responsible for a masters course on the Semantic Web at EPU Nice - Sophia Antipolis and also teaches in Licence Pro at IUT Nice-Sophia Antipolis and at ENSI Bourges.
  

  Rose Dieng-Kuntz was a research director at INRIA-Sophia-Antipolis and leader of the Acacia knowledge management project. She graduated from Ecole Polytechnique and ENST, obtained Doctorate in Computer Science from University Paris-Sud. She had organised 20 conferences and workshops, was member of 55 program committees, chaired or co-chaired JAVA'93, EKAW'2000, ECAI'2002, IC'2003, and COOP2004. She was a series editor at IOS Press and had published 8 books as author or editor and 95 papers on Knowledge Engineering, Knowledge Management, Ontologies, Semantic Web, Conceptual Graphs and Multi-Agent Systems.

  The Edelweiss research group and project at INRIA Sophia-Antipolis (previously known as Acacia) aims at offering methodological and software support for knowledge management (KM), based on a corporate memory approach. Its research topics concern ontologies, corporate Semantic Webs, multi-expertise, multiple viewpoints, multiple ontologies, ontology-guided information retrieval and multi-agent systems for distributed memory.