Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them.

The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.

1;Preface;7 2;Acknowledgements;11 3;Contents;13 4;Introduction;27 4.1;Introduction;27 4.2;Bioinformatics;28 4.3;Systems Biology;33 4.4;Research Areas for Analysis;39 4.5;Collaborative Research;40 4.6;European Commission Research Projects;43 4.7;A Practical Guide to Project Websites, Participants, Coordinators, Publications;44 4.8;Key Sources;47 5;Part I Fundamental Collaborative Research and Computational Biology;49 5.1;Bioinformatics;51 5.1.1;Introduction;51 5.1.2;Genome Annotation;52 5.1.3;Bioinformatics Tools For Annotation;58 5.1.4;Gene Definition/Alternative Transcripts and Splicing;63 5.1.5;Gene Regulation and Expression;65 5.1.6;Functional Annotation of Proteins;68 5.1.7;Post-translation Modification, Membrane and Localisation Prediction;70 5.1.8;Protein Complexes, Networks and Pathways;73 5.1.9;Encyclopaedia of DNA Elements;75 5.2;Systems Biology;79 5.2.1;Introduction;79 5.2.2;Cell Cycle;80 5.2.3;P53;84 5.2.4;Spindle Formation and Imaging;86 5.2.5;Signalling and Control;88 5.2.6;Metabolic Regulation;93 5.2.7;Circadian Clock;96 5.2.8;Multiple Pathway Integration;97 5.2.9;Cellular Systems Biology;100 5.2.10;Local and Worldwide Scientific Collaboration;101 5.2.11;A Major FP7 Initiative in Systems Biology;104 5.3;Developmental Biology and Ageing;111 5.3.1;Introduction;111 5.3.2;Plant Development;112 5.3.3;Stem Cells and Development;116 5.3.4;Mitochondria and Ageing;117 5.3.5;Nuclear Receptors and Ageing;119 5.3.6;Implementation in the Seventh Framework Programme;120 6;Part II Resources Supporting Bioinformatics and Systems Biology Research;123 6.1;Databases, Computational Tools and Services;125 6.1.1;Introduction;125 6.1.2;Major Gateway to Collaborative Research;126 6.1.3;Distributed Development of Resources;129 6.1.4;Distributed Annotation System;131 6.1.5;Database Grid Integration;132 6.1.6;Ontologies;139 6.1.7;Text Mining;140 6.1.8;Systems Biology Toolboxes;141 6.2;Supporting Infrastructures;149 6.2.1;Introduction;149 6.2.2;Wet-Laboratory Research Infrastructures;150 6.2.3;Research Infrastructures: Future Priorities;155 6.2.4;Medical Information Systems;158 6.2.5;Knowledge Management Systems;158 6.2.6;Education;160 7;Part III Disease-Related Collaborative Research and Computational Biology;163 7.1;Infectious and Major Diseases;165 7.1.1;Introduction;165 7.1.2;Viral Pathogens;168 7.1.3;Bacterial Pathogens;170 7.1.4;Cardiovascular-Pulmonary Diseases and Diabetes;173 7.1.5;Neurological Diseases;176 7.1.6;Immunology;179 7.1.7;Drug Development;179 7.1.8;Implementation in the Seventh Framework Programme;188 7.2;Cancer;191 7.2.1;Introduction;191 7.2.2;Nature of Cancer and Biology and Genetics of Cells and Organisms;194 7.2.3;Tumour Viruses;195 7.2.4;Cellular Oncogenes;196 7.2.5;Growth Factors and Their Receptors;199 7.2.6;Cytoplasmic Signalling Circuitry;199 7.2.7;Cell Cycle;200 7.2.8;Tumour Suppressor Genes;201 7.2.9;p53 and Apoptosis;202 7.2.10;Cell Immortalisation, Tumourigenesis and Senescence;205 7.2.11;Multistep Tumourigenesis;206 7.2.12;Genomic Integrity and the Development of Cancer;207 7.2.13;Angiogenesis and Lymphangiogenesis;207 7.2.14;Metastasis;209 7.2.15;Tumour Immunology and Immunotherapy;210 7.2.16;Implementation in the Seventh Framework Programme;210 7.3;Genetic Variation and Diseases;213 7.3.1;Introduction;213 7.3.2;Genetic Variation Workshop;214 7.3.3;Status of Genetic Variation Research;215 7.3.4;Genotype to Phenotype;217 7.3.5;Data and Analysis Challenges;218 7.3.6;Databases;221 7.3.7;Data Generation;225 7.3.8;The Way Forward;227 7.3.9;Research in the Fifth Framework Programme and the Sixth Framework Programme;229 7.3.10;A Major Seventh Framework Programme Initiative in Genetic Variation;233 8;Part IV Science Management, Perspectives and Conclusions;239 8.1;Science Management;241 8.1.1;Introduction;241 8.1.2;How To Participate and Develop Proposals;246 8.1.3;Evaluation of Proposals;254 8.1.4;Project Negotiation;257 8.1.5;Operating Project Attributes and its Management;261 8.1.6;Contractual and Financial Ob