Collaborative Computational Technologies for Biomedical Research

Methods, Processes, and Tools for Collaboration "e;The time has come to fundamentally rethink how we handle the building of knowledge in biomedical sciences today. This book describes how the computational sciences have transformed into being a key knowledge broker, able to integrate and operate across divergent data types."e; Bryn Williams-Jones, Associate Research Fellow, Pfizer The pharmaceutical industry utilizes an extended network of partner organizations in order to discover and develop new drugs, however there is currently little guidance for managing information and resources across collaborations. Featuring contributions from the leading experts in a range of industries, Collaborative Computational Technologies for Biomedical Research provides information that will help organizations make critical decisions about managing partnerships, including: Serving as a user manual for collaborations Tackling real problems from both human collaborative and data and informatics perspectives Providing case histories of biomedical collaborations and technology-specific chapters that balance technological depth with accessibility for the non-specialist reader A must-read for anyone working in the pharmaceuticals industry or academia, this book marks a major step towards widespread collaboration facilitated by computational technologies.

Methods, Processes, and Tools for Collaboration"The time has come to fundamentally rethink how we handle thebuilding of knowledge in biomedical sciences today. This bookdescribes how the computational sciences have transformed intobeing a key knowledge broker, able to integrate and operate acrossdivergent data types."--Bryn Williams-Jones, Associate ResearchFellow, PfizerThe pharmaceutical industry utilizes an extended network ofpartner organizations in order to discover and develop new drugshowever there is currently little guidance for managing informationand resources across collaborations.Featuring contributions from the leading experts in a range ofindustries, Collaborative Computational Technologies for BiomedicalResearch provides information that will help organizations makecritical decisions about managing partnerships, including:* Serving as a user manual for collaborations* Tackling real problems from both human collaborative and dataand informatics perspectives* Providing case histories of biomedical collaborations andtechnology-specific chapters that balance technological depth withaccessibility for the non-specialist readerA must-read for anyone working in the pharmaceuticals industryor academia, this book marks a major step towards widespreadcollaboration facilitated by computational technologies.

FOREWORD xiAlpheus BinghamPREFACE xvCONTRIBUTORS xixPART I GETTING PEOPLE TO COLLABORATE 11. The Need for Collaborative Technologies in Drug Discovery 3Chris L. Waller, Ramesh V. Durvasula, and Nick Lynch2. Collaborative Innovation: The Essential Foundation of Scientific Discovery 19Robert Porter Lynch3. Models for Collaborations and Computational Biology 39Shawnmarie Mayrand-Chung, Gabriela Cohen-Freue, and Zsuzsanna Hollander4. Precompetitive Collaborations in the Pharmaceutical Industry 55Jackie Hunter5. Collaborations in Chemistry 85Sean Ekins, Antony J. Williams, and Christina K. Pikas6. Consistent Patterns in Large-Scale Collaboration 99Robin W. Spencer7. Collaborations Between Chemists and Biologists 113Victor J. Hruby8. Ethics of Collaboration 121Richard J. McGowan, Matthew K. McGowan, and Garrett J. McGowan9. Intellectual Property Aspects of Collaboration 133John WilbanksPART II METHODS AND PROCESSES FOR COLLABORATIONS 14710. Scientific Networking and Collaborations 149Edward D. Zanders11. Cancer Commons: Biomedicine in the Internet Age 161Jeff Shrager, Jay M. Tenenbaum, and Michael Travers12. Collaborative Development of Large-Scale Biomedical Ontologies 179Tania Tudorache and Mark A. Musen13. Standards for Collaborative Computational Technologies for Biomedical Research 201Sean Ekins, Antony J. Williams, and Maggie A. Z. Hupcey14. Collaborative Systems Biology: Open Source, Open Data, and Cloud Computing 209Brian Pratt15. Eight Years Using Grids for Life Sciences 221Vincent Breton, Lydia Maigne, David Sarramia, and David Hill16. Enabling Precompetitive Translational Research: A Case Study 241Sándor Szalma17. Collaboration in Cancer Research Community: Cancer Biomedical Informatics Grid (caBIG) 261George A. Komatsoulis18. Leveraging Information Technology for Collaboration in Clinical Trials 281O. K. BaekPART III TOOLS FOR COLLABORATIONS 30119. Evolution of Electronic Laboratory Notebooks 303Keith T. Taylor20. Collaborative Tools to Accelerate Neglected Disease Research: Open Source Drug Discovery Model 321Anshu Bhardwaj, Vinod Scaria, Zakir Thomas, Santhosh Adayikkoth, Open Source Drug Discovery (OSDD) Consortium, and Samir K. Brahmachari21. Pioneering Use of the Cloud for Development of Collaborative Drug Discovery (CDD) Database 335Sean Ekins, Moses M. Hohman, and Barry A. Bunin22. Chemspider: a Platform for Crowdsourced Collaboration to Curate Data Derived From Public Compound Databases 363Antony J. Williams23. Collaborative-Based Bioinformatics Applications 387Brian D. Halligan24. Collaborative Cheminformatics Applications 399Rajarshi Guha, Ola Spjuth, and Egon WillighagenPART IV THE FUTURE OF COLLABORATIONS 42325. Collaboration Using Open Notebook Science in Academia 425Jean-Claude Bradley, Andrew S. I. D. Lang, Steve Koch, and Cameron Neylon26. Collaboration and the Semantic Web 453Christine Chichester and Barend Mons27. Collaborative Visual Analytics Environment for Imaging Genetics 467Zhiyu He, Kevin Ponto, and Falko Kuester28. Current and Future Challenges for Collaborative Computational Technologies for the Life Sciences 491Antony J. Williams, Renée J. G. Arnold, Cameron Neylon, Robin W. Spencer, Stephan Schürer, and Sean EkinsINDEX 519