Collaborative Computational Technologies for Biomedical Research

Methods, Processes, and Tools for Collaboration "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."—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.

FOREWORD xi Alpheus Bingham PREFACE xv CONTRIBUTORS xix PART I GETTING PEOPLE TO COLLABORATE 1 1. The Need for Collaborative Technologies in Drug Discovery 3 Chris L. Waller, Ramesh V. Durvasula, and Nick Lynch 2. Collaborative Innovation: The Essential Foundation of Scientific Discovery 19 Robert Porter Lynch 3. Models for Collaborations and Computational Biology 39 Shawnmarie Mayrand-Chung, Gabriela Cohen-Freue, and Zsuzsanna Hollander 4. Precompetitive Collaborations in the Pharmaceutical Industry 55 Jackie Hunter 5. Collaborations in Chemistry 85 Sean Ekins, Antony J. Williams, and Christina K. Pikas 6. Consistent Patterns in Large-Scale Collaboration 99 Robin W. Spencer 7. Collaborations Between Chemists and Biologists 113 Victor J. Hruby 8. Ethics of Collaboration 121 Richard J. McGowan, Matthew K. McGowan, and Garrett J. McGowan 9. Intellectual Property Aspects of Collaboration 133 John Wilbanks PART II METHODS AND PROCESSES FOR COLLABORATIONS 147 10. Scientific Networking and Collaborations 149 Edward D. Zanders 11. Cancer Commons: Biomedicine in the Internet Age 161 Jeff Shrager, Jay M. Tenenbaum, and Michael Travers 12. Collaborative Development of Large-Scale Biomedical Ontologies 179 Tania Tudorache and Mark A. Musen 13. Standards for Collaborative Computational Technologies for Biomedical Research 201 Sean Ekins, Antony J. Williams, and Maggie A. Z. Hupcey 14. Collaborative Systems Biology: Open Source, Open Data, and Cloud Computing 209 Brian Pratt 15. Eight Years Using Grids for Life Sciences 221 Vincent Breton, Lydia Maigne, David Sarramia, and David Hill 16. Enabling Precompetitive Translational Research: A Case Study 241 Sándor Szalma 17. Collaboration in Cancer Research Community: Cancer Biomedical Informatics Grid (caBIG) 261 George A. Komatsoulis 18. Leveraging Information Technology for Collaboration in Clinical Trials 281 O. K. Baek PART III TOOLS FOR COLLABORATIONS 301 19. Evolution of Electronic Laboratory Notebooks 303 Keith T. Taylor 20. Collaborative Tools to Accelerate Neglected Disease Research: Open Source Drug Discovery Model 321 Anshu Bhardwaj, Vinod Scaria, Zakir Thomas, Santhosh Adayikkoth, Open Source Drug Discovery (OSDD) Consortium, and Samir K. Brahmachari 21. Pioneering Use of the Cloud for Development of Collaborative Drug Discovery (CDD) Database 335 Sean Ekins, Moses M. Hohman, and Barry A. Bunin 22. Chemspider: a Platform for Crowdsourced Collaboration to Curate Data Derived From Public Compound Databases 363 Antony J. Williams 23. Collaborative-Based Bioinformatics Applications 387 Brian D. Halligan 24. Collaborative Cheminformatics Applications 399 Rajarshi Guha, Ola Spjuth, and Egon Willighagen PART IV THE FUTURE OF COLLABORATIONS 423 25. Collaboration Using Open Notebook Science in Academia 425 Jean-Claude Bradley, Andrew S. I. D. Lang, Steve Koch, and Cameron Neylon 26. Collaboration and the Semantic Web 453 Christine Chichester and Barend Mons 27. Collaborative Visual Analytics Environment for Imaging Genetics 467 Zhiyu He, Kevin Ponto, and Falko Kuester 28. Current and Future Challenges for Collaborative Computational Technologies for the Life Sciences 491 Antony J. Williams, Renée J. G. Arnold, Cameron Neylon, Robin W. Spencer, Stephan Schürer, and Sean Ekins INDEX 519