Collaborative Computational Technologies for Biomedical Research

SEAN EKINS, MSc, PhD, DSc, is the Principal at Collaborations in Chemistry, and Collaborations Director at Collaborative Drug Discovery, Inc., as well as an Adjunct Associate Professor in the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy. He has published more than 170 papers and book chapters on computational and in vitro drug discovery approaches and has previously edited or co-edited three books for Wiley. MAGGIE A. Z. HUPCEY, PhD, is a chemist working within the Life Sciences and Healthcare Practice of PA Consulting Group in Princeton, New Jersey. She has worked on collaborative projects for the design and development of new products and processes in the medical device, drug delivery, and drug discovery fields, including presubmission and post-launch regulatory compliance activities.ANTONY J. WILLIAMS, PhD, FRSC, is currently Vice President, Strategic Development, at the Royal Society of Chemistry and holds an adjunct position at UNC-Chapel Hill. He has written chapters for many books and published more than 100 peer-reviewed papers and book chapters on NMR, predictive ADME methods, Internet-based tools, crowdsourcing, and database curation. He is an active blogger and participant in the Internet chemistry network.

"The book is of interest to researchers developing IT systems in the pharmaceutical industry, and for those participating in drug discovery collaborations." (Book News, 1 October 2011) "What unveiled itself as I turned the pages was ... a truthful, meaningful accounting of an evolving social science, perhaps a hope that the pure thrill of crowdsourcing may accelerate the process of discovery while preserving a free market economy.... The book contains... [contributions from a] multi-national task force if you will of some of the world's finest minds in life and physical science and ‘cloud-native' knowledge-sharing." (Untangled Health, 11 August 2011)

• FOREWORD xiAlpheus Bingham PREFACE 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