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.

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