Table of Contents
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