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:
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Serving as a user manual for collaborations
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Tackling real problems from both human collaborative and data and informatics perspectives
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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.
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
