Collaborative Computational Technologies For Biomedical Research

This work offers guidelines for managing information and resources for collaboration in the pharmaceutical industry. Contributors include experts from pharmaceutical companies, software companies, government institutes, nonprofits, and academia. They offer insight on how to use computational technologies to manage partnerships in the pharmaceutical industry and provide case histories of biomedical collaborations. Technology chapters have been written to be accessible to nonspecialist readers. The book can be used as a quick-start guide for new labs, companies, and partnerships, and as a manual for troubleshooting existing partnerships. The first part of the book offers models for collaboration and computational biology and discusses ethics and intellectual property. The second section gives more details on methods and processes for collaborations, with examples from biomedicine in the Internet age, collaborative development of large-scale biomedical ontologies, and collaboration in cancer research. A section on tools for collaboration covers electronic laboratory notebooks, the use of the cloud for development of a collaborative drug discovery database, and a platform for crowdsourced collaboration to curate data derived from public compound databases. B&w charts and screen shots are included. The book is of interest to researchers developing IT systems in the pharmaceutical industry, and for those participating in drug discovery collaborations. Ekins works in drug discovery and teaches in the Department of Pharmaceutical Sciences at the University of Maryland. Annotation c2011 Book News, Inc., Portland, OR (booknews.com)

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 (Alpheus Bingham).

PREFACE.

CONTRIBUTORS.

PART I GETTING PEOPLE TO COLLABORATE.

1. The Need for Collaborative Technologies in Drug Discovery (Chris L. Waller, Ramesh V. Durvasula, and Nick Lynch).

2. Collaborative Innovation: The Essential Foundation of Scientific Discovery (Robert Porter Lynch).

3. Models for Collaborations and Computational Biology (Shawnmarie Mayrand-Chung, Gabriela Cohen-Freue, and Zsuzsanna Hollander).

4. Precompetitive Collaborations in the Pharmaceutical Industry (Jackie Hunter).

5. Collaborations in Chemistry (Sean Ekins, Antony J. Williams, and Christina K. Pikas).

6. Consistent Patterns in Large-Scale Collaboration (Robin W. Spencer).

7. Collaborations Between Chemists and Biologists (Victor J. Hruby).

8. Ethics of Collaboration (Richard J. McGowan, Matthew K. McGowan, and Garrett J. McGowan).

9. Intellectual Property Aspects of Collaboration (John Wilbanks).

PART II METHODS AND PROCESSES FOR COLLABORATIONS.

10. Scientifi c Networking and Collaborations (Edward D. Zanders).

11. Cancer Commons: Biomedicine in the Internet Age (Jeff Shrager, Jay M. Tenenbaum, and Michael Travers).

12. Collaborative Development of Large-Scale Biomedical Ontologies (Tania Tudorache and Mark A. Musen).

13. Standards for Collaborative Computational Technologies for Biomedical Research (Sean Ekins, Antony J. Williams, and Maggie A. Z. Hupcey).

14. Collaborative Systems Biology: Open Source, Open Data, and Cloud Computing (Brian Pratt).

15. Eight Years Using Grids for Life Sciences (Vincent Breton, Lydia Maigne, David Sarramia, and David Hill).

16. Enabling Precompetitive Translational Research: A Case Study (Sándor Szalma).

17. Collaboration in Cancer Research Community: Cancer Biomedical Informatics Grid (caBIG) (George A. Komatsoulis).

18. Leveraging Information Technology for Collaboration in Clinical Trials (O. K. Baek).

PART III TOOLS FOR COLLABORATIONS.

19. Evolution of Electronic Laboratory Notebooks (Keith T. Taylor).

20. Collaborative Tools to Accelerate Neglected Disease Research: Open Source Drug Discovery Model (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 (Sean Ekins, Moses M. Hohman, and Barry A. Bunin).

22. Chemspider: a Platform for Crowdsourced Collaboration to Curate Data Derived From Public Compound Databases (Antony J. Williams).

23. Collaborative-Based Bioinformatics Applications (Brian D. Halligan).

24. Collaborative Cheminformatics Applications (Rajarshi Guha, Ola Spjuth, and Egon Willighagen).

PART IV THE FUTURE OF COLLABORATIONS.

25. Collaboration Using Open Notebook Science in Academia (Jean-Claude Bradley, Andrew S. I. D. Lang, Steve Koch, and Cameron Neylon).

26. Collaboration and the Semantic Web (Christine Chichester and Barend Mons).

27. Collaborative Visual Analytics Environment for Imaging Genetics (Zhiyu He, Kevin Ponto, and Falko Kuester).

28. Current and Future Challenges for Collaborative Computational Technologies for the Life Sciences (Antony J. Williams, Renée J. G. Arnold, Cameron Neylon, Robin W. Spencer, Stephan Schürer, and Sean Ekins).

INDEX.