Collaborative Computational Technologies for Biomedical Research

Edited by Sean Ekins, Maggie A.Z. Hupcey and Antony J. Williams

With a Foreword by Alpheus Bingham

Wiley Series on Technologies for the Pharmaceutical IndustrySean Ekins, Series Editor

Biomedical research has become increasingly driven by creating and consuming tremendous volumes of data. At the same time the pharmaceutical industry is utilizing an extended network of partner organizations of various sorts in order to discover and develop new drugs. There is currently little if any guidance for managing information and computational resources across collaborations.

Methods, Processes and Tools for Collaborations

The book is divided into four sections:

Part I. Getting People To CollaboratePart II: Methods And Processes For CollaborationsPart III. Tools For CollaborationsPart IV. The Future Of Collaborations

This book tackles a real set of problems thoroughly from both the human collaborative, the data and informatics side, and is very relevant to activities of running a laboratory or a collaborative R&D project.

This book provides the reader with state of the art practical advice. Collaboration will only increase in the future and scientists will be relying on computational applications to enable this.

PART I: GETTING PEOPLE TO COLLABORATE

1. The Need for Collaborative Technologies in Drug DiscoveryChris L. Waller, Ramesh V. Durvasula and Nick Lynch

2. Collaborative Innovation: the Essential Foundation of Scientific DiscoveryRobert Porter Lynch

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

4. Precompetitive Collaborations in the Pharmaceutical IndustryJackie Hunter

5. Collaborations in ChemistrySean Ekins, Antony J. Williams and Christina K. Pikas

6. Consistent Patterns in Large Scale CollaborationRobin W. Spencer

7. Collaborations Between Chemists and Biologists Victor J. Hruby

8. Ethics of CollaborationRichard J. McGowan, Matthew K. McGowan and Garrett J. McGowan

9 Intellectual Property Aspects of CollaborationJohn Wilbanks

PART II: METHODS AND PROCESSES FOR COLLABORATIONS

10. Scientific Networking and CollaborationsEdward D. Zanders

11. Cancer Commons: Biomedicine in the Internet AgeJeff Shrager, Jay M. Tenenbaum, and Michael Travers

12. Collaborative Development of Large-Scale Biomedical OntologiesTania Tudorache and Mark A. Musen

13. Standards for Collaborative Computational Technologies for Biomedical ResearchSean 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 StudySándor Szalma

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

18. Leveraging Information Technology for Collaboration in Clinical TrialsO.K. Baek

PART III. TOOLS FOR COLLABORATIONS

19. The Evolution of Electronic Laboratory NotebooksKeith T. Taylor

20. Collaborative Tools to Accelerate Neglected Disease Research: the Open Source Drug Discovery Model Anshu Bhardwaj, Vinod Scaria, Zakir Thomas, Santosh Adayikkoth, Open Source Drug Discovery (OSDD) Consortium and Samir K. Brahmachari 21. Pioneering Use of the Cloud for Development of the 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 AcademiaJean-Claude Bradley, Andrew S.I.D. Lang, Steve Koch and Cameron Neylon

26. Collaboration and the Semantic WebChristine Chichester and Barend Mons

27. A Collaborative Visual Analytics Environment for Imaging GeneticsZhiyu He, Kevin Ponto and Falko Kuester

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

Target Audience

We have aimed for a complete volume that can be read by all interested in biomedical research and development and with each chapter edited to ensure consistency across the common theme of collaboration and with appropriate explanatory figures and key references. We are confident this book will become a valuable reference work for those interested in collaborative approaches to biomedical research.

The time has come to fundamentally re-think 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

Considering the present state the pharmaceutical industry finds itself in, the promise of innovative medicines for children and our children's children may well depend on finding new collaborative paradigms with attendant business models. The material for this genesis, though nascent, may well be found in these pages.

- Alpheus Bingham, Cascade Consulting; InnoCentive, Inc.; Monitor Talent

Sean Ekins, MSc, PhD, DSc is the Principal at Collaborations in Chemistry; Collaborations Director at Collaborative Drug Discovery, Inc., SVP at ACT LLC; Adjunct Associate Professor in the Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy. Dr. Ekins has published >150 papers and book chapters on computational and in vitro drug discovery approaches and 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 in Princeton, NJ. 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 pre-submission and post-launch regulatory compliance activities.

Antony J Williams, PhD, FRSC is currently VP, 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 >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.

About the Authors

Related books by these authors

Related websites for these authors

http://www.collaborations.com/CHEMISTRY.HTM

http://myprofile.cos.com/ekinssean

http://www.amazon.com/Sean-Ekins/e/B003BFP2E0

http://www.chemconnector.com/chemunicating/

http://www.chemspider.com/blog/

Acknowledgments

All contributors to the book

www.tagxedo.com

Contact us @

ekinssean@yahoo.comhupcey@yahoo.comtony27587@gmail.com