The Ferryman

Ensemble, Integrated and Systems Dynamics Approaches to Systems Biology

In our InnovationWell session chaired by Keith Elliston (Co-Founder, President and Chief Executive Officer of Genstruct, Inc.) taking place the morning of 14 October 2008 at Bryn Mawr, we will have the following 3 systems biology perspectives presented:

Darius M. Dziuda (Central Connecticut State University), Ensemble Classifiers and Biomarker Discovery
Frank Tobin (Tobin Consulting), Integrative Mathematical Modeling of Biological Systems
David S. Lester (Innovative Technologies in Health and Wellness, Inc.), Using a Systems Approach to Determine Diabetic Patient Interventions and Outcomes

The perspectives will be followed by a knowledge café discussion, lunch and in the afternoon a further related session on computational biology chaired by Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.):

http://barryhardy.blogs.com/theferryman/2008/08/computational-b.html

A description of the session with presentation abstracts follows.  Please add your comments, discussion or questions at the end of the post.

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

InnovationWell Systems Biology KM Knowledge Management bioinformatics Computational Biology Translational Medicine Molecular Medicine biology pharmaceutical pharma meeting workshop training Critical Path toxicology Life Sciences Drug Discovery Research and Development Drug Development Healthcare Innovation Innovation Management events

Schedule for InnovationWell and eCheminfo Autumn 2008 Community of Practice Meeting

I provide below a schedule for the upcoming InnovationWell and eCheminfo Community of Practice meetings at Bryn Mawr.

I also include a location map here which may be useful upon arrival:

Download bryn_mawr_campus_map_douglas_connect_meeting.pdf

[Please follow continuation here to view schedule.]

The Push and Pull of Knowledge Management in R&D

Knowledge Management in the pharmaceutical industry has been undergoing a transition over the past 5-10 years. With recent changes occurring in the industry, shifts in the research focus at both large pharmaceuticals and small-mid size pharmaceuticals and biotechs are becoming more common. The way we view the information food chain has had to change. We are in a world where we need to have greater flexibility and easier access to data than ever before. We are typically working with external as well as internal collaborators on our project teams.

On the 13 October 2008 at the InnovationWell Community of Practice Meeting at Bryn Mawr College, Philadelphia, we will run a workshop on the Push and Pull of Knowledge Management in R&D, which will be chaired by John Conway (Accelrys) and Frank Hollinger (Sphaera Pharma).

The objective of the workshop will be to discuss how Knowledge Management Systems are being developed in this new age, how they are being used and what changes we as a community should be pushing for in the next generation of systems. Keeping an eye toward doing things ‘right’ while remaining cost conscious, we are often presented with a challenge to put the ‘best’ system in place. Participants will discuss ways forward in solving this problem within organizations, collaborations and discovery teams.

User Perspectives will be used to seed discussions on current and future research needs in Knowledge Management in R&D support systems, which will be carried out using a wiki-supported Knowledge Cafe format.

Program & Schedule
09.00 Frank Brown (Accelrys), Data is only Valuable if you can Extract the Information
09.30 Chris Culberson (Merck Research Laboratories), WISK: What I Should Know – Mining Chemical Transformations to see What Really Works

10.00 Ralph T. Mosley (Pharmasset), Going Big to Small: What happens when you leave Big Pharma?
10.30 Coffee Break
11.00 Knowledge Cafe on Perspectives
12.30 Group Discussion
13.00 Lunch
14.00 Tim McIntyre (GlaxoSmithKline), Workflow Application Enhances Productivity
14.30 Chris Smith (Pfizer), Risk-based Decision Making based on Complex Physical Chemical, Environmental Fate and Toxicological Effect Data Sets for Pharmaceutical Products and their Intermediates
15.00 Barry Hardy (Douglas Connect), Knowledge-Oriented Collaboration in Virtual Organisation Structures
15.30 Coffee Break
16.00 Knowledge Cafe on Perspectives
17.30 Group Discussion
18.30 Knowledge-sharing Dinner

A description of the abstracts for the session perspectives follows:

The Push and Pull of Knowledge Management in R&D 

http://innovationwell.net/COMTY_kmworkshopbm08

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

Computer-based Predictive Toxicology: Advances and Impact of Cheminformatics on the Safety-oriented Design of New Products

Current advances in computer-based predictive toxicology offer the potential to create more advanced environments for the screening and prediction of safety issues due to chemical and drug adverse side effects, drug-drug and chemical-system interactions, and chemical and drug toxicologies in the environment and the human body.  Advances in this growing field also offer the potential to replace or reduce the need for animal testing and to reduce later stage clinical trial failures or new product development rejection. Acceleration of progress in practical applications requires the creation of interoperable environments, knowledge sharing, data integration, algorithm development, and extensive validation and testing. 

Numerous opportunities exist in this field for scientific advances, but also for innovation, service and product development, and value creation. Additionally, significant collaboration approaches are a scientific, industry and society imperative to advance this field and the safety of new products and all society members.  Collaborative approaches need to support the multidisciplinary networking and collaboration between computer scientists, biologists, chemists, toxicologists, product development and clinical and environmental researchers, and to network groups, centers, initiatives, projects and data into interoperable semantic frameworks, systems, knowledge bases and virtual organisations.

At our Predictive Toxicology session chaired by Artem Cherkasov (University of British Columbia) running 17 October 2008 at Bryn Mawr recent developments in the field of predictive toxicology will be presented and discussed.

The session will be preceded the evening of October 16 by a Knowledge Café to discuss Collaboration Opportunities in Predictive ADME & Predictive Toxicology.

A description of the session with presentation abstracts follows.  Please add your comments, discussion or questions at the end of the post.

Predictive Toxicology

http://innovationwell.net/COMTY_confprogr08predtox

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

Predictive ADME: guiding the lead development and optimization process

The prediction of absorption, distribution, metabolism, and excretion (ADME) properties has become increasingly important as failures late in the drug discovery process become more costly. Increasingly, stringent in vitro and in vivo requirements have been placed on the hit-to-lead and lead optimization stages of the drug discovery process. Although it is tempting to dismiss ADME modeling and simply conduct an in vitro or in vivo experiment to get “the correct answer”, this approach is not practical. A skilled, competent medicinal chemist working on a lead optimization program can easily conceive of far more compounds than can reasonably be synthesized during the time of a lead optimization effort. In vivo studies are expensive and time-consuming and may become the rate-limiting step for some projects, particularly for small pharmaceutical companies. Rather than providing “the correct answer”, modeling provides a means of “stacking the deck” in favor of the medicinal chemistry effort, increasing the likelihood that a given compound will show the desired effect in vitro or in vivo.

At our Predictive ADME session chaired by Anthony Klon running October 16 at Bryn Mawr recent developments in the predictive modeling of ADME properties will be presented and discussed. Speakers will present their research into modeling microsomal stability, drug-drug interactions, and membrane transport processes such as blood-brain barrier penetration, intestinal absorption, and skin penetration. One topic of the accompanying discussions will be the appropriateness of relevant biological endpoints for ADME/PK modeling.

The session will be followed in the evening by a Knowledge Café to discuss Collaboration Opportunities in Predictive ADME & Predictive Toxicology.

A description of the session with presentation abstracts follows.  Please add your comments, discussion or questions at the end of the post.

Predictive ADME

http://innovationwell.net/COMTY_confprogr08adme

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

Computational Biology: Data Mining in Biomedical Research

Biomedical research, be it in the biopharmaceutical industry, academia or governmental laboratories, is becoming an information driven science. An enormous amount of data is either present in published literature and patents or being generated using high-throughput technologies (such as DNA sequencing, microarrays, genome-wide association, proteomics etc.). The resulting computational biology challenges currently involve the development of intelligent data mining methodologies for these high-dimensional data and the development of databases that facilitate the hosting and integration of these diverse data-sets. The computational advances being made in these areas are significantly impacting biomedical research ranging from fundamental biological findings that relate genes and environment to disease all the way to molecular biomarkers for drug efficacy or toxicity.

In our InnovationWell session chaired by Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.) taking place 14 October 2008 at Bryn Mawr, we have gathered a set of top researchers who have significant experience in the areas of data mining and integration. Presentation and discussion topics will include: molecular network reconstruction from genetically segregating populations (Paul McDonagh), the use of molecular networks for environmental risk assessment (Stephen Edwards), semantic web technologies for modeling biological pathways (Christopher Bouton), application of integrated genomics and genetics in pharmaceutical discovery (Debraj GuhaThakurta), and comparative genomics in drug discovery (James Brown).

A description of the session with presentation abstracts follows.  Please add your comments, discussion or questions at the end of the post.

Computational Biology

http://innovationwell.net/comty_confprogr08compbio

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

Knowledge Management in Translational Medicine

Healthcare is a highly complex, information-driven industry, and effective knowledge management is at the heart of the drug discovery and development process. Translational medicine is becoming increasingly important within the pharmaceutical industry where it is defined by a variety of initiatives designed to facilitate the transfer of knowledge from the bench to the bedside and back.

On the 15 October 2008 at the InnovationWell Community of Practice Meeting at Bryn Mawr College, Philadelphia, I will chair a day-long session where we have brought together a diverse set of speakers representing a broad spectrum of activities across the pharmaceutical workflow – from target identification to clinical trials. Each presentation will describe specific examples of advances in translational medicine brought about by practical approaches to improved knowledge management. Sometimes these advances will be technology-based, sometimes they will have resulted from innovative forms of collaboration and the use of Web 2.0 tools. Together we hope these speakers will stimulate discussion and the transfer of insights and ideas illustrating the potential of knowledge management tools and techniques to drive advances in translational medicine.

A description of the session with presentation abstracts follows:

Knowledge Management in Translational Medicine

http://innovationwell.net/COMTY_confprogr08kmtransmed

(Please follow continuation here to read abstracts.  Comments can be made at the end.)

Innovation in Life Science & Healthcare R&D

This year's InnovationWell Autumn Community of Practice Meeting will take place 14-17 October 2008 at Bryn Mawr College, Bryn Mawr, Philadelphia, USA to discuss the following areas of Innovation in Life Science & Healthcare R&D:

Critical Path Advances in Drug Development, Innovation & Knowledge Management in R&D and Translational Medicine, Computational Biology, Predictive ADME, Predictive Toxicology, Metabolomics, Biomarkers, Systems Biology

Program Summary
Systems Biology, chaired by Keith Elliston (Genstruct)
Computational Biology, chaired by Debraj Guhathakurta (Merck)
Knowledge Management in Translational Medicine, David Bousfield (Ganesha Associates)
Applications of Metabolomics to Drug Discovery & Development, chaired by Bruce Kristal (Brigham and Women's Hospital)
Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery)
Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia)

Pre-Conference Workshop, 13 October 2008
Knowledge Management in R&D
chaired by John Conway (Accelrys) and Frank Hollinger (FRESH Directions Consulting)

Speakers
Keith Elliston (Genstruct), Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.), Stephen W. Edwards (U.S. Environmental Protection Agency), Paul McDonagh (Gene Network Sciences), Christopher M.L.S. Bouton (Pfizer), James R. Brown (GlaxoSmithKline), John Wilbanks (Creative Commons), Barry Bunin (Collaborative Drug Discovery), Michael Liebman (Windber Research Institute), Jerry Wright (Johns Hopkins Medical Institutions), Anastasia Christianson (AstraZeneca), James Golden (Science Applications International Corporation), John Speakman (National Cancer Institute), William Hayes (Biogen Idec), Andrew McMurry (Harvard Medical School), Eugene Clark (Partners Healthcare), Alvin Berger (Metabolon), John Newman (USDA), Bruce Kristal (Brigham and Women's Hospital), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI), Alex Tropsha (UNC), Barry Hardy (Douglas Connect), Weida Tong (FDA)

CFP
We invite contributed papers from members of academic, government research and commercial organizations on areas of new research and innovation relevant to innovation and knowledge management in the life sciences. The work presented should involve innovative new method development or application in the areas of systems biology, translational medicine, knowledge management, computational biology, metabolomics, predictive ADME, predictive toxicology or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome.

Abstracts (300-500 words) should be submitted to innovationwell -[at]-douglasconnect.com by 31 July 2008, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 August 2008.

Bursary
Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants should be working in a relevant area of research related to life science, healthcare, and drug product discovery and development at the postdoctoral, graduate student and senior undergraduate levels.

To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations related to R&D (300-500 words) to innovationwell -[at]- douglasconnect.com by 31 July 2008. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of attendance at the meeting on their research and career progress. Authors will be notified of acceptance by 15 August 2008.

Poster Session
All InterAction Meeting registrants are eligible to present a Conference Poster. The Poster Sessions will take place in the evenings in Thomas Great Hall on campus, where refreshments and dinner are also served. Poster Abstracts (300-500 words) with Title, Institution, Authors and Contact Information should be submitted to barry.hardy -[at]-
douglasconnect.com Abstracts will be considered based on date of submission and quality, and will be reviewed and accepted as they are received. To be considered for the formal program, they should be submitted at the very latest by 31 August 2008.

Download Program Brochure as pdf:

Download InnovationWell-BM08-Final1.pdf

Contact:
Program: Dr. Barry Hardy, InnovationWell Community of Practice, Douglas Connect. Tel: +41 61 851 0170. barry.hardy -[at]- douglasconnect.com

Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. InnovationWell -[at]- douglasconnect.com or please visit:

http://InnovationWell-BM810.eventsbot.com

InnovationWell meeting Computational Biology Translational Medicine Systems Biology ADME Predictive ADME Predictive Toxicology Innovative Medicines Community of Practice workshop conference management executive Bryn Mawr Philadelphia Critical Path biomarkers metabolomics toxicology personalised medicine KM Life Sciences Pharma Drug Discovery Drug Safety Research and Development Drug Development Healthcare Innovation Knowledge Management events

SYNERGY Knowledge Assessment Launch

SYNERGY, a new 3 year European-funded Seventh Framework Research Project which commenced on the 1 February 2008, will research the knowledge sharing and collaboration support needs of stakeholders working collaboratively both internally within organisations, and within partnerships and new virtual network and business models. The project offers end user organisations an opportunity to participate in this leading edge research to address their unique requirements, to undergo a knowledge assessment of their collaboration needs, and the potential to pilot and test utility-based services developed during the project.

Swiss-based Douglas Connect will lead the SYNERGY workpackage on knowledge assessment, piloting and testing activities of application cases within industry and business contexts. To provide an opportunity for organisations to learn more about the initiative and the potential benefits of participation to them, Douglas Connect will hold a launch and networking event and Knowledge Café at the Radisson SAS Hotel in Basel, March 6 starting at 15.00. If interested in attending please contact Nicki Douglas of Douglas Connect, (Email: Nicki.Douglas –(at)- douglasconnect.com; Tel: +41 61 851 0461) to request a guest pass.

Following short presentations to inform, the event will feature peer-to-peer based Knowledge Café discussions on SYNERGY which will be facilitated by:

Prof. Keith Popplewell, Jaguar Cars Professor of Engineering Manufacture and Management, Coventry University, UK

Dr. Barry Hardy, Founder, InnovationWell & Knowledge Assessment Leader, Douglas Connect

Dr. Nenad Stojanovic, FZI Competence Center for Business Software, Forschungszentrum Informatik an der Universität Karlsruhe, Germany

Dr. Asha Nagesser, Managing Director, INSIDEAN GmbH

Richard Zbinden, CEO, Software for Corporate Leaders LLC

A more detailed agenda and project overview is provided in the continuation below.

Knowledge-oriented Collaboration: SYNERGY research project summary

SYNERGY, a new 3 year European-funded Seventh Framework Research Project commencing on the 1 February 2008, will research the knowledge sharing and collaboration support needs of stakeholders working collaboratively both internally within organisations, and within partnerships and new virtual network and business models. The project offers end user organisations an opportunity to participate in this leading edge research to address their unique requirements, to undergo a knowledge assessment of their collaboration needs, and the potential to pilot and test utility-based services developed during the project.  A summary of the project extracted from the formal technical proposal is provided below. (in continuation text)