October 06, 2008

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.)

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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.]

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August 27, 2008

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

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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.)

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June 13, 2008

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:

September 21, 2007

Productivity Gains enabled by ICT and KM Support Systems

Knowledge Management (KM) has from the start been a major theme of our InnovationWell community activities.  Knowledge Management in R&D was the topic of our very first InnovationWell conference held at the end of 2003, progressed in 2004 by the theme of Integrating Knowledge in the Life Science Product Life Cycle, to Drug Safety Knowledge Management and Knowledge-based Innovation in 2005, and to Critical Path and Translational Medicine applications in 2006.  More recently we have addressed additional critical knowledge management support areas of culture, collaboration, leadership, trust, innovation etc.  In these meeting sessions I have enjoyed both excellent dialogues and meeting many interesting, competent, thoughtful and inspiring people.  As we now move into becoming a community of research in addition to a community of practice, these conversations are having a significant influence on the research proposals and projects we are pursuing, and I am very much looking forward to the launch of our initial related collaborative research projects starting in 2008.

It is interesting to note from the Economist survey “Foresight 2020: Examining the Economic, Industry, and Corporate Trends of the Future” that healthcare industry executives singled out knowledge management as the highest priority area for productivity gains in the next 15 years.  Such recognition is also reflected in the key role knowledge management plays in the Critical Path Initiative and that it is one of the key 4 pillars of the Innovative Medicines Initiative launching in 2008.

Next month at Bryn Mawr (15-16 October) we return to the topic of KM in R&D by taking a look at existing ICT solutions supporting R&D activities including the increasing deployment of Collaborative electronic Research & Development (CeR&D) and Electronic Laboratory Notebook (ELN) systems.  We will additionally explore the emerging roles and impact of approaches emerging from semantic web research, social software, web services and utility computing and Web 2.0/3.0 that are complimentary with structured IT systems to enable increased productivity and innovation success within the context of the ever increasing importance of collaboration within and between organisations working in increasingly networked global research initiatives and projects.  Cross-disciplinary thinking from fields such as organisational development and culture, cognitive science and innovation management will I maintain play key influencing roles on future integrating architectures supporting knowledge management, transfer and sharing to enable the hoped-for productivity gains of executives.

The workshop at Bryn Mawr will have a strong emphasis on peer-to-peer discussions with each workshop session involving a facilitated Knowledge Café discussion. On Monday evening we will have a Knowledge Dinner with good food and conversation menus at the Alumni House, whereas on Tuesday evening we will have a poster session, drinks reception and buffet dinner in Thomas Great Hall.

For Poster Presentations, you can present as a traditional poster or setup a computer-based presentation of software for discussion.  Wireless and Internet connectivity are available. Abstracts ca. 300-500 words should be sent to me.

We will discuss and share experiences with current information and communications technology (ICT) supporting R&D, to discuss current requirements and short term needs with electronic laboratory notebook (ELN) systems, collaboration support and knowledge tools supporting R&D, and to create a shared vision and roadmap for next generation knowledge management (KM) support systems. A wiki will be opened prior to the workshop to commence group documentation of supporting materials and to help to populate the workshop program with introductory materials, suggestions, ideas and experiences.  The wiki will continue to be available after the workshop for supporting continuing interactions in 2008.

Presentations to seed Discussions
Dimitris K. Agrafiotis, Vice President of Informatics, Johnson & Johnson Pharmaceutical Research & Development, LLC; The ABCD ELN: Towards a Fully Integrated Discovery Enterprise
Frank Guerino, CEO, TraverseIT; Semantic-based Frameworks for Enterprise Content Management
Carl Elkin, Principal Scientist, Schering-Plough; Building Knowledge Infrastructure: A Bottom-up Wiki in a Large Company
David Gilmour, CEO, Tacit; Peer-to-Peer Knowledge Sharing - Implications for Enterprise Knowledge Management
Alex Heiphetz, CEO, Delta L Training; Training Simulations and Metrics in Second Life
Marisol Wesson, CEO, TMS; Enterprise Knowledge Portals and Application Integration for supporting Collaboration
Richard Lysakowski, President, CENSA; Collaborative eR&D - Vision and Strategy to Product Realities
Jeff Spitzner, CSO, Rescentris; Research Knowledge Management for the Post-ELN Era: Envisioning a Multi-Scale 'Scientist's Desktop' with Unified Information Services, Management and Collaboration
Gladys Range, Consulting Engineer; GVR Systems Automation, Semantic Knowledge Infrastructures and Services for R&D

Program Brochure: http://barryhardy.blogs.com/theferryman/files/KMWorkshopBrynMawr07web2.PDF

More Information at: http://www.innovationwell.net/COMTY_kmworkshopbrynmawr07

June 12, 2007

Advancing best practices in predictive ADME and Toxicology

On the 17-19 October 2007 we will host a joint eCheminfo and InnovationWell Community of Practice Workshop and Forum at Bryn Mawr College, Philadelphia to discuss and advance best practices in predictive ADME and Toxicology, to develop best practices for comparison studies and validation, to review latest developments in method development and applications related to drug discovery and development, and to discuss the potential for collaborations between initiatives and international cooperation.

This conference, forum and workshop activity will consist of the following parts:

1. Workshops to discuss developments, challenges and  potential for collaborations. (afternoons of October 17-19).

2. Conference sessions on latest ADMET methods and application developments with presentations and panel discussions. (mornings of October 18 and 19)

3. Hands-on Workshop sessions with drug discovery informatics software (running during afternoons throughout week)

4. Evening Poster Sessions on latest modelling developments (evenings of October 17 and 18)

Workshop Facilitators
Joseph Tomaszewski (NCI), Artem Cherkasov (University of British Columbia), Dennis Pelletier (Pfizer), Richard Beger (FDA), Anthony Klon (Pharmacopeia Drug Discovery), Tony Hopfinger (University of New Mexico College of Pharmacy), Joseph Contrera (FDA), Christoph Helma (University of Freiburg and in silico toxicology), Vladimir Poroikov (Russian Academy of Sciences), Judith Madden (Liverpool John Moores University), Ann Richard (EPA)

(continued ...)

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March 28, 2007

International Cooperation in Predictive Toxicology

A variety of initiatives of relevance to the development of ADME/Toxicology resources of value to supporting improved productivity in drug discovery and development are in progress in different organisations and countries.  There is potential for great benefits for collaboration and alignment between such initiatives so as to support the robust development of the emerging field of predictive toxicology and to advance goals related to heathcare safety and development as expressed in the FDA's Critical Path Initiative in the USA and the EU's Innovative Medicines Initiative in Europe.

To further development and progress in this area we are scheduling the following activity:

International Forum & Workshop on Cooperation on ADME/Tox
18-19 October 2007
to take place at the Community of Practice Meeting, Autumn 2007
a joint InnovationWell and eCheminfo InterAction Meeting
Bryn Mawr College, Philadelphia
http://www.echeminfo.com/COMTY_conferences

This forum and workshop will have an agenda developed by workshop leaders to address ways forward for international cooperation and including discussion of the following topics:

  • latest advances in QSAR and ADME/Tox methodologies and resources
  • impact of government and regulatory policy and legislation in the US and Europe
  • potential and barriers for replacing animal testing by alternative approaches
  • actions for data integration and knowledge sharing between initiatives
  • the role of semantic web approaches in uniting structured data from multiple resources
  • the role of natural language processing for processing unstructured information
  • extraction of data from the scientific literature
  • methods and procedures for secure testing of commercial data that could be acceptable to industry
  • application of advanced search and agent technologies
  • frameworks for computational model testing and validation
  • impact of knowledge management approaches
  • collaboration and community support structures and environments

The agenda of the forum and workshop will be designed by a set of workshop leaders so as to maximise interaction, discussion, issue resolution, and action plans for cooperation.  In addition to presentations on latest developments, workshop activities will address specific challenges to progress in the field and areas where collaboration can support integration and alignment of programs and resources and reduction of duplication.  An Innovation Cafe format will be used in which the group will define a scenario in which optimum confidence in predictive toxicology methods has been reached and will then prioritize steps for achieving that goal.  The resulting roadmap should provide action plans where cooperation between initiatives can accelerate the contribution of predictive toxicology methods to enhanced confidence in safety of new healthcare products and progressing the goal of reduction and replacement of animal testing by computational methods.  Virtual communication and collaboration approaches will be used pre- and post-event to maximise the benefit of the workshop.

Workshop leaders are being invited from the US and Europe and will include representatives from industry, government and academia.

Barry Hardy

Community of Practice Manager

October 26, 2006

InnovationWell Membership & Workshop Activity for 2007

During November I will be planning the program for the following InnovationWell workshop in Oxford (cross-industry sector) and InterAction Meeting in Bryn Mawr (life science/pharma/healthcare sector). Please contact me with your interests and proposals!

Knowledge Assessment & Performance Improvement of Collaborative Work and Innovation Activities

InnovationWell Workshop & Innovation Café, accompanied by pre-meeting
2 day hands-on workshop activities on collaborative systems and ELNs
20-22 June 2007, Oxford University, Oxford UK

Innovation in Life Science & Healthcare Research & Product Development
InnovationWell Community of Practice InterAction Meeting
15-18 October 2007, Bryn Mawr College, Philadelphia, PA, USA
Themes: FDA Critical Path Themes, Knowledge Management, Translational Research, Biomedical Informatics, Metabolomics, Biomarkers, Toxicology, Patient & Drug Safety

InnovationWell Gold membership
This entitles members to access InnovationWell meeting proceedings including audio, access to our Executive Insights reports from meeting and community of practice activities, and additional member discounts on meeting and training registration fees.

Download InnovationWell2007MembershipForm.pdf

Barry Hardy

Email: barry.hardy *[at]* douglasconnect.com

October 10, 2006

Metabolomics and its role in progressing Drug Development and Safety on FDA's Critical Path

Metabolomics is an FDA-identified Critical Path Opportunity (1) offering a toolkit which can be potentially applied to identification of safety biomarkers, diagnostic monitoring of patient response to drug treatment, lead optimization through toxicity assessment in non-clinical drug development, biochemical pathway studies in cells, animals and humans, patient stratification, and insights on and tracking of mechanisms associated with the onset of disease or following therapeutic intervention.

However, despite its above promise, the challenges in the complexity of the biological systems studies, the experimental spectroscopy methods used and the datasets generated has restricted to this point the full commercial application of metabolomics methods in the pharmaceutical industry and in healthcare. 

The complexity of the interpretation of metabolomics data points to the need for improved data analytics and visualisation methods in decision making processes and situations (2).  The importance of the value-added of the integration of metabolomics data with other proteomic and genomic data to provide a more integrated, accurate and broader view of the state of the biological system studied points to the importance of explicit knowledge management techniques in critical path areas of clinical research and drug development (3) to the application of semantic web, ontology and web service approaches (4) and to the adoption of these approaches in the day-to-day scientific research activity as supported by electronic laboratory notebooks and collaboration systems (5).  It also points again to the importance of co-operation on the always difficult agreement area of the definition of standards and data integration.

I also find it quite interesting that two different fields (knowledge management and metabolomics) share a common critical concept: that of context. Context is critical in the human area of knowledge management and transfer in social ecosystems and its poor treatment a reason why many early IT and informatics approaches to knowledge management worked poorly.  In the biological situation of a cell or animal, metabolomics provides the critical biochemical context and data to match it, and can do so in a dynamic way over time and can track perturbations in the behaviour of such a complex system.

Recent progress in the metabolomics field includes new advances in spectroscopic and statistical and analytical techniques that strengthen and expand the accuracy and scope of the analysis possible.  But the progress also increasingly includes significant application experience which already has included a significant role in the 2005 Nobel Prize in Medicine award for assigning the causative role of H. pylori bacterium in peptic ulcers and gastritis, and more recently has been applied to patient stratification in Lou Gehrig’s disease, identification of off-targeted side effects for several drugs and new chemical entities, has been applied in diagnostic roles on serum samples of diabetics and non-diabetics, the development of biomarkers for prediction of drug-induced liver injury and to insight into toxic effects from urine analysis.

Richard Beger (FDA) has pointed out (6,7) that the development of NMR- based multi-dimensional quantitative spectrometric data-activity relationships (QSDAR) provides models which could be useful for estimating chemical toxicity, risk assessment of environmental contaminants and drug-lead identifications, and that such models of biological activity should be more objective and overcome some of the unreliabilities of traditional Quantitative Structure-Activity Relationship (QSAR) approaches (8).  He also indicates that Metabolomics can play an important role in the creation of better evaluation tools and models for diseases, better identification and quantification of safety biomarkers, and improving the measurement of patient response. The voluntary submission of genomics data (VGDS) to the FDA is now accepting both proteomics and metabolomics data sets (9).

In response to such demand and interest, and in addition to significant activity in academic research, a number of companies including Metabolon, Leco, Blue Gnome, Bio-Rad and Chenomx are increasingly offering commercial solutions and services in metabolomics to industry.

I provide below a description of the presentation, discussion and workshop activity for the InnovationWell Session on Application of Metabolomics to Drug Discovery & Development which will take place on Wednesday 18th October ’06 at the InnovationWell meeting at Bryn Mawr. (Follow the Continuation…)

Barry Hardy

References
1. FDA Critical Path Opportunities Report, http://www.fda.gov/oc/initiatives/criticalpath
2. Decision Support in Drug Discovery & Development, http://barryhardy.blogs.com/theferryman/2006/09/decision_suppor.html
3. Knowledge Management in Translational Research, http://barryhardy.blogs.com/theferryman/2006/09/utilising_knowl.html
4. Semantic Web & Drug Development, http://www.innovationwell.net/COMTY_semweb/
5. KM in R&D and ELNs, http://www.innovationwell.net/COMTY_conferenceopenevent/
6. Richard D. Beger, Drug Discovery Today, Vol. 11, pp 429-435, May (2006).
7. R. D. Beger, D. A. Buzata, J.G. Wilkes, Drug Discovery Handbook, Ed. Shayne C. Gad, John Wiley & Sons, pp 227-285  (2005)
8. Predictive Toxicology, http://barryhardy.blogs.com/cheminfostream/2006/09/appyling_predic.html
9. FDA’s Critical Path Initiative: Opportunities for Metabolomics http://www.innovationwell.net/COMTY_mebegerr/

(continued…)

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Communities of Practice