The Ferryman

Collaborative Development of Predictive Toxicology Applications

I enclose here an abstract and copy of the presentation for the Plenary Lecture "Collaborative Development of Predictive Toxicology Applications" that I presented in Istanbul on 6 July 2009 at the Fifth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (CMTPI 2009).

Presentation

Download OpenTox-CMTPI 2009 Presentation 90706

Abstract

Collaborative Development of Predictive Toxicology Applications

Barry Hardy*^a, Christoph Helma^b, Nina Jeliazkova^c, Romualdo Benigni^d, Stefan Kramer^e, Andreas Karwath^f, Haralambos Sarimveis^g, David Gallagher^h, Vladimir Poroikovⁱ, Sunil Chawla^j, Sylvia Escher^k

This lecture will provide a perspective on the growing significance of community and collaboration approaches in predictive toxicology.  In part these challenges are technical and involve progressing issues related to cross-organisational, enterprise and application interoperability. Additional challenges include the development and application of best practices related to knowledge management, culture, organizational and industry development.

The EC-funded FP7 project “OpenTox” (www.opentox.org) is developing an Open Source-based predictive toxicology framework that provides a unified access to toxicological data and (Quantitative) Structure-Activity Relationship i.e., (Q)SAR models. OpenTox provides tools for the integration of data, for the generation and validation of (Q)SAR models for toxic effects, libraries for the development and integration of (Q)SAR algorithms, and scientifically sound validation routines. OpenTox will support the development of applications for non-computational specialists in addition to interfaces for risk assessors, toxicological experts and model and algorithm developers.

OpenTox is relevant for the implementation of REACH as it allows risk assessors to access experimental data, (Q)SAR models and toxicological information from a unified interface that adheres to European and international regulatory requirements including OECD Guidelines for validation and reporting.  The OpenTox framework is being populated initially with data and models for chronic, genotoxic and carcinogenic effects. These are the endpoints where computational methods promise the greatest potential reduction in animal testing required under REACH. Initial research has defined the essential components of the framework architecture, approach to data access, schema and management, use of controlled vocabularies and ontologies, web service and communications protocols, and selection and integration of algorithms for predictive modelling.  The initial results of this research and next steps will be discussed.

OpenTox has been initiated as a collaborative project involving a combination of 11 different enterprise, university and government research groups to design and build the initial framework.  Additionally numerous organizations with industry, regulatory or expert interests are being included from the start in providing guidance and direction.  The goal is to expand OpenTox as a community project enabling additional expert and user participants to be involved in developments in as timely a manner as possible. To this end, our agreed upon intention is to carry out developments in an open and transparent manner from the early days of the project, and to open up discussions and development to the global community at large, who may either participate in developments or provide user perspectives.  Cooperation on data standards, data integration, ontologies, integration of algorithm predictions from different methods, and testing and validation all have significant collaboration opportunities and benefits for the community.  Additionally, practices for building effective collaborations from the OpenTox community approach will be discussed.

About OpenTox

OpenTox - An Open Source Predictive Toxicology Framework, www.opentox.org, is funded under the EU Seventh Framework Program: HEALTH-2007-1.3-3 Promotion, development, validation, acceptance and implementation of QSARs (Quantitative Structure-Activity Relationships) for toxicology, Project Reference Number Health-F5-2008-200787 (2008-2011).

Project Partners

Douglas Connect^a, In Silico Toxicology^b, Ideaconsult^c, Istituto Superiore di Sanita'^d, Technical University of Munich^e, Albert Ludwigs University Freiburg^f, National Technical University of Athens^g, David Gallagher^h, Institute of Biomedical Chemistry of the Russian Academy of Medical Sciencesⁱ, Seascape Learning^j and the Fraunhofer Institute for Toxicology & Experimental Medicine^k

Advisory Board
European Centre for the Validation of Alternative Methods, European Chemicals Bureau, U.S Environmental Protection Agency, U.S. Food & Drug Administration, Nestle, Roche, AstraZeneca, LHASA, Leadscope, University of North Carolina, EC Environment Directorate General, Organisation for Economic Co-operation & Development, CADASTER and Bayer Healthcare

*Contact Address: Dr. Barry Hardy, OpenTox Project Coordinator and Director, Community of Practice & Research Activities, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland

 

Growing significance of communities and collaboration in discovery and development

Just saw an article I wrote for Future Science has come out as a Perspective:

Growing significance of communities and collaboration in discovery and development
Barry Hardy, Future Medicinal Chemistry, June 2009, Vol. 1, No. 3, Pages 435-449.
http://www.future-science.com/toc/fmc/1/3

Sorry, but I don't have the budget just right now to take the Open Access option, but there is some other open material available at the above link.

In summarising the drivers for the growing significance of communites and collaboration I introduced:

The benefits of community participation or collaboration should outweigh the costs to support a rational decision to pursue such routes.  Lions usually prefer to hunt as a group as the shared food from group kills offers a better return and lower risk than hunting alone; in a similar manner organisations may also choose to collaborate to have greater success in acquiring new resources or income. The current convergence of a number of factors appears to be driving up the R&D collaboration benefit/cost ratio. The drivers include:

1.      Scientific research is becoming more complex and multi-disciplinary, requiring researchers to move more away from “working in the expert’s box”.

2.      Our work, economy and society are becoming more knowledge-oriented. (I define knowledge here as including understanding gained from experience and involves individual and collective knowledge in addition to explicit knowledge such as intellectual property (IP).)

3.      Business models in the chemistry and pharmaceutical industry that worked fine historically, e.g., manufacturing products based predominantly on patents related to chemistry, appear to be increasingly lacking.

4.      The goals of translational and personalized medicine have stronger requirements for networked and collaborative approaches over discipline and time than the historically relatively linear drug discovery and development process.  Integrated services offer greater future value creation than stand-alone products.

5.      Patient Safety has become an issue of growing concern requiring new more integrative approaches to data, knowledge and disciplines.

6.      Computational Science continues to grow in importance, fueling overlaps and interactions between scientific disciplines including that of computer science.

7.      The maturing of the Internet-based World Wide Web including enhanced usability, services, social software and the semantic web, provide new community and collaboration resource opportunities.

8.      Challenging problems we face as a race such as global warming, energy management, population growth, and sustainable development are often linked to healthcare issues and are demonstrating the need and benefit for greater cooperation and at larger scales.

9.      Continuing education and learning throughout life has been growing in importance as knowledge workers go through greater numbers of career and job changes than in the industrial age.

10.  Work can increasingly be done anywhere on the planet where the best combination of costs and skills are available.  As Thomas Friedman discussed in his recent book, the “world is now flat” (1). A work objective can be broken into a workflow of numerous tasks, each of which may be done in different locations or by different organizations or individuals.

And I will add three more uncertain or controversial factors here:

11.  There is a growing importance of small and medium size enterprises (SMEs) collaborating in knowledge-oriented activity and growth in the global economy.

12.  As our modern life seems increasingly less rewarding beneath the surface, we need, search for and find new happiness from the benefits of taking advantage of new collaboration opportunities through interacting with others more.  In addition to needing better conversations for learning, work and self-development, we also simply need them psychologically and to feel good.  (Happier workers are also more productive ones.)

13.  Enabling international cooperation, collaboration and knowledge transfer in socio-economic areas such as healthcare, including building shared cultural meaning between different countries, races and cultures will significantly progress the security and prosperity of the world we leave to our children, whereas other current flawed political, military and unsustainable economic strategies will not.

Welcome your feedback and additions...

The Ferryman

(1) Friedman TL, “The World is Flat”, Picador, (2005).

Dear Michael, Thanks, Respects and Inspiration to you (Michael Jackson)

Thanks Michael for all those great music videos in the 80's.  You were a leader, an innovator, doing completely new and great things back then.  You entertained us when we took a break from our studies in college in the early 80s, and tried out this new MTV experience at the time.  (It was much more interesting back then!)  You were a Thriller!

Respects to you Michael, we played and danced to your songs last night, and were not alone.

Inspiration Michael, if we can take inspiration from your tragedy and Childhood legacy you could not shake off, it is that we should take some more time to reach out to our family, friends and contacts.  Even if it is that business partner, don't just always email them, get on the Skype with them, talk and get some understanding, build some shared meaning, reach out and support. As you said:

You are not alone, I am here with you
Though you're far away, I am here to stay
You are not alone, I am here with you
Though we're far apart, You're always in my heart

And if you want to collaborate folks in this flatter world don't be alone and far away. Reach out!

The Ferryman

Collaboration Support and Context: future directions shown by Google Wave and Colayer

It has become apparent from experiences in recent years that successful knowledge management strategies need to address the issue of successfully connecting people to people.  To accomplish effective knowledge work, workers have to increasingly collaborate and this collaboration may increasingly span different organisational entities, time and space in a flatter world.  Collaboration systems have been developed for years and the explosion of Web 2.0 solutions and services has provided many additional approaches for connecting people though blogs, wikis, social networking sites etc.  Yet when I look at my current interactions, projects and collaborations what do I see: many people still often prefer to send that email with an attachment, and I am not unguilty myself in this email culture.  As a project coordinator I can then be left with the job of having the additional task of getting the message or document on that wiki that we are using to support the collaboration, but which many seem to find difficult to incorporate into their way of working.  One could take a draconian approach with project rules, but that often may not be feasible or successful. 

Also as we sign up for more social networking sites, collaboration spaces, wikis etc., we have an accompanying increase of emails with links, alerts, updates, news summaries etc.  So our email noise and traffic has been increasing.  This has led me to a survival strategy of restricting my social network signups or ignoring many such Web 2.0 generated emails.  But one still has to keep an eye on the important messages one should not miss.  The end result is often one of increased administration rather than that of enhanced people-to-people connections, co-working, better knowledge management and effective collaboration.

So I found it interesting recently to see that an extensive conversation had started on Colayer which has been supporting our eCheminfo and InnovationWell community activity about the new Google Wave announcement at their recent developer conference.  So I went to see it myself on You Tube at http://www.youtube.com/watch?v=v_UyVmITiYQ  As both an indicator of what we could be using soon for collaboration, an exciting Open Source initiative and perhaps the most high impact development in the IT industry this year, it is really worth taking a look. Plus they organised a very good demo - they kept my interest and attention for 80 minutes!  A lot of the concepts are what attracted me to Colayer when we were initiating our community activity end of 2003.  Perhaps the time has finally come that we will have a new wave of innovative collaboration support solutions accompanied by user adoption and we could possibly overcome the poor existing email work practices and email overload.

Maintaining the context of our conversations is what is a key principle here, and the Google Wave demonstration shows the integration of many activities which are often fragmented across a variety of tools and locations into the one context.  So I can email, message, edit documents, add images, conduct searches, carry out surveys, track issues all in this one context and can export in real time the integrated knowledge products to other contexts, e.g.  as I am typing  a message or adding an image it can be simultaneously updated on an external third party blog, and other collaborators can even join me in real time for that work.

Since moving to Switzerland in 2001 I have had numerous conversations over the years with Colayer founder Markus Hegi who has been promoting and developing such concepts with his Colayer approach and his declaration that “email be dead soon”.  However, although I have always been able to communicate with him and his coworkers at Colayer without using email, I have not found email dying with many of my other situations and work contacts and like many have an increasingly severe email overload problem!

There are two Colayer concepts I would like to mention here which I think are particularly powerful  for collaboration support.  One concept is that of what Colayer calls the “Times Page”.  On Colayer all conversations and contexts take place in different communications areas called “comties”, each which can have a different topic context e.g., for a project or interest or discussion topic.  When you visit Colayer you can take a “Times page” view of all new messages and content that have been added since your last visit.  You can also control what you want displayed and prioritized on your Times page.  So it is like obtaining a morning newspaper view of communication activity ordered by context.  This contrasts greatly the unstructured dump of a couple of hundred messages into my inbox, which filters do not seem to have helped very much either.  This is an example view of what such a Times Page view looks like:

Now if we could get a critical mass of people collaborating through such a Colayer and Times Page view or through a Google Wave, would that not be a significant step forward?  Disregarding here all the technical issues on approaches to applications, the concept seems extremely sound from the knowledge management point of view.  We just need significant adoption from users to take off and perhaps that is now finally coming!

A second Colayer concept I would like to mention here is that of the shuttle or idea weaver shuttle.  The shuttle takes you to any location of conversation or content where you can subsequently add your content, conversation or images in a collaborative context.  Again we are freed from the isolation, torture and desolation of our fragmented  email box to interact in a much more collaborative place, to weave our ideas with those of others, and to experiencing that place of knowledge co-creation with our collaborators.   Here is an example of what such a virtual conversation accompanied by shuttle navigation looks like:

Working this way is however new to many people who have become used to spending most of their day immersed in a desktop application or email box. We must unlearn our immersion in these isolated environments and learn to spend more time in our collaboration work spaces.  Sometimes we may also need to disconnect from the noise of the collaboration space, to focus on our individual knowledge work, but that should not be the paradigm for all work, especially as we have increasing collaborative activity. We also need to continue to blend the right balance of our face-to-face and virtual activity.  It is still very hard to beat the conversation of a small group discussing a topic around a table.

In an essay on a “New Renaissance Period in Science” 15 years ago when I was in a relatively colourful and idealistic mindset at Oxford I wrote:

The hype of the information age is transforming itself into the reality for the computer user. It is becoming increasingly common for a researcher to have the ability to convert a structure from a remote database into manipulatable graphical images on a screen. Computer simulation, information technology and electronic publishing technology will converge into an era of interactive communication of a type never before possible. Authors will become publishers, readers will readily be able to swop roles with authors by interactively viewing data from a research paper and starting their own simulated experiment, to ask "what if?" questions about changes in experimental conditions or model parameters, to add their contribution to the growing "live" paper, to forward their own interpretation.

and

The best technology of the future will increasingly involve an understanding of the human condition. Its explanation and presentation may intertwine with the arts for poetic interpretation and communication like never before. We will be pilgrims of knowledge freed from the chains of rigid discipline, we must leave the command science approach behind to pursue more flexible and dynamic structures, to explore avenues that transcend old boundaries. We will solve new problems in new ways and do so with passion and conviction. In a New Renaissance period we will view a rich colorful world through our kaleidoscopes.

and we have had such developments happen but only in part 15 years later.  As an older and less idealistic writer I will rephrase the last quote into a more realistic expectation for coming years:

The best collaboration technology of the future will increasingly involve an understanding of the human condition. Interaction and knowledge exchange between people will intertwine with communications like never before. We will be pilgrims of knowledge freed from the chains of email boxes, we must leave the "send email" approach behind to pursue more flexible and dynamic structures, to explore avenues that transcend these old boundaries. We will solve new problems in new ways and shared contexts and do so with passion and conviction. In a New Renaissance period of the Knowledge Web we will view a rich colourful world through our kaleidoscopes.

Perhaps then my virtual co-working will become more like sharing that conversation with you on the river ferry in Basel and we will be happier co-creating the shared answers to our questions.

Barry aka The Ferryman

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.]

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, Collaboration & Leadership

We are holding a Knowledge Cafe and networking event at the Merian Hotel, Basel, Switzerland 17.00-20.00, Wednesday 23 April 2008, on the topic of Knowledge & Collaboration.

We will additionally extend the use of supporting the face-to-face cafe conversations with the virtual collaboration tool of a wiki as I used at the Autumn 2007 InnovationWell meeting at Bryn Mawr. (more information on that in a later post)

The Café discussions will be peer-to-peer based and will be co-moderated by:

Beat Knechtli, Director and CKO, PricewaterhouseCoopers
Pavel Kraus, President, Swiss Knowledge Management Forum and Senior Partner, aht'intermediation
Douglas Weidner, President, International Knowledge Management Institute
Barry Hardy, Founder and Director, InnovationWell & Douglas Connect
Chris Pallaris, ISN Chief Editor, Swiss Federal Institute of Technology (ETH Zurich)
Hannes Gassert, CTO, Liip
Nicolette Liller, Microsoft
Asha Nagesser, Managing Director, INSIDEAN
Marco Bettoni, Director of Research & Consulting, Swiss Distance University of Applied Sciences (FFHS)
Richard Zbinden, CEO, Software for Corporate Leaders

The following Guest Seminar will be presented:
17.00 Process-Oriented Knowledge Management
Michael Wyrsch, Vice-President & Leader of the Knowledge Management Competence Center Switzerland, Credit-Suisse

During the Café starting at 18.00, table discussions will include the following Knowledge & Collaboration sub-topics:

Knowledge Sharing, Innovation Networks, Leadership Support, Organisational Complexity & Context, Productivity & Teams, Group Decision-Making, Collaboration Patterns & Roles, Social Networks and Web 2.0, Culture & International Collaboration, and Cooperative Sustainable Development.

The Cafe is free to attend. Light refreshments will be provided. If interested in attending please contact Nicki Douglas (Tel: +41 61 851 0461. Email: Nicki.Douglas –(at)- douglasconnect.com) to reserve a guest place.

The event is co-organised by Douglas Connect, the International Knowledge Management Institute, the Swiss Knowledge Management Forum (SKMF), and the Gurteen Knowledge Community.

Knowledge & Leadership
In 2007 the Basel Knowledge Café focused on *Knowledge & Leadership* whose results formed the basis for an article series being published in KM Review:

B. Hardy; Linking Trust, Change, Leadership & Innovation – Ingredients of a Knowledge Leadership Support Framework; KM Review, Nov/Dec 2007, Vol 10, Issue 5, pp 18-23.

B. Hardy; Collaboration, Culture, and Technology – Contributions to Confidence in Leadership Support; KM Review, Jan/Feb 2008, Vol 10, Issue 6, pp 18-23.

A short summary with photos is posted on the The Ferryman Blog at http://barryhardy.blogs.com/theferryman/2007/06/knowledge_and_l.html

The Café also contributed significantly to the formation of the KLeaders practice and interest group, which has since been working together on developing the ideas of the KLeaders Leadership Practice and Support Framework, and which is currently collaborating on research and network proposals. If you are interested in this research and innovation activity, please contact Dr. Barry Hardy (barry.hardy –(at)- douglasconnect.com, +41 61 851 0170) to discuss your needs or contributions.

Knowledge Collaboration Leadership Knowledge Cafe Douglas Connect KM Institute KM Institute Switzerland meeting workshop training management executive CKM KM Knowledge Management Knowledge Management Training Management Training Basel Innovation Switzerland events

The Science of Knowledge Management?

Is knowledge management a science? How should we define it? These questions may look simple but are not so easy to answer for both individuals and the collective.  How can we apply the scientific method in a constructive way to knowledge management activities such as successfully managing communities of practice, transforming community of practice activity to community of innovation activity, or building next generation IT systems for the more successful support of knowledge management activities such as organisational culture transformation, innovation, change management, collaboration, sustainable trust between stakeholders, and leadership transparency? (as discussed in our Knowledge Cafe last week in Basel (agenda)

(If interested in this topic and wishing to add to the discussion, please follow the links and read on!)

InnovationWell Interest List and Signup

You can join our InnovationWell interest list (managed by Constant Contact) to be kept posted on news related to our community of practice activities using the following signup form:

Join Our Mailing List

Email:

Barry Hardy

InnovationWell Community of Practice

Program for InnovationWell & eCheminfo InterAction Meetings

I summarise below the list of sessions with over 100 top speakers and discussion leaders for the program listing for the upcoming Autumn InterAction Meetings taking place in Philadelphia and Basel. Please add a traceback or link for other like-minded folk to find!

I also provide an electronic brochure for download here for the InnovationWell Autumn Program on Knowledge-based Innovation in Life Science Product Development:

Download InnovationWell-ProgramAutumn05.PDF

And the equivalent eCheminfo brochure on Drug Discovery:

Download eCheminfo-ProgramAutumn05.pdf

Note: The poster sessions will be run as electronic poster sessions using tabletop spaces, a wireless network and Internet facilities at the meetings, in addition to virtual access through the website, i.e., the posters will be electronic but the access can be face-to-face or virtual. You can participate in person and virtually in the poster sessions.  We can supply nourishment and refreshments locally; remote participants may have to order out! [We also expect, subject to on-site testing, to have live conference call capabilities for remote participating members to join local discussions.]  Anyone interested in presenting such an "electronic poster" should directly contact us via email at innovationwell at douglasconnect.com

Look forward to seeing you in Philadelphia or Basel!

Barry Hardy
Community of Practice Manager
Douglas Connect
http://douglasconnect.com/
+41 61 851 0170 (office)

InnovationWell & eCheminfo InterAction Meetings
Philadelphia, US, 11-12 October 2005 and Basel, Switzerland, 9-10 November
List of Sessions with Speakers & Schedule (InterAction Autumn Meetings)
http://innovationwell.net/ and http://echeminfo.com/

Registration to attend the meetings or to access virtually is available through the websites or through contacting Nicki Douglas [nicki.douglas at douglasconnect.com]

InnovationWell eCheminfo meeting workshop conference management executive drug safety KM Life Sciences Pharma Drug Discovery Drug Development Healthcare Innovation Informatics Knowledge Management events

…PROGRAM LISTING CONTINUING IN FULL POSTING…..