Cheminfostream

The Ferryman and Spela

Barry is now a lucky, happy and just married man to Spela

http://barryhardy.blogs.com/theferryman/2012/11/a-shared-moment-of-great-happiness.html

Innovation in Predictive Toxicology

The preliminary program with schedule for the #OpenTox InterAction Meeting in Munich in August has been loaded at:
Innovation in Predictive Toxicology
9-12 August, Munich, Germany
http://www.opentox.org/meet/opentox2011/opentox2011

Abstracts for the poster session and awards are still being accepted through June at:
https://www.easychair.org/conferences/?conf=opentox2011

There is no registration fee to attend the conference but places are limited to 100 attendees.
Please complete the registration application form while still available at:
https://www.surveymonkey.com/s/opentox2011

Innovation in Predictive Toxicology

We are holding an OpenTox InterAction Meeting, in Munich, Germany (10-12 August 2011 on Innovation in Predictive Toxicology.

Further information including a preliminary list of speakers and topics, and links to abstract submission and registration forms is located at:
http://www.opentox.org/meet/opentox2011

Abstract submissions should be completed by 30 April for consideration for the conference program and bursary awards. Poster abstracts will continue to be accepted through 30 June, to be eligible for meeting-based review and innovation merit awards.

Registration should be completed using the form located at
https://www.surveymonkey.com/s/opentox2011

Registration involves no fee, but please note that places are limited to 100 participants, and we will have to close registration once our confirmed invitation and acceptance list is full.

A pre-conference OpenTox workshop on new developments in methods, REACH-relevant models and applications will be held 9 August.

AXLR8 2010 report on Alternative Testing Strategies

The AXLR8 2010 report on Alternative Testing Strategies is now available at:
http://axlr8.eu/axlr8-2010-progress-report.pdf

This book provides a very useful reference and comprehensive summary of all recent/current significant Alternative Testing R&D FP6/7 projects in Europe, plus additional perspectives on other initiatives e.g., in US, Japan etc. It includes a chapter on #OpenTox.

Barry

Barry Hardy PhD
Director, Community of Practice & Research Activities
and OpenTox Project Coordinator (www.opentox.org)

Collaborative Development and Use of Predictive Toxicology Applications

I have made a copy of the slides used in the OpenTox presentation on 19 September at the EuroQSAR meeting in Rhodes available at:

Development and Use of Predictive Toxicology Applications
Barry Hardy, Christoph Helma, Nina Jeliazkova, Olga Tcheremenskaia, Stefan Kramer, Haralambos Sarimveis and Andreas Karwath
http://www.opentox.org/home/documents/presentations/rhodesworkshoppressept2010/view

We then spent the afternoon overcoming various challenges in working groups!

 

Afterwards we had some chance for reflection on the water as we sailed down the coast.

Collaborative development of predictive toxicology applications

The following initial paper on OpenTox has now been published and is available in preliminary form:

Collaborative development of predictive toxicology applications
Barry Hardy, Nicki Douglas, Christoph Helma, Micha Rautenberg, Nina Jeliazkova, Vedrin Jeliazkov, Ivelina Nikolova, Romualdo Benigni, Olga Tcheremenskaia, Stefan Kramer, Tobias Girschick, Fabian Buchwald, Joerg Wicker, Andreas Karwath, Martin Gutlein, Andreas Maunz, Haralambos Sarimveis, Georgia Melagraki, Antreas Afantitis, Pantelis Sopasakis, David Gallagher, Vladimir Poroikov, Dmitry Filimonov, Alexey Zakharov, Alexey Lagunin, Tatyana Gloriozova, Sergey Novikov, Natalia Skvortsova, Dmitry Druzhilovsky, Sunil Chawla, Indira Ghosh, Surajit Ray, Hitesh Patel and Sylvia Escher
Journal of Cheminformatics 2010, 2:7 (31 August 2010)
http://www.jcheminf.com/content/2/1/7

Please feel free to circulate in the community and to your contacts who might be interested. Thanks!

And a special thanks to all who have contributed to advancing this work, including our advisors, and growing community of friends, interactions and partners!

Barry

OpenTox Links - Creating a Linked Data and Resource Infrastructure for Predictive Toxicology and Safety Assessment

We have had a lot of activity in recent months on the OpenTox project with regards to developing a linked data and resource infrastructure for the support of interdisciplinary predictive toxicology research and safety assessment.  I enclose several links below including our recent overview workshop presentation in Potsdam, reports, demonstrations, technical links and interest groups.  A paper will be published as an Open Access publication in coming weeks (reference below).

 

We welcome your joining this community and movement to work towards the common goal of safer products and a safer environment, supported by new alternative and advanced methods.

 

Barry 

 

Predictive Toxicology Workshop in Oxford (2-6 August 2010)
Strategies: http://barryhardy.blogs.com/theferryman/2010/05/developing-new-predictive-toxicology-strategies.html

Program (pdf): http://barryhardy.blogs.com/files/echeminfopredictivetoxbrochure-ox810-web1.pdf

Program (eCheminfo website): http://echeminfo.com/COMTY_oxfordadmet10

Registration: http://echem2010-admet.eventsbot.com/

 

OpenTox Links

 

Your Resources
If you have a useful resource you would like to see integrated into OpenTox, e.g., a database from your project to which an OpenTox web service could be added, please contact me to discuss.

 

OpenTox Workshop in Potsdam, 30 May 2010
Program:
http://www.opentox.org/data/blogentries/public/opentoxworkshoppotsdam2010

OpenTox Presentation:
http://www.opentox.org/home/documents/presentations/opentoxpresPotsdam30May2010/view 

 

OpenTox Reports
http://www.opentox.org/home/documents/Reports

 

OpenTox Demos
(Please keep in mind these are early prototype applications and may not have features you want.  We welcome requests from you for what you additionally need in these applications or others.)
http://www.opentox.org/toxicity-prediction

 

OpenTox Signup & Mailing List
Complete the form at http://www.opentox.org/join_form

Note: If you have a general interest and want to receive a monthly news update e.g., on new applications, data resources, ontology developments, news etc., select the "I'm interested in OpenTox news"

option.  We also welcome including news from other projects in the newsletter.  Do not select the option "I'm interested in OpenTox Technical Development" unless you are doing technical computing work

in the field as this list is quite technical and busy!

 

OpenTox Collaboration Pool
If you are interested in joining virtual organisation collaborations in predictive toxicology supported by OpenTox, complete the form linked from:
http://www.opentox.org/data/blogentries/public/opentoxcollaborationpool

 

Technical Development Details including API
http://www.opentox.org/dev

http://www.opentox.org/dev/apis

 

Publication Reference
Collaborative Development of Predictive Toxicology Applications, B. Hardy, N. Douglas, C. Helma, M. Rautenberg, N. Jeliazkova, V. Jeliazkov, I. Nikolova, R. Benigni, O. Tcheremenskaia, S. Kramer, T. Girschick, F. Buchwald, J. Wicker, A. Karwath, M. Gütlein, A. Maunz, H. Sarimveis, G. Melagraki, A. Afantitis, P. Sopasakis, D. Gallagher, V. Poroikov, D. Filimonov, A. Zakharov, A. Lagunin, T. Gloriozova, S. Novikov, N. Skvortsova, D. Druzhilovsky , S. Chawla, I. Ghosh, S. Ray, H. Patel, S. Escher, accepted 3 June 2010 for Open Access publication in J. Chemical Informatics http://www.jcheminf.com/ (2010).

 

Satisfying REACH Requirements in Predictive Toxicology

The OpenTox workshop on "Satisfying REACH Requirements in Predictive Toxicology" to be held at the ISS in Rome 10-11 September 2009. 

Participants at the workshop will involve cross-industry users and regulatory experts in addition to solution developers and providers who will discuss the requirements and use cases of users in chemical toxicology evaluation and risk assessment, and including satisfaction of current and future requirements of the REACH legislation using alternative testing methods. The workshop format involves short presentations to provide user, regulatory and solution needs perspectives, followed by knowledge cafe discussions discussing use cases, challenges, issues, solutions, collaboration opportunities and ways forward in small groups.

PROGRAM

Thursday 10 September

08.30 Welcome Coffee

09.00 Introduction & Workshop Overview, Barry Hardy (OpenTox and Douglas Connect, Switzerland)

09.15 The Use of Computational Methods for the in silico  Prediction of Chemical Properties in REACH, Andrew P Worth (Systems Toxicology Unit, Institute for Health and Consumer Protection, European Commission -Joint Research Centre, Italy)

09.40 Automated Workflows for Hazard Assessment, Elena Fioravanzo (S-IN Soluzioni Informatiche, Italy)

10.05 OpenTox Predictive Toxicology Use Cases, Barry Hardy (OpenTox and Douglas Connect, Switzerland)

10.30 Coffee Break

11.00 Knowledge Café Discussions

12.30 Group Discussion

13.00 Lunch

14.00 Opportunities for using  Systems Biology Data for in silico  Modeling of Personalized Medicine, Richard D. Beger  (Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, USA)

14.25 A Framework for Using Structural, Reactivity, Metabolic and Physicochemical Similarity to Evaluate the Suitability of Analogs for SAR-based Toxicological Assessments, Joanna Jaworska (Procter & Gamble, Modeling & Simulation, Biological Systems, Brussels Innovation Center, Belgium)

 14.50 Integration of Integrated Assessment Tools for Environmental Risk Assessment, Willie Peijnenburg (National Institute for Public Health and the Environment, The Netherlands)

15.15 Prediction of Animal Toxicity Endpoints for ToxCAST Phase I Compounds using a Combination of Chemical and Biological in vitro Descriptors, Alex Tropsha (Carolina Center for Computational Toxicology and Carolina Environmental Bioinformatics Research Center, University of North Carolina at Chapel Hill, USA)

15.40 Coffee Break

16.00 Knowledge Café Discussions

17.30 Group Discussion

18.00 Close

 

Friday 11 September

08.30 Welcome Coffee

09.00 Predictive Toxicology for Cosmetics - An Industry Perspective, Stephanie Ringeissen (Safety Research Department, L’Oréal R&D, France)

09.25 OECD (Q)SAR Application Toolbox: Progress and Ongoing Developments, (OECD, Paris, France)

09.50 Italian Specialty Chemical Industry Perspective on Predictive Toxicology, Maurizio Colombo (Health & Safety Evaluation, Industrial Regulation Management, Lamberti S.p.A., Italy)

10.15 Coffee Break

10.45 Knowledge Café Discussions

12.00 Group Discussion

12.30 Lunch

13.30 The Italian Chemical Industry and the REACH impact on SMEs, Antonio Conto (Chemsafe Srl, Italy)

13.55 Classification- and Regression-Based QSAR of Chemical Toxicity on the Basis of Structural and Physicochemical Similarity, Oleg Raevsky (Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds of Russian Academy of Sciences, Moscow, Russia)

14.20 Analysis of Toxcast Data and in vitro / in vivo Endpoint Relationships, Romualdo Benigni (Istituto Superiore di Sanità, Italy)

14.45 Coffee Break

15.15 Knowledge Café Discussions

16.30 Group Discussion

17.00 Close

More Information including Abstracts:

http://www.opentox.org/data/blogentries/public/opentoxworkshoprome09

eCheminfo Virtual Community Activities in Cheminformatics

When I started the eCheminfo community of practice in late 2003 we focused initially on using the approach of virtual conferencing and communications to get the community started.  More recently I have given more attention to developing face-to-face conference and workshop activity and initiating collaborative research. While on this journey it has been personally rewarding to have met and made contact with hundreds of scientists in the international community and to additionally be involved in supporting their networking, career development and research in drug design, discovery and modelling. It has also been rewarding to have just met so many great people and to have had the chance to interact with them, be it on a computer, in a workshop exercise, or on a punt trying to get down the river as we usually do when we are in Oxford.  So far we seem to be better on computer-based physics than boat physics!

And so I have come full circle and can see the need to prioritise the virtual community aspects of eCheminfo further again, to support the continuation of all these worthwhile interactions in the community.  So LinkedIn is one place to start.  I have been on there for some years and we have had a group area, but have not really done much with it.  It has primarily been useful for some introductions between people.  However recent feature additions for discussion, posting of news, job announcements etc. have been added, so it seems worthwhile to try using it more for supporting continuing interactions in the community.  So I am initiating today invitations to the eCheminfo community to join us there for discussion, news and networking on what is happening in the world of drug discovery informatics, cheminformatics, bioinformatics, etc.  Use of the group is intended for scientific and professional exchange purposes only.  As included in our mission we encourage cross-disciplinary cross-sector participation so from medicinal chemists in the pharmaceutical industry through toxicologists in government institutes through PhD students working on their modelling research problems are welcome!

To request joining the eCheminfo LinkedIn group please follow the following link and introduce yourself with a group joining request:

https://www.linkedin.com/e/gis/1173/77EB680070FF/

I also really welcome suggestions from the community there on what you would like to see as further developments in coming years!

Barry

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.]

Chemogenomics eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop training Oxford Critical Path toxicology Bursary Life Sciences Pharma Drug Discovery Research and Development Drug Development Healthcare Innovation Knowledge Management events