Cheminfostream

ToxBank builds on and extends OpenTox framework

On the Ferryman the approach and experience on the building of a data and analysis architecture based on Open Standards is discussed.

http://barryhardy.blogs.com/theferryman/2013/10/building-a-data-and-analysis-architecture-based-on-open-standards.html

OpenTox USA 2013 speaker program

The OpenTox USA 2013 speaker program is available.

http://barryhardy.blogs.com/theferryman/2013/09/opentox-usa-2013-program-and-goals.html

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

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).

 

Integrated Predictive Toxicology Application Development

I have posted a copy of the slides I used at the recent EBI-EMBL industry forum on toxicoinformatics:
Integrated Predictive Toxicology Application Development
http://www.opentox.org/home/documents/presentations/integtoxdev/view
which summarises our philosophy, approaches and current status on OpenTox.

For those of you in the community interested in closer involvement with OpenTox development and application use cases, joining related new initiatives and proposals, discussing our collaborating more closely with your own project, taking a leadership role etc., please feel free to contact me with your interests and motivations, and we could for example have a chat via Skype, get introduced and discuss your needs or ideas.

Barry

Contact Barry Hardy in his role as OpenTox Coordinator
at Barry.Hardy !-(at)-* douglasconnect.com

Visit and register to the OpenTox community at
www.opentox.org

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