Cheminfostream

Presentations in Boston on OpenTox, eCheminfo, ToxBank, eNanoMapper

I look forward to the interactions in Boston in coming days dedicated to innovation and particularly to our honouring JC Bradley and open science (which drives and accelerates our progress)!

http://barryhardy.blogs.com/theferryman/2015/08/innovation-from-discovery-to-application.html

eCheminfo Drug Design Meeting, Johns Hopkins, 9 - 11 Feb 2015

Join us at Johns Hopkins 9 -11 February 2015 to discuss anti malarial kinase inhibitor design, ADME and toxicity modelling, macromolecular target structure analysis and applying new quantum mechanics methods to drug design.

More information at

http://www.echeminfo.com/events/drug-discovery-usa-2015

and

http://www.scientistsagainstmalaria.net/

Goodbye Patrik, we will miss you.

Patrik Rydberg

1976-02-26 – 2013-11-29

I heard the sad news of your sudden death today Patrik. We will miss your science, your fun and your company. We will remember the good times. Below we are setting out on what became a tradition at eCheminfo summer workshops in Oxford: the start of the week evening punting trip, this one in 2009.

Your RIP Notice:
http://www.familjesidan.se/details/381613

 

 

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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

Interoperable Approach to Collaborative Drug Design and Predictive Toxicology

I gave a talk at at the IQPC Predictive Toxicology Conference in London, UK on 24 February. In this presentation I discuss the critical role of interoperability in collaboration situations in drug design and predictive toxicology. I reflect on the inspiration of the Tamboti Tree Use Case from our recent conservation work trip to South Africa. The role of intereroperability and ontology development in the OpenTox predictive toxicology framework is discussed.  The evolution of development and prototyping within OpenTox has demonstrated its potential as a Semantic Web for Predictive Toxicology, alternative testing methods and risk assessment. Several recent OpenTox interoperations have been achieved including with Bioclipse, CDK, ToxCast, and Leadscope. OpenTox will provide a valuable open standards based foundation on which to create services and link resources for the new ToxBank infrastructure project.

I provide an overview of the approach used in the FP7 Synergy project where we have established a Scientists Against Malaria virtual organisation which is carrying out a number of modelling and experimental drug design activities against a kinase target in Plasmodium, the parasite that causes malaria. We use an ontological approach to interoperate between a collaborative electronic notebook, Synergy collaboration services and event-driven recommendation rules for consensus formation and traffic light discussion and decision making on conflicting predictions or experimental results.

The presentation is available from:

http://www.opentox.org/home/documents/presentations/hardyiqpcpresentationfeb2011/view

Advancing Collaborative Drug Discovery & Safety Infrastructure

I will deliver an OpenTox seminar at the IQPC (Pharma IQ)  Predictive Toxicology conference taking place in London 23-24 Feb 2011, in which I will present on recent developments with regards to OpenTox interoperability advances, and particularly to support of collaborative drug discovery projects.  Also of interest to the increasing support by OpenTox of in vitro methods is a significant program on stem cell technology.  The conference will address the accuracy of drug safety testing through the integration of advanced prediction methods, including stem cell based assays and screening into safety evaluation strategies. The main conference will take place in London on 23rd-24th February 2011 and new for this year, there will be a pre-conference focus day on 22nd February 2011 dedicated to the use of stem cells as a tool to enhance predictive toxicology.
http://www.predictivetoxicology.co.uk/Event.aspx?id=394530

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

ICT Support Role in Collaborative Drug Design and Predictive ADME/Tox projects

During April - October 2010 we will be running two pilots which will create two virtual organisations (VOs) of research partners who will collaborate on a drug discovery and a predictive toxicology project.

We are currently seeking Expressions of Interest in the ICT support role for the pilots which should be submitted by 17.00 CET, 19 February 2010 through the following form:
https://www.surveymonkey.com/s/QSHKDCH 

The VOs will be created from partners from Douglas Connect Collaboration Pools, who will bring contributing knowledge, computational or experimental capabilities to the partnership for the duration of the projects:

a) Drug Design project will examine the application of a variety of leading modelling and design approaches to novel target kinases, to experimentally test predictions, and to initiate a best practices virtual screening resource.

b) Predictive Toxicology project will apply a combination of in silico and in vitro approaches to predict in vivo toxicity including exposure.

The ICT support role will support the informatics requirements of the researchers in organising, processing and sharing data, and in collaborative analysis and decision making.

The VOs will be supported by knowledge-oriented collaboration services developed under the FP7 Synergy research project, including a reactive complex event driven engine, collaboration moderator, collaboration pattern services and partner knowledge base.
Summary on Synergy project: http://barryhardy.blogs.com/theferryman/2008/02/knowledge-orien.html 

The Predictive Toxicology VO will be supported by distributed REST-driven web services for data management, model building, validation and reporting, developed under the OpenTox Framework (http://www.opentox.org/)

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

Tel: +41 61 851 0170
Email: barry.hardy -(at)- douglasconnect.com

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

eCheminfo Autumn Community of Practice meeting 2007

The eCheminfo Autumn Community of Practice meeting will take place the week of October 15 at Bryn Mawr College, Philadelphia to discuss latest research applications, methods and best practices in drug discovery informatics, design and modelling.

The following conference sessions will be held:
16 October: Virtual Screening, chaired by Christopher Austin (NIH) and Ajay Jain (UCSF)
16 October: Structural Biology, chaired by Max Cummings (Tibotec Pharmaceuticals)
17 October: Structure-based Drug Design, chaired by Jose Duca (Schering-Plough)
17 October: Fragment-based Drug Discovery, chaired by Maria Kontoyianni (Crystax Pharmaceuticals)
18-19 October: Predictive ADME/Toxicology, chaired by Tony Hopfinger (University of New Mexico College of Pharmacy)

Additional workshop activity on virtual screening best practices, knowledge management in R&D and advances in predictive ADME and toxicology will also be held.

Conference speakers include:
Stephen Burley (SGX Pharmaceuticals), Georgia McGaughey (Merck), Charles Lesburg (Schering-Plough), Rick Beger (FDA), Marc Nicklaus (NIH), Woody Sherman (Schrodinger), Daniel Cheney (Bristol Myers Squibb), Paul Labute (Chemical Computing Group), Ajay Jain (UCSF), Alan Cheng (Amgen), Tony Hopfinger (University of New Mexico), Anthony Klon (Pharmacopeia Drug Discovery), Artem Cherkasov (University of British Columbia), Dennis Pelletier (Pfizer), Chaohong Sun (Abbott), Xavier Barril (University of Barcelona), Jose Duca (Schering-Plough), Terry Stouch (JCAMD), Natasja Brooijmans (Wyeth), Gerard Kleywegt (University of Uppsala), Vladimir Poroikov (Russian Academy of Sciences), Christoph Helma (in silico toxicology), Ann Richard (EPA), Judy Madden (Liverpool John Moores University), Julian Tirado-Rives (Yale), Heather Carlson (University of Michigan), Joseph Tomaszewski (NCI), Joseph Contrera (FDA), Christopher Austin (NIH), Jerome Hert (UCSF), Renate Sekul (Graffinity), Gunther Stahl (Tripos), John W Liebeschuetz (CCDC), Wilfried Langenaeker (Silicos), Zsolt Zsoldos (SimBioSys), Paul Hawkins (OpenEye Scientific Software), François Delfaud (MEDIT), Anatoly Ruvinsky (University of Kansas), Robin Taylor (CCDC), Eric Jamois (Strand Life Sciences), David Gilmour (Tacit), Alex Heiphetz (Delta L Training), Frank Guerino (TraverseIT), Salvatore Alesci (Wyeth), Darius Dziuda (CCSU), Laszlo Boros (Sidmap) Fred Cohen (Fast Track Systems), Alex Tropsha (UNC), Dimitris Agrafiotis, (Johnson & Johnson), Carl Elkin (Schering-Plough)

Poster Session
We will be running poster sessions in the evenings at the meeting with themes: knowledge management (Tuesday), drug design (Wednesday) and drug development and ADMET (Thursday). This option is available to all meeting attendees. Please send your abstract and biography of ca. 300-500 words each to eCheminfo -(at)- douglasconnect.com for approval.

Program Brochure:

Download eChemProgramBrynMawr07-web2.PDF

More information at http://echeminfo.com/COMTY_conferences

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