Cheminfostream

eCheminfo Drug Design workshop, bursary

We are returning to Oxford for another hands-on eCheminfo drug design workshop week this summer running from 29 July - 2 August 2013.

The deadline for bursary applications is 19 April. Please see http://www.echeminfo.com/?q=drugdiscovery2013 for more details and application form. We have tried to keep the application process simple.

We will link the case study work closely this year with the anti-malarial kinase drug design activity we initiated with SAM (http://www.scientistsagainstmalaria.net/).

We published a short article last month in Drug Discovery Today on our approach to collaboration and knowledge infrastructure (http://www.sciencedirect.com/science/article/pii/S1359644613000391).

In the Oxford workshop this year we plan to look at additional new kinase targets and to put a process in place to experimentally test most promising predictions.

Please contact me to discuss your interest in this program or related disocvery initiatives:

Barry Hardy, PhD,

Director, Research and Practice

Douglas Connect GmbH, Baermeggenweg 14, 4314 Zeiningen, Switzerland

Em: Barry Hardy -(at)-! douglasconnect.com

Tel: +41 61 851 0170

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

OpenTox 2011 Poster Session in Predictive Toxicology

You can preview the abstracts of the posters to be presented at the #OpenTox 2011 Poster Session in Predictive Toxicology in Munich on the 11th August at:

http://www.opentox.org/meet/opentox2011/poster-session

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.

OpenTox Tutorials, Validation Report Generation, Demonstration Server, Evaluation and Improved APIS and Interfaces

I have made the following OpenTox reports available for download from the OpenTox Reading Room (http://www.opentox.org/home/documents):

OpenTox Tutorials
http://www.opentox.org/data/documents/development/opentoxreports/opentoxreportd62

Automated Validation Report Generation
http://www.opentox.org/data/documents/development/opentoxreports/opentoxreportd52

Prototype Demonstration Server
http://www.opentox.org/data/documents/development/opentoxreports/opentoxreportd23

Prototype Evaluation, Improved API and Interface Designs
http://www.opentox.org/data/documents/development/opentoxreports/opentoxreportd13

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 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.

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
www.opentox.org/home/documents/presentations/rhodesworkshoppressept2010/view

We also ran a Knowledge Fair at the workshop with a number of interactive hands-on activities:
www.opentox.org/data/blogentries/public/opentoxworkshoprhodes2010

We should be making related virtual versions on guidance and exercises available through the OpenTox website in coming weeks.