The Ferryman

OpenTox workshop at SETAC Africa, Buea

The #OpenTox workshop at the SETAC Africa conference in Buea today will feature hands on use of ToxPredict, ToxCreate and Bioclipse.

Also, for the first time we will run the OpenTox software and infrastructure using a local virtual appliance installation.

Participants can copy all the setup and Open Source software onto their machines and we can work on getting it running!

The Knowledge Ferry - an Open Knowledge Community

Consider joining our Open Knowledge Community if you are interested in sharing experiences on knowledge - how to accelerate its flow, nourish greater sharing, somehow imperfectly "manage" it.  Join us for an interesting ride on the new Knowledge Ferry at: 

http://knowledgeferry.ning.com/

The Ferryman

Continuous rain will gradually break the hard stones

Continuous rain will gradually break the hard stones in the river bed so that the knowledge flow may accelerate and the ferry we are on together may reach its destination of wisdom. 

Collaborative Ontology Development for Predictive Toxicology

We have established two resource initiatives for the scientific community to collaborate on the creation, integration and use of common terminologies, vocabularies and ontologies for application in predictive toxicology (including reuse of existing medical, biological and chemical ontologies):

OpenTox Collaborative Ontology Development (based on Collaborative Protege):

http://www.opentox.org/dev/ontology/collaborative_protege

OpenToxipedia (based on Semantic Media Wiki)

http://www.opentoxipedia.org/index.php/Main_Page

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 Workshop in Potsdam to discuss collaborative approach to linking resources to improve human safety

On Sunday May 30 we host an OpenTox Workshop near Berlin in Potsdam that will bring many leading international research program directors and leaders together to discuss how collaboration and the increased linking of resources over the World Wide Web could progress human safety research and safety assessment.  By linking resources and data increasingly powerful computer-based models can be built for predicting and avoiding unwanted adverse toxic side effects of drugs, chemicals, ingredients in soaps and cosmetics, pesticides etc. thus enhancing human safety and protecting the environment better.  Such methods should also eventually lead to the replacement of many animal experiments.

More details on program can be located at:

http://www.opentox.org/data/blogentries/public/opentoxworkshoppotsdam2010

Developing new Predictive Toxicology Strategies

I have now posted the detailed program for the eCheminfo predictive toxicology and ADME workshop which take place in Oxford 2 - 6 August 2010 at
http://barryhardy.blogs.com/theferryman/2010/05/predictive-toxicology-echeminfo-2010-oxford-workshop-program.html

and you can also download a copy of the program from here as a pdf:

Download ECheminfoPredictiveToxBrochure-OX810-web1

During the workshop we will apply a variety of design, informatics and modelling methods to predictive toxicology problems guided by workshop leaders with expertise in the approaches used. A case study approach will additionally be followed so that groups can work together throughout the week on their case study problems. The case studies will also be developed virtually before the workshop week with support extended afterwards for further work including experimental testing of interesting results and hypotheses developed. The virtual aspects of the case study work will additionally be supported by the Synergy and OpenTox infrastructures and related Collaboration Pool and pilot collaboration study.

Case studies will focus on the development of innovative integrated testing strategies applied to the problem of predicting the toxicity of a molecule.  Such strategies are becoming an increasingly important part of drug design strategies so as to remove toxic liabilities as early as possible in the design processs. REACH legislation is also requiring organisations in coming years to carry out a more extensive safety testing of all chemical ingredients in a variety of products ranging from consumer products to food to agrochemicals. Related to this activity is the relatively unsatisfactory use of animal experiments to predict human toxicity, which are not only complex and expensive, but also often do not predict human effects well, if at all. 
Hence new approaches combining computational modelling, in vitro assays, systems biology, stem cell technology etc. are required.

We will apply techniques to the study of existing knowledge (e.g., from adverse events, biological literature, pathway models etc.) to help support mechanism-based hypotheses and strategies. Modelling techniques based on data-mining, database searching, and read-across will be applied to chemical categories. Integrated QSAR-based models supported by the new OpenTox infrastructure will be used to build properly validated models including estimation of applicability domain. We will also research ADME and kinetics properties of structures as relevant to their toxicity profiles. We will attempt to predict primary metabolities based on P450 metabolism simulation and model the potential toxicities of metabolites. Population-varied physiologically-based ADME Simulations will be carried out for in vitro-in vivo extrapolation, exposure estimation and to study the variation across individuals and populations.  We will also apply workflow techniques to the combination of methods and Bayesian networks to the evolution of weight of evidence based consensus predictions.

The most promising strategies and predictions developed will be used to design experimental human toxicity-oriented in vitro assays which will be run after the workshop as part of the virtual case study extension work.  Both computational and experimental work will be documented according to industry best practices in a collaborative electronic laboratory notebook.  We will attempt to develop new combined in silico - in vitro strategies superior to existing approaches which should help advance the field and industry testing and regulatory needs.

Through the time spent working and discussing together combined with the availability of a variety of leading software and expert support from workshop leaders, workshop participants should take home ideas and learning to help accelerate their own projects related to safety design and risk assessment. The location and atmosphere in Oxford is also an ideal background for networking, getting to know your peers and joining the ongoing eCheminfo community of practice activities. As is often common with eCheminfo gatherings the workshop usually attracts a variety of backgrounds including industry, academia and government research instititutes and from many different countries. We also welcome the participation of non-modelling specialists from different areas of chemistry, biology and toxicology to participate and bring an interdisciplinary interaction to the collaborative group work.

I hope you can join us!
Barry

Neglected diseases, HIV, and development work on the ground in communities

Neglected diseases such as parasitic infections reek havoc on many communities in different parts of the world.  As part of our committment to responsible, sustainable development and a community culture, we will make neglected disease problems, where we evaluate we can make a significant difference, a goal of our collaborative virtual organisations in years to come.  Please contact me to discuss your ideas and also consider joining the new Collaboration Pools summarised at bottom of this post.  We can also work together on new funding opportunities.

However and also, my experiences in Africa, for example on our conservation trip to the remote Caprivi Delta region of Namibia:
http://barryhardy.blogs.com/theferryman/2009/02/experiences-from-expedition-work-in-the-caprivi-delta.html
(please keep in mind this post was based on a summary for my younger son for awareness!), was that "small contributions" can make a big difference.  One story from that trip was the inability of a local clinic to deal with the torn foot of one of our party, and we ended up stitching him up with a veterinary kit back at base camp. Once that was done, how would he get around we asked, as there were no crutches to be had locally?!  Discussing the incident around the camp fire afterwards, we came up with the simple solution of each throwing some money into a "needles and crutches" hat, and that was able to buy needles and crutches for the local clinic to keep them going for a couple of years, and it could be directly organised.  So in this reality-focused context something like $200 made a bigger difference on the real problem for the future than a (possibly failed) major $100m program.  A bit of a stretched analogy, but you probably get the point.

We intend to continue our support of sustainable development work in the community in Caprivi in community-involved wild life conservation development, and look forward to our next trip, and others in the community who might be interested.  Let me know, if this might be for you too.

Here I would like to draw attention to a new local initiative in the area to help support the families affected by a widespread HIV infection epidemic.  There is need for education, healthcare, and support of the many orphans left behind by parents who simply die from untreated HIV infection.  Consider what you might do by volunteering some simple help and support to the work out there.  The new center is called TAG Volunteers (TAG for think-act-grow):
 
http://www.tagvolunteer.com/
 
I vouch this is a real legitimate project as Ronel, the woman setting it up, was also very much involved in competently running the important activities at our base camp on our last visit, such as getting something to eat when we got back very tired and hungry from our trips into the bush!

Welcome your feedback.  If you do decide to take some time out to volunteering in some way, I suspect you will find it rewarding.  And it is also at the same time such a special and beautiful country to experience!

Barry

Collaboration Pools:

OpenTox - predictive toxicology
https://www.surveymonkey.com/s/M7TFM6C

eCheminfo - drug discovery
https://www.surveymonkey.com/s/V6T2YSD
 
InnovationWell - life science innovation and knowledge management
https://www.surveymonkey.com/s/782L9DZ

InnovationWell Collaboration Pool Formation

We are establishing an InnovationWell Collaboration Pool of individuals and organisations who have an interest in collaborating together in areas of healthcare and life science innovation. For example, a selection of Pool members could participate in a collaborative life science, systems biology or predictive toxicology project, develop a funding proposal or response to a call opportunity together, or develop an innovation or best practice.

To join the InnovationWell Collaboration Pool please complete the short form located at https://www.surveymonkey.com/s/782L9DZ

Collaborations will take a virtual organisation approach, i.e., partners can bring contributing knowledge, computational or experimental capabilities to a partnership for the duration of a project or other endeavour.

We will run two such virtual organisation (VO) projects for the first time this year starting later this Spring:
A) Drug Design project which 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 to apply a combination of in silico and in vitro approaches to predict in vivo toxicity including exposure.

Both VOs will be supported by a variety of leading modelling and design software, informatics infrastructure, and collaborative content management and electronic lab notebook systems.

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.

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/)

We will also consider incorporation of Case Studies into the eCheminfo Drug Discovery and Predictive ADME/Tox workshops to be held in Oxford this summer. See http://echeminfo.com/

Barry Hardy PhD
InnovationWell 

Douglas Connect
Switzerland

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