The Ferryman

New OpenTox Exercises

Try out some new #OpenTox predictive toxicology exercises!

Based on our recent OpenTox 2011 workshop activities, we have set
up several demonstration applications and exercises at the following
address:
http://www.opentox.org/meet/opentox2011/exercises

I hope you can try an exercise there of interest to you!

You can provide feedback via the evaluation form at:
https://www.surveymonkey.com/s/652XY7C

Please feel free to contact me your questions and suggestions!

OpenTox 1.0 - what we have reached on its third birthday

 


On the eve of its 3rd birthday, I told the story so far of our development of OpenTox in Slovenia last week.

The lecture (slides and video) recorded at the Josef Stefan institute in Ljubljana on "OpenTox - the creation of a semantic web for toxicology" is available at:
http://videolectures.net/solomon_hardy_semantic/

I look forward to that future "Sixth Sense" journey interoperating with OpenTox to revisit the Tamboti Trees in South Africa and the Mopane Trees in Namibia, and to test the delivery of safety advice from the distributed semantic knowledge of OpenTox 3.0 use cases in the field :)!

Innovation Questions for the field of Predictive Toxicology

What are key innovation questions for the field of predictive toxicology? I propose we discuss the following questions at our Knowledge Cafe at the #OpenTox 2011 meeting in Munich. We can use the discussions as a basis to formulate an innovation white paper to provide direction to innovators who can accelerate developments in the field with strategy and technology development.

A. Mechanistic Strategies - What are the key innovations needed to accelerate progress?

B. Predictive Metabolism - What is needed for a complete and reliable prediction of metabolites?

C. Computational Chemistry - Emerging challenges and opportunities in receptor-mediated predictive toxicology

D. Systems Biology - How can we bridge the divide between modelling molecular pathways and quantitative prediction at the organelle level?

E. Integrated Analysis - Experimental designs for optimising biomarker discovery

F. Kinetics - Extrapolating in vitro data to model human hazard and exposure

G. Weight of Evidence - Developing holistic approaches to compound profiling and prioritisation-based decision making

H. Read Across and Categories - What are the key components for a more rigorous approach to a best practice?

I. Regulatory Needs - How do we accelerate the acceptance of emerging scientific methods in regulatory applications?

J. High Content Assays - What information can they provide today and what are the key gaps requiring new innovation?



OpenTox Services and Applications

I have posted a presentation summarising recent developments in #OpenTox services and applications, as reported at the AXLR8 meeting in Berlin at:

http://www.opentox.org/data/documents/development/presentations/opentoxpresAXLR82011/view

Developments include:

- OpenTox data infrastructure based on Ambit containing quality labelled data for over 185, 000 chemicals

- Development of OpenTox ontology including ToxML conversion

- Deployment of Authorisation & Authentication (A&A) services

- Extension of ToxPredict to 23 endpoints (as of May 2011) with A&A deployed

- Extension of ToxCreate to include confidences and ToxPredict integration with A&A deployed

- Development of Validation & Reporting services (including QMRF and QPRF)

- QPRF reporting with Q-edit

- Read Across (alpha prototype)

- CheS-Mapper for chemical dataset visualisation

- Descriptor calculations with ToxDesc, IBMC Desc and MaxTox

- Bioclipse-OpenTox interoperation

- Deployment in Scientists Against Malaria drug discovery collaboration

- Development and testing of Taverna workflows across OpenTox resources

Greetings from OpenTox class in Buea, Cameroon

#OpenTox A la Koh! Njuah! Aleh Aleh! Greetings from the #SETAC #Africa workshop group here to the #OpenTox community. We find the tools interesting and would like more workshop activity and tutorials in the future. We are interested in applying tools to assessing the quality of our water, pollution from pesticides, effects of petroleum products on our communities. We are interested in assessing toxicity data, predicting acute toxic effects, evaluating longer term effects on human health such as development and reproductive toxicity, and applying ecotoxicity models for environmental risk assessment of our ecosystems.

OpenTox workshop, SETAC Africa - day 1

We managed to get quite a bit of software installed at the #OpenTox workshop at SETAC, Africa on Tuesday on about 25 laptops or so belonging to the group. But we still have to get a couple of final machines to setup.

As now we can work on some problems, we decided at day's end we could continue the workshop again today, although that was not originally planned, but why not. Perhaps we can run all week, until we all get tired out :)!

Our main challenge and delay with the Virtual Appliance installation was the final installation patch Roman and Nina discovered was needed over the weekend, as this was required to fix the removal of ontology service files from the temp directory upon a virtual machine restart. At least we can fix that bug in a nicer way for next time.

However yesterday, the final installation step required going onto the net for every machine in turn, which took most of the afternoon! We did not have any internet for several hours, but we finally were able to send a group member Anyi with cash down to a provider office to charge an account she had, which we were able to use in the afternoon (Thanks Anyi for saving the day!). It was not so reliable or fast a connection but we eventually got through on it, but only one machine could be on at a time.

It will be helpful if we can figure out the shared file folders facility between the Virtual Appliance for linux and Windows - but did not have time to do that yet.

Also, we installed and ran Bioclipse live over the one internet connection at the end of the afternoon and had it go out and fetch OpenTox resource and model information, and live for an example. We did it (just about)! I pointed out the new login profile setup Egon has just recently setup, and perhaps we can get that done for the group today.

Philip Judson also joined us and we were able to get Derek and Meteor setup on machines too. Based on his experience, he gave a nice overview on some factors we have to reflect on in using such in silico programs and methods!

Eventually the bus came and took us home - tired but at least installed :)! We will try to continue today!!

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!

Innovation in Predictive Toxicology (#OpenTox Munich meeting program)

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

Using Induced Pluripotent Stem Cells to Identify New Treatments for ALS

Adult skin cells can be manipulated to generate induced pluripotent stem cells (iPSCs) to produce motor neurons and astrocytes, cells at risk in ALS.  This link below includes an informative webinar on a new research project being carried out by iPerian to use iPSCs to develop cell lines which could be used for new drug candidate screening.

http://www.alsa.org/news/archive/stem-cells-derived-from-skin.html

The ALS Association has awarded a one-year grant to iPierian to support the identification of a “cellular phenotype,” which represents differences in motor neurons or astroglial cells derived from ALS patients, versus healthy controls.  This phenotype would be the basis for drug screening to identify potential disease-modifying drug candidates for ALS.

OpenTox presentation at ACS 2011 Spring meeting

A recording of the OpenTox presentation on OpenTox as an Open Source platform and semantic web for toxicity prediction, delivered by David Gallagher and Sunil Chawla at the ACS Spring 2011 meeting, is available at the following link: 

http://www.softconference.com/ACSchem/sessionDetail.asp?SID=250349