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!

Womenware

I have been fortunate to have had numerous interesting and engaging conversations with Dana Winner during our recent work together in the Middle East. I anticipate an interesting and stimulating read in her new book just out called "Womenware". See http://www.amazon.com/Hardware-Software-Womenware-ebook/dp/B005NW1WVG/ref=sr_1_1?s=digital-text&ie=UTF8&qid=1316365083&sr=1-1 for details on the Kindle version. I have just been able to download a version to a reader on my laptop. Now I just need some more reflective space and reading time!

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?



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 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!

Knowledge Management Training Week 2011, Lucerne, Switzerland

We will hold our Knowledge Management Training Week this year in Switzerland in Lucerne the week of the 12 -1 6 September 2011. Consider joining us for what has become a memorable highlight on the annual calendar which is led by several experienced practitioners and usually joined by a diverse group of international and interacting professionals.

More information at:

http://www.douglasconnect.com/km/km-training

or you can read some of my previous posts on this activity at:

http://barryhardy.blogs.com/theferryman/km_institute/

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



Scientists Against Malaria initiative: the story of our development journey to our initial results

I presented our initial story, work and results on the "Scientists Against Malaria" project at the BIO-IT 2011 conference in Boston, 13 April 2011, in the Collaborative Drug Design session.

We selected our target Plasmodium Kinase which had no protein structure or known ligand at the start of the project in June 2010, carried out a variety of predictive model building, created a design library, expressed the protein and developed an assay, and obtained initial micromolar hits.  In parallel a support infrastructure was built including industry standard systems e.g., documented evidence captured in collaborative lab notebook system (CERF), and innovative approaches, e.g., ontology-based interoperability to complex event driven services and collaboration patterns supported by SYNERGY.

OpenTox will contribute to the Scientists Against Malaria initiative through the holistic incorporation of predictive toxicology modelling of drug design libraries.

We are currently proceeding with further computational and lab experiments.

Slides:

Download SYN SAM BIO-IT 110409 2.0

Poster:

Download SYN&SAM poster BioIT 1

Background "Meet your Future Patients" post:

http://barryhardy.blogs.com/theferryman/2011/04/meet-your-future-patient-realities-in-malaria.html

"Meet your Future Patient" Realities in Malaria

While presenting for the first time on the initial results of our "Scientists Against Malaria" drug design initiative at the Bio-IT conference in Boston this week, I used a few slides from our trip to the Caprivi Delta, Namibia to draw attention to the realities and important issues on the ground of the children needing solutions in such regions.

 

While on a start-up conservation field trip in a remote region of Namibia, we visited many local villages: you can consider the children here as an introduction to your ‘future patients’ for malaria treatment. Malaria is a common infection in this region which has many wetlands and a strong wet season.

 

Families and village communities form a critical part of the social fabric in this region. Unfortunately a high HIV infection rate is having devastating impact on such communities. Infections go untreated and many children lose their parents.

 

We visited a local school where we had lively interactions with the children who demonstrated their talents with enthusiasm and energy. Education requires healthy families and children so that children can attend such schooling for sufficiently long periods of time to develop stronger educational foundations to navigate the issues of this coming century for their community.

 

This next generation of the community is however growing up with the challenges of malaria and little medical care.

A family we interviewed with proudly showed us their material possessions. The current cost of our anti-malarials for just two weeks would exceed their entire annual income.

 

We can work on biodiversity conservation (e.g., recent rhino rescue work in Thanda shown). But we need a healthy, educated community involvement for it to be sustainable. Criminal groups who exploit these communities and regions for poaching must be resisted through capacity building. In collaboration together in areas of health, education and business we can build a more promising future for both the people and their rich and valuable biodiverse environment.

 

Consider the following realities and joining us in our collaborative work to invent new ones!