The Ferryman

Predictive Toxicology Ontology Perspectives and Roadmap

Re: #OpenTox, ontology, new predictive toxicology systems

The following papers are now available from the new issue of Altex:

Toxicology ontology perspectives
This article provides an overview of some of the leading developments in
incorporating ontology into new knowledge-based systems in predictive toxicology.

http://www.altex.ch/en/index.html?id=16&aid=3

A toxicology ontology roadmap
In this article we lay out the main justifications and needs for ontology
development to enable the building of interoperable predictive toxicology systems
and services for industry to design and test safer products.

http://www.altex.ch/en/index.html?id=16&aid=2

OpenTox Toxicology Ontology Development

This article is just out online describing initial #OpenTox ontology work:

#OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337268/

Our Valentine's Message to you today Nicki

Our love is a little more painful today Nicki but we will continue to be inspired by your spirit and vision in times to come. Tonight let's first close our eyes and talk with you as we enter the early hours and your dancing begins. Let the cats of the world gather around in the deep of the night with us and see again that yes there is a planet still alive and not yet quite amused to death.

 

 

 

All my Love Barry

 

Nicki Douglas

I bring unfortunate news that we lost Nicki Douglas through a sudden
death this week. We will have an open house tomorrow Friday 10 Feb from
14.00 - 20.00 at Baermeggenweg 14, Zeiningen in Switzerland so that
friends and family will have a chance to say goodbye to her.

Barry

#OpenTox - #Bioclipse Cloud article

The final version of our first #OpenTox - #Bioclipse paper on getting our tox cloud working with the Bioclipse workbench for interactive design for safety purposes is now available in open access. See http://www.biomedcentral.com/1756-0500/4/487

Updated progress of Scientists Against Malaria initiative

I presented a progress update on our Scientists Against Malaria drug discovery initiative at the BIO-IT Europe conference in October. You can download the presentation as a pdf:

Collaborative Virtual Organisation and Infrastructure for Anti-Malarial Drug Design

OpenTox 2011 Technical Reports

The following #OpenTox 2011 technical reports in predictive toxicology are now available:

OpenTox D1.4 Report on Evaluation of the Final Implementation

OpenTox D2.4 Report on Final Framework

OpenTox D3.4 Report on Final Database with Additional Content

OpenTox D4.3 Report on Final Version of (Q)SAR algorithms

OpenTox D5.3 Report on Validation Against Confidential Data

OpenTox D5.4 Report on Final Validation Routines with Facilities to Validate Against Confidential Data

Bioclipse and OpenTox partner up to create a unique workbench semantic web combination

#OpenTox and #Bioclipse have partnered up on a new open platform we hope you will try out!

We describe the combination of the Bioclipse workbench and distributed OpenTox web services to create a unique safety assessment exploration and design environment for chemists, biologists and toxicologists in the following new paper:

Computational toxicology using the OpenTox application programming interface and Bioclipse

BMC Research Notes 2011, 4:487

http://www.biomedcentral.com/1756-0500/4/487

I believe future developments of this platform are looking promising. Welcome your feedback!

Barry

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!