The Ferryman

Knowledge Management Training, 6-10 May 2013

We will run our international Knowledge Management Training week again in Switzerland 6-10 May 2013.

Topics: 
Knowledge Management (KM) Concepts, KM Practices, Business Case, Strategy, Program Planning, KM Frameworks, KM & Organisational Culture & Development, Change Management for KM Programs, Leadership and Competencies for KM Knowledge Assessment, Metrics, Enterprise Knowledge Management, Process-oriented Knowledge Management, Knowledge Mapping, Benchmarking, Expertise Location, Search, Personal Knowledge Management, Web 2.0, Communities, Collaboration 

More Information: 
http://douglasconnect.com/km/km-training
http://douglasconnect.com/events/Basel2013

Program Brochure (pdf): 
http://douglasconnect.com/sites/default/files/KMTrainingBrochure-Swiss-Basel-2013.pdf

A Shared Moment of Great Happiness

Barry Hardy and Spela Predan, Just Married.

 

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

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

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 :)!

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!

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