The Ferryman

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

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!!

"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!

 

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

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

Dear Michael, Thanks, Respects and Inspiration to you (Michael Jackson)

Thanks Michael for all those great music videos in the 80's.  You were a leader, an innovator, doing completely new and great things back then.  You entertained us when we took a break from our studies in college in the early 80s, and tried out this new MTV experience at the time.  (It was much more interesting back then!)  You were a Thriller!

Respects to you Michael, we played and danced to your songs last night, and were not alone.

Inspiration Michael, if we can take inspiration from your tragedy and Childhood legacy you could not shake off, it is that we should take some more time to reach out to our family, friends and contacts.  Even if it is that business partner, don't just always email them, get on the Skype with them, talk and get some understanding, build some shared meaning, reach out and support. As you said:

You are not alone, I am here with you
Though you're far away, I am here to stay
You are not alone, I am here with you
Though we're far apart, You're always in my heart

And if you want to collaborate folks in this flatter world don't be alone and far away. Reach out!

The Ferryman

Walking with Lions and Licked By Cheetahs; a visit with the Mukuni Project in Zambia

On the way back home in November from our expedition in Namibia, we stayed a few days in Livingstone in Zambia. As the rains had been falling on and off for two weeks, the Victoria Falls there were very pretty when we visited them.  But the really interesting experience was discovering and visiting a new lion and cheetah re-introduction initiative: the Mukuni Project.

More on our experience there below!