Thursday, May 31, 2012

Three projects improving openModeller

In general, programmers are not good at advertising their work as they are always busy implementing new things, fixing bugs, interacting with users and writing reports. So, the fact that you don't see any news here for some time doesn't mean that there's no activity going on. Actually, right now there are many exciting activities related to openModeller being carried out. This post gives you an overview of what's happening. There are currently three projects promoting specific improvements in openModeller. An extension to the INCT - Virtual Herbarium funded by the Brazilian government will soon release a web application to generate niche models for species of the Brazilian Flora. The Random Forests algorithm (already released in version 1.2) was implemented as part of this project. In this new system, all models will be generated by openModeller, but this effort will actually be carried out in a partnership with another project called EUBrazil-OpenBio . This second project is being jointly funded by the Brazilian government and the European Commission, and it involves several institutions from both sides. It has the ambitious goal of creating a Virtual Research Environment offering access to biodiversity data and tools, including niche modelling. In this particular case, the main idea is to investigate different ways of efficiently running openModeller on the Cloud, including parallelization strategies. It will also develop an advanced web interface (similar to openModeller Desktop) to generate niche models. The same project is also funding a new implementation of the Maximum Entropy algorithm in openModeller. Preliminary results look promising (you can check here ), indicating that we will finally be able to produce similar results to the original Maxent software. The third project,BioVeL, is entirely funded by the European Commission. CRIA is participating with many European institutions. Here, the main idea is to enhance existing tools and services so that researchers can use a workflow management tool (in this case Taverna) to design and run complex tasks related to bioinformatics and biodiversity informatics. BioVeL will promote many improvements in the openModeller Web Service inteface including not just functionality but also documentation and tests. We already managed to run the first niche modelling workflows and we hope to soon release them to the public.

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