openModeller 1.5 released

Version 1.5 of the openModeller framework and command line tools is now available for download. This release contains a new algorithm to generate virtual niches and a decent description was finally included for the Niche Mosaic algorithm. The Web service contains a few changes and a new scheduler compatible with HTCondor DagMan. The most important changes are on the Windows installer, which now: 1) includes some MSVC DLLs that could be missing in some machines, 2) fixes a problem that could erase the content of the PATH environmental variable, and 3) contains a new option to install the Python module.

New video showing the ENM workflow running on the BioVeL portal

The ENM workflow uses the openModeller Web Service to perform ENM tasks:

openModeller 1.4 released

Version 1.4 of the openModeller framework and command line tools is now available for download. This release contains a new "meta" algorithm that can use several algorithms behind the scenes to generate a consensus model. A new command-line tool (om_evaluate) can be used to return raw model values given a set of points and an environmental scenario. A new version of the web service (OMWS 2.0) is also available, including new operations - one of them allowing whole experiments to be specified in a single request. A new raster driver now allows remote files to the fetched and used. There were also many changes in the framework itself. Click here to get more information about this release and download it.

First BioVeL workflow based on openModeller is available

The first ecological niche modelling workflow based on the openModeller web service was released as part of the BioVeL project. The workflow can be run either directly from the BioVeL Portal or from the Taverna workbench. In the later case, besides downloading and installing the software on your machine, you need to install the Taverna interaction plugin and you need to run the workflow with an active Internet connection in order to interact with the web service (models are generated, tested and projected remotely).

The workflow contains several interactions where you can choose an algorithm, set the parameter values, choose a layer set for model creation, choose or create a mask, decide if you want to run 10-fold cross validation and also project the model as many times as you want.

All results are available in the end of the workflow as separate "output ports". Projections can be visualized during the workflow on the last step through a specific interface called BioSTIF, also developed as part of the project.

For those using Taverna workbench, the workflow can be downloaded from myExperiment here.

If you are in London this week for INTECOL 2013, there will be demonstrations of the workflow there. Just look for the BioVeL booth for more information.

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.

openModeller 1.2 released

Version 1.2 of the openModeller framework and command line tools is now available for download. This release contains the new algorithm Random Forests and new versions of ENFA, Maxent and Environmental Distance. There were also changes in the Web Service, command line interface and the framework itself. Click here to get more information about this release and download it.

openModeller 1.1 released

Version 1.1 of the openModeller framework and command line tools is now available for download. This release includes two new algorithms - ENFA (Ecological Niche Factor Analysis) and Niche Mosaic - and a new version of the Maximum Entropy algorithm based on the Maxent paper (Phillips et al., 2006). It also contains a few adjustments in other existing algorithms (GARP, AquaMaps, ANN, CSM and Mahalanobis distance).

More details can be found here.