tag:blogger.com,1999:blog-70512576887270272252024-02-20T17:30:37.420-03:00openModeller NewsRenato De Giovannihttp://www.blogger.com/profile/02303051776283592123noreply@blogger.comBlogger32125tag:blogger.com,1999:blog-7051257688727027225.post-41154925252904259522015-01-08T17:30:00.001-02:002015-01-08T17:30:46.877-02:00openModeller 1.5 releasedVersion 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.Renato De Giovannihttp://www.blogger.com/profile/02303051776283592123noreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-64350101023523906292014-10-24T09:17:00.001-02:002014-10-24T09:17:37.499-02:00New video showing the ENM workflow running on the BioVeL portal<p>The ENM workflow uses the openModeller Web Service to perform ENM tasks:</p>
<br />
<iframe allowfullscreen="" frameborder="0" height="315" src="//www.youtube.com/embed/eZ6g7XpRC9E" width="560"></iframe>Renato De Giovannihttp://www.blogger.com/profile/02303051776283592123noreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-12575556188692698132014-04-02T09:35:00.000-03:002014-04-02T09:35:02.145-03:00openModeller 1.4 released<div style="text-align: justify;">
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 <a href="http://sourceforge.net/projects/openmodeller/files/openModeller/1.4.0/">here</a> to get more information about this release and download it.
</div>
Renato De Giovannihttp://www.blogger.com/profile/02303051776283592123noreply@blogger.com6tag:blogger.com,1999:blog-7051257688727027225.post-88980109162265873852013-08-19T19:29:00.000-03:002013-08-19T19:31:37.662-03:00First BioVeL workflow based on openModeller is availableThe first ecological niche modelling workflow based on the openModeller web service was released as part of the <a href="http://biovel.eu/">BioVeL</a> project. The workflow can be run either directly from the <a href="http://portal.biovel.eu/">BioVeL Portal</a> or from the <a href="http://www.taverna.org.uk/download/workbench/">Taverna workbench</a>. 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).<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.myexperiment.org/workflows/3355.html" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="320" src="http://www.myexperiment.org/workflows/3355/versions/13/previews/medium" width="177" /></a></div>
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. <br />
<br />
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.<br />
<br />
For those using Taverna workbench, the workflow can be downloaded from myExperiment <a href="http://www.myexperiment.org/workflows/3355.html">here</a>.<br />
<br />
If you are in London this week for <a href="http://www.intecol2013.org/">INTECOL 2013</a>, there will be demonstrations of the workflow there. Just look for the BioVeL booth for more information.Renato De Giovannihttp://www.blogger.com/profile/02303051776283592123noreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-63066580669190591132012-05-31T10:40:00.000-03:002013-05-29T10:41:15.574-03:00Three projects improving openModellerIn 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 <a href="http://inct.florabrasil.net/">INCT - Virtual Herbarium</a> 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 <a href="http://www.eubrazilopenbio.eu/">EUBrazil-OpenBio</a> . 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 <a href="http://wiki.eubrazilopenbio.eu/index.php/OpenModeller_Maxent">here</a> ), indicating that we will finally be able to produce similar results to the original Maxent software. The third project,<a href="http://www.biovel.eu/">BioVeL</a>, 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 <a href="http://www.taverna.org.uk/">Taverna</a>) 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.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-89892989598616637842011-10-03T10:39:00.000-03:002013-05-29T10:40:18.925-03:00openModeller 1.2 releasedVersion 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 <a href="http://sourceforge.net/projects/openmodeller/files/openModeller/1.2.0/">here</a> to get more information about this release and download it.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-79074035197543114172010-02-15T10:39:00.000-02:002013-05-29T10:39:35.842-03:00openModeller 1.1 releasedVersion 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).<br />
<br />
More details can be found <a href="http://sourceforge.net/projects/openmodeller/files/openModeller/1.1.0/NOTES.txt/view">here</a>. Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-19210455406909934532009-08-21T10:38:00.000-03:002013-05-29T10:38:31.778-03:00New publication explains openModeller in detailIf you want to know how openModeller works and why it was created, GeoInformatica has just published a new paper as an electronic Online First article with this information:<br />
<br />
<a href="http://www.springerlink.com/content/n805714x26265573/">http://www.springerlink.com/content/n805714x26265573/</a> <br />
<br />
Now the following reference can be used to cite openModeller:<br />
<br />
Muñoz, M.E.S., Giovanni, R., Siqueira, M.F., Sutton, T., Brewer, P., Pereira, R.S., Canhos, D.A.L. & Canhos, V.P. (2009) "openModeller: a generic approach to species' potential distribution modelling". GeoInformatica. DOI: 10.1007/s10707-009-0090-7<br />
<br />
As soon as it gets published in a paginated issue, you will be able to add volume number and page range to the citation. The publications section will be updated accordingly when the corresponding journal issue gets compiled.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-56413787575322151492009-05-22T10:36:00.000-03:002013-05-29T10:36:59.805-03:00openModeller 1.0 is availableThis release contains only a few adjustments and minor feature enhancements, but it consolidates all work that was done during the last 4 years as part of a thematic project funded by Fapesp. Some people are still working on additional features that will hopefully be incorporated in future releases, such as a new version of the maximum entropy algorithm (Maxent), a new algorithm called Niche Mosaic and paralellized versions of GARP.<br />
<br />
Version 1.0 includes adjustments in algorithms (ANN and SVM), command line tools (om_model and om_niche) and ROC curve procedures. It also contains improvements in the modelling protocol, and model statistics (possibility to use lowest presence threshold).<br />
<br />
More details about this release can be seen <a href="http://sourceforge.net/project/shownotes.php?group_id=101808&release_id=684403">here</a>.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-2319322302589693862009-01-15T10:35:00.000-02:002013-05-29T10:48:37.522-03:00Version 0.7.0 of the openModeller library releasedVersion 0.7.0 of the openModeller library is now available. This release contains the following main changes/features:<br />
<ul>
<li>New algorithm using Artificial Neural Networks;</li>
<li>New option to generate distribution maps directly in ARC/Info ASCII grid format (byte or floating point);</li>
<li>New keywords "Spatially unique" and "Environmentally unique" can be used to filter input points when using om_console;</li>
<li>Change in AUC calculation: when no absences are provided, instead of using 1-specificity after generating pseudo-absences, it now uses the proportion of points predicted present for a large number of random background points;</li>
<li>New method in the RocCurve class to calculate partial area ratio;</li>
<li>New parameters to om_test: <span style="font-family: Courier New, Courier, monospace;">--calc-matrix</span>, <span style="font-family: Courier New, Courier, monospace;">--calc-roc</span>, <span style="font-family: Courier New, Courier, monospace;">--num-background</span> and <span style="font-family: Courier New, Courier, monospace;">--max-omission</span>.</li>
</ul>
<br />
Please note that the previous release (0.6.1) also includes these changes:<br />
<ul>
<li>Many adjustments in the command line tools;</li>
<li>New method in the modelling service to perform external tests;</li>
<li>Possibility for the modelling server to submit jobs to Cluster nodes via Condor.</li>
</ul>
<br />
More details about the latest release can be found <a href="https://sourceforge.net/project/showfiles.php?group_id=101808&package_id=116659&release_id=653929">here</a> .Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-16212216063265593352008-10-06T10:32:00.000-03:002013-05-29T10:32:40.124-03:00How to add new algorithms in openModellerA new document is available to help those who are interested in adding new algorithms in openModeller. All algorithms must be written in C++. Apart from that, the framework is quite flexible to accommodate new algorithms since they are completely free to decide how distribution models will be represented. The new manual is available <a href="http://openmodeller.sourceforge.net/alg_manual.html">here</a>. Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-48237918049290266612008-08-20T10:31:00.000-03:002013-05-29T10:32:17.891-03:00openModeller being used by the GBIF data portalThe <a href="http://www.gbif.org/">Global Biodiversity Information Facility</a> (GBIF) recently released a new version of its <a href="http://data.gbif.org/">data portal</a> allowing users to generate niche models in real time. After searching for occurrence records, users have the option to create a niche model when visualizing results.<br />
<br />
The data portal uses a Java client that can communicate with a remote modelling service through the openModeller Web Service protocol (OMWS). The Java client was developed by the <a href="http://www.colorado.edu/">University of Colorado</a>, and the modelling service by <a href="http://www.cria.org.br/">CRIA</a>. Initially, models are being generated only for present time using the Envelope Score algorithm.<br />
<br />
GBIF is the world largest biodiversty data portal, currently serving more than 140 million specimen/observation records of which 80% are georeferrenced.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-41063391630889769162008-07-08T10:29:00.000-03:002013-05-29T10:50:10.138-03:00Version 0.6.0 of the openModeller library releasedVersion 0.6.0 of the openModeller library is now available. This release contains mainly new features, including:<br />
<ul>
<li>Drivers to directly read occurrences from GBIF or TAPIR/DarwinCore providers.</li>
<li>A new command-line tool (om_points) that can be used to retrieve occurrence data using any of the available drivers.</li>
<li>A new command-line tool (om_algorithm) to get information about the available algorithms.</li>
<li>A new Maximum Entropy algorithm with two training methods: GIS (Generalized Iterative Scaling) and L-BFGS (Limited-Memory Variable Metric).</li>
</ul>
<br />
The GARP Best Subsets algorithm was also changed to accept the "max threads" parameter, which can be used to speed up the modelling process in multi-processor machines.<br />
<br />
More details about this release can be found here:<br />
<br />
<a href="https://sourceforge.net/project/showfiles.php?group_id=101808&release_id=611859">https://sourceforge.net/project/showfiles.php?group_id=101808&release_id=611859</a>Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-55854943098365987882008-04-24T10:26:00.000-03:002013-05-29T10:28:33.867-03:00Released version 0.5.3 of the libraryA new version of the openModeller library is available. This release (0.5.3) contains many bugfixes and a new algorithm called Aquamaps. The algorithms "minimum distance" and "distance to average" were removed since EnvironmentalDistance now provides the same functionality. The TerraLib drivers were updated for compatibility with TerraLib 3.2.0. There are two new classes for pre-analysis on input layers to perform jackknife and chi-square (only available as library classes - their functionality still need to be exposed in the command-line and/or Desktop interfaces).<br />
<br />
More details about this release can be found here:<br />
<br />
<a href="http://sourceforge.net/project/shownotes.php?group_id=101808&release_id=587262">http://sourceforge.net/project/shownotes.php?group_id=101808&release_id=587262</a>Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-65016058043888474992007-10-26T10:24:00.000-02:002013-05-29T10:51:21.976-03:00openModeller Desktop version 1.0.6 ReleasedIt is our great pleasure to announce the immediate availability of openModeller Desktop Version 1.0.6 <a href="http://openmodeller.sf.net/">openModeller</a>is a generic framework for carrying out fundamental niche modelling experiments - typically used to predict species distribution given a set of environmental raster layers. The openModeller Desktop application builds on the openModeller library by providing a user friendly graphical user interface for carrying out niche modelling experiments.<br />
<br />
This release introduces several new features including:<br />
<ul>
<li>Improved mapping capabilities - you can now specify occurrence symbol size and colour, and overlay a context layer (such as country boundaries) on your output map.</li>
<li>Experiments run in their own thread.- this makes for a more responsive user interface and you can look at completed models whilst the experiment is still running.</li>
<li>Web Service modelling improvements - improvement have been made to allow better job progress reporting when running as a web sevice.</li>
<li>Absence modelling is now supported - previous versions of openModellerDesktop did not handle absence data properly so absence modelling was not available.</li>
<li>GBIF Rest Data Fetcher (work sponsored by GBIF with our thanks!) - it is now possible to retrieve occurrence data using the new GIF Rest query service. The data fetcher has also had various cosmetic and useability improvements, and now functions as a wizard.</li>
<li>New algorithms - openModeller Desktop now ships with two new algorithms (Support Vector Machines and Bioclim Score).</li>
<li>Thresholding tool - you can now compute 'hotspot' models showing the predicted species count per cell by aggregating many model outputs into a single raster file. The threshold tool can also be used for 'concensus' modelling where many algorithms are used for a single species and all the resulting probability distribution maps are combined to provide a map indicating where most algorithms are in agreement that a species will ocurr at a given cell.</li>
</ul>
<div>
<br /></div>
The release also includes numerous improvements, bug fixes and stability improvements. openModeller Desktop is available in source form, and as binary executables for Microsoft Windows, Mac OS X, and Ubuntu 7.10 GNU/Linux. All versions can be obtained from our <a href="http://sourceforge.net/project/platformdownload.php?group_id=101808&sel_platform=4998">download page</a>. As an open source project, we provide support for using openModeller via our mailing lists and bug tracker:<br />
<div>
<ul>
<li>For general enquiries <a href="http://lists.sourceforge.net/mailman/listinfo/openmodeller-users">subscribe</a> to our users mailing list.</li>
<li>For developer related enquiries <a href="http://lists.sourceforge.net/mailman/listinfo/openmodeller-devel">subscribe</a> to our separate developers list.</li>
<li>If you think you have found a bug, please report it using our <a href="http://sourceforge.net/tracker/?group_id=101808&atid=631036">bug tracker</a>. When reporting bugs, please include some contact information in case we need help with replicating your issue.</li>
</ul>
<h4>
<br /></h4>
<h4>
Known Issues</h4>
The threshold tool can crash with large datasets, this will be addressed in next release.</div>
Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-21028419312488679942007-05-08T10:22:00.000-03:002013-05-29T10:51:35.955-03:00Released version 0.4.2 of the libraryA new version of the openModeller library is available. This release (0.4.2) contains some bugfixes and two new features:<br />
<ul>
<li>ROC curve was included in the model statistics (AUC is now automatically calculated by om_console, which generates pseudo-absence points if no real absence points are provided).</li>
<li>Metric Chebyshev can be selected as a parameter in the Environmental Distance algorithm.</li>
</ul>
<br />
For developers, the Log object is now a singleton instead of a global variable.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-67338584950231632342007-04-20T10:19:00.000-03:002013-05-29T10:20:34.721-03:00openModeller Desktop version 1.0.5 ReleasedIt is our great pleasure to announce the immediate availability of openModeller Desktop Version 1.0.5 <a href="http://openmodeller.sf.net/">openModeller</a>is a generic framework for carrying out fundamental niche modelling experiments - typically used to predict species distribution given a set of environmental raster layers. The openModeller Desktop application builds on the openModeller library by providing a user friendly graphical user interface for carrying out niche modelling experiments. This release introduces several new features including improved reporting, automated retrieval of locality data from online databases such as GBIF, Mac OS X build, and many other enhancements. The release also includes numerous bug fixes and stability improvements. openModeller Desktop is available in source form, and as binary executables for Microsoft Windows, Mac OS X, and as a GNU/Linux distribution independent application bundle. All versions can be obtained from our <a href="http://sourceforge.net/news/submit.php?group_id=101808">download page</a>. As an open source project, we provide support for using openModeller via our mailing lists and bug tracker:<br />
<ul>
<li>For general enquiries <a href="http://lists.sourceforge.net/mailman/listinfo/openmodeller-users">subscribe</a> to our users mailing list.</li>
<li>For developer related enquiries <a href="http://lists.sourceforge.net/mailman/listinfo/openmodeller-devel">subscribe</a> to our separate developers list.</li>
<li>If you think you have found a bug, please report it using our <a href="http://sourceforge.net/tracker/?group_id=101808&atid=631036">bug tracker</a>. When reporting bugs, please include some contact information in case we need help with replicating your issue.</li>
</ul>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://openmodeller.sourceforge.net/images/stories/releases/openModellerDesktop1.0.5/openModeller1.0.5.mac.thumb.png" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Report view for a completed experience (Mac OS X version)</td></tr>
</tbody></table>
Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-24273177443316531842007-03-12T10:14:00.000-03:002013-05-29T10:14:41.599-03:00Released version 0.4.1 of the libraryA new version of the openModeller library is available. This release (0.4.1) includes some changes and new features:<br />
<ul>
<li>New algorithm EnvironmentalDistance supporting three different metrics: Euclidean, Mahalanobis and Gower. When used with Gower and maximum distance of 1, this algorithm should be equivalent to DOMAIN.</li>
<li>It is now possible to specify absence points in the localities file, which has a new format: four mandatory columns (id, label, longitude and latitude) and one optional column (abundance). Absences are indicated with abundance equal to zero. All values must now be separated by TABs, so labels (usually scientific names) can contain spaces. The new column "id" is used to identify the individual records.</li>
<li>For developers, there's initial support to cmake (should compile on GNU/Linux and Mac OS X).</li>
</ul>
Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-77668894292243324572007-01-09T10:12:00.000-02:002013-05-29T10:12:56.654-03:00Source code migration from CVS to SubversionToday we have finally migrated the openModeller source code from CVS to Subversion. This change affects developers only. Subversion will allow improved management of the openModeller source code. The instructions under the <a href="http://openmodeller.sourceforge.net/index.php?option=com_content&task=view&id=21&Itemid=7">resources page</a> have been updated with subversion specific details.<br />
<br />
Please let us know if you have any problems accessing the source code via Subversion. Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-42085226947058465792007-01-08T10:10:00.000-02:002013-05-29T10:10:55.651-03:00openModeller Desktop version 1.0.4 ReleasedWe are very pleased to announce the <a href="http://sourceforge.net/project/showfiles.php?group_id=101808">immediate availability</a> of openModeler Desktop version 1.0.4. This release contains a critical bug fix for the layerset manager in the 1.0.3 release and includes no new features. We encourage you to upgrade to this version at the first possible opportunity!<br />
<br />
Currently the openModeller Desktop application is available as a Microsoft Windows setup file or in source form. Future releases will include binaries for GNU / Linux and Mac OS X. <br />
<br />
We invite you to join our mailing lists, IRC channel and other community <a href="http://openmodeller.sourceforge.net/index.php?option=com_content&task=view&id=21&Itemid=7">resources</a> if you need help using the openModeller Desktop application, or would like to discuss issues relating to openModeller.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-34825532204056994332007-01-02T10:08:00.000-02:002013-05-29T10:46:42.849-03:00openModeller Desktop version 1.0.3 ReleasedWe are very pleased to announce the <a href="http://sourceforge.net/project/showfiles.php?group_id=101808&package_id=142057&release_id=475226">immediate availability</a> of openModeler Desktop version 1.0.3. This release contains several bug fixes and adds some two new features:<br />
<ul>
<li>The extracted environmental variables for the occurrence sites used in a given model can be exported as a Comma Separated Values (CSV) file.</li>
<li>The occurrence sites are displayed as an overlay on top of the probability surface in the model map display.</li>
</ul>
<br />
We encourage you to upgrade from version 1.0.2 if you installed it since this version also fixes some issues that caused the application to crash when changing the modelling plugin.<br />
<div>
<br />
Currently the openModeller Desktop application is available as a Microsoft Windows setup file or in source form. Future releases will include binaries for GNU / Linux and Mac OS X. <br />
<br />
We invite you to join our mailing lists, IRC channel and other community <a href="http://openmodeller.sourceforge.net/index.php?option=com_content&task=view&id=21&Itemid=7">resources</a> if you need help using the openModeller Desktop application, or would like to discuss issues relating to openModeller.</div>
Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-32867471120881448392006-12-14T10:02:00.000-02:002013-08-19T18:29:26.403-03:00openModeller Desktop version 1.0.2 ReleasedThe openModeller team is pleased to announce version 1.0.2 of the openModeller Desktop graphical user interface for openModeller. This is the first public release of the new user interface which replaces the previous wizard based version.<br />
<br />
<h4>
Main Features</h4>
<div>
<ul>
<li><b>A layerset manager.</b> This is for creating named collections of layers for use in modelling experiments. Having layers organised in named sets removes the tedium of repeatedly having to select layers from the file system for different model runs.</li>
<li><b>An algorithm profile manager.</b> Algorithm profiles let you store the custom parameters you use for running models in a reusable way.</li>
<li><b>An experiment designer.</b> The experiment designer allows you to set up an experiment consisting of multiple species and algorithm profiles.</li>
<li><b>An experiment browser.</b> Once an experiment is completed the experiment browser presents the list of algorithm profiles and the species names in a tree view. Clicking on an item in the experiment tree shows a detailed report for that model. The report includes all the details of which algorithm was used, which parameters for the algorithm were changed, which layers were used, the model duration and so on.</li>
<li><b>A map browser.</b> The map browser allows you to pan and zoom on the model's map image.</li>
<li><b>Translations.</b> The openModeller Desktop application is available with Brazillian Portuguese and English translations.</li>
<li><b>Modelling Plugins.</b> The actual modelling work is managed by plugins. This release includes a 'local' plugin that uses the recent 0.4.0 openModeller library release, and a 'web service' plugin that allows models to be run on a remote server.*</li>
</ul>
<b>Note:</b> The web service plugin is still considered experimental.<br />
<br />
<h4>
Availability</h4>
</div>
<div>
The software is available in <a href="http://downloads.sourceforge.net/openmodeller/openModellDesktopSourceVersion1.0.zip?use_mirror=osdn">source form</a> (all platforms) and as a <a href="http://downloads.sourceforge.net/openmodeller/openModellerDesktopSetup1.0.2.exe?use_mirror=osdn">binary installer</a> package for Microsoft Windows. In future releases we will make binaries available for Mac OS X and GNU/Linux. If you are an Ubuntu Linux user, <a href="http://openmodeller.cria.org.br/wikis/omgui/InstallFromScratchOnUbuntuDapper">step by step instructions</a> for building the application on your system are available.<br />
<br />
<h4>
Screenshots</h4>
</div>
<div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://openmodeller.sourceforge.net/screenshots/layerset_manager.jpg" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Layer Set Manager Window</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://openmodeller.sourceforge.net/screenshots/algorithm_manager.jpg" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Algorithm Profile Manager</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://openmodeller.sourceforge.net/screenshots/experiment_designer.jpg" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Experiment Designer Window</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://openmodeller.sourceforge.net/screenshots/main_window.jpg" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Experiment Browser / Main Window</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://openmodeller.sourceforge.net/screenshots/map_viewer.jpg" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Map Viewer</td></tr>
</tbody></table>
<h4>
</h4>
<h4>
<br /></h4>
<h4>
Tutorial Video</h4>
A <a href="http://openmodeller.cria.org.br/images/openModellerDesktopVideoHighQuality.mpg">tutorial video</a> is available (~124mb!) which will help in getting started with openModeller Desktop.<br />
<br />
<h4>
</h4>
<h4>
Known Issues</h4>
</div>
<div>
This is a first public release and the software has some known issues. These include application crash when switching plugins. Restart the application when ever you switch plugins and it should function normally after the restart. We encourage you to report any bugs you find on the <a href="http://sourceforge.net/tracker/?group_id=101808&atid=631036">project bug tracker</a>. You can also use the bug tracker to browse the list of known issues.</div>
Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-6975955706421530202006-12-06T09:14:00.000-02:002013-05-29T09:17:08.175-03:00Released version 0.4 of the libraryA new release of the openModeller library is now available. Version 0.4 contains major feature enhancements and also some bugfixes. This release includes integration with <a href="http://www.terralib.org/">TerraLib</a>, which is a complete framework for developing GIS tools. The main changes are:<br />
<div>
<ul>
<li>In addition to GDAL, openModeller's IO functions now work with Terralib raster and point data.</li>
<li>Refactoring of the SOAP interface which now covers all modelling functionality, allowing remote interaction with a modelling service.</li>
<li>The new version of GARP (v3) has been re-enabled.</li>
<li>The default output map file type was changed to ERDAS Imagine ".img" to achieve wider compatibility with GIS software. This format provides a floating-point representation in each raster cell (reflecting probability of presence).</li>
<li>Several fixes in the SWIG-Python binding.</li>
<li>An installation issue with the RPM packages was fixed.</li>
</ul>
The work has been funded by <a href="http://www.fapesp.br/">FAPESP.</a></div>
Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-54791435805051066752006-11-22T09:12:00.000-02:002013-05-29T09:13:26.191-03:00Preview of openModeller DesktopA preview snapshot of the next generation openModeller Desktop is <a href="http://www.cria.org.br/~timlinux/openModellerDesktopSetup.exe">available for download</a> (windows only). Please note the software is still not feature complete or stabilised so just treat this as a preview. This is only for early adopters interested to see where we are headed with the next generation openModeller Desktop application. More than likely you will find bugs and crashes, and we invite you to submit these to our <a href="http://sourceforge.net/tracker/?group_id=101808&atid=631036">bug queue</a>. I have made a short video which should provide a sufficient overview for getting started. The video in .avi file (requires a media player capable playing quicktime) is available <a href="http://www.cria.org.br/~timlinux/omgui1.avi">here</a>.Anonymousnoreply@blogger.com0tag:blogger.com,1999:blog-7051257688727027225.post-64721229104153729932006-10-16T09:11:00.000-03:002013-08-19T18:39:30.276-03:00openModeller at TDWG2006<div class="separator" style="clear: both;">
</div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><img border="0" src="http://openmodeller.sourceforge.net/img/mobo_gardens.gif" style="margin-left: auto; margin-right: auto;" /></td></tr>
<tr><td class="tr-caption">Missouri Botanical Gardens, US</td></tr>
</tbody></table>
<br />
Tim Sutton and Renato De Giovanni are attending <a href="http://tdwg2006.tdwg.org/">TDWG2006</a> (TDWG is the Taxonomic Databases Working Group) this week. Tim will be <a href="http://openmodeller.sourceforge.net/files/openModeller_tdwg2006.ppt">presenting</a> our proposal for a standard API for performing Ecological Niche Modelling over the Internet. There is a <a href="http://openmodeller.cria.org.br/wikis/omgui/OpenModeller_Standard_Web_Services_API">draft</a> of the API available on the openModeller wiki, as well as a <a href="http://openmodeller.cria.org.br/wikis/omgui/Use_Case_Scenario_for_Open_Modeller_Web_Services_API">use case diagram</a>.Anonymousnoreply@blogger.com0