Pack: ENM components

Created: 2013-12-06 17:57:57      Last updated: 2014-11-17 19:06:40
Information Live view

Title: ENM components


Information Description

ENM Components is a set of Taverna components (sub-workflows) specialized in ecological niche modelling (ENM) tasks. They simplify the creation of new workflows by encapsulating details that may not be trivial to implement and they can be reused across different workflows. To use ENM components on new workflows with the Taverna workbench, just click on “import new service” on the “service panel”, choose “component service”, select “myExperiment” as the registry and “ENM components” as the family. This will add a new entry in the service panel from where each component can simply be dragged into the workflow being designed. To facilitate connecting different components, most ports with the same data type were assigned the same name. To inspect the functionality of a given component and even run it, choose "Open component" under the "Components" menu and run it as a normal workflow. All ports have example values that can be used as a test.

Most of the functionality on this pack uses the openModeller web service (OMWS version 2.0), so almost everything will only work with an Internet connection. The default service being used is hosted by CRIA and runs on a single machine. The service is free and open to the public, without restrictions. However, if you plan to make intensive use of it, such as submitting thousands of job requests in a short period of time, it is advisable to contact CRIA before. For more information about the service: http://modeller.cria.org.br

To check if the service is online you can use the corresponding biodiversitycatalogue entry here.

If you wish to use another service endpoint - as there are other services available that are compatible with the same protocol (you could even install your own copy of the service, if necessary) - there is currently no plugin or easy trick in Taverna to do this. Each service call in each component would need to be manually changed. There is a special workflow being developed by Alan R. Williams from the University of Manchester that can do this, but you would first need to create your own copy of the whole ENM components family.

Since the web service uses openModeller behind the scenes, you can also find more information about the available modelling algorithms in the openModeller web site documentation section.

There are a number of environmental layers available on the server. CRIA is keen to include more layers there if they can be useful to other people - please contact them in that case. The service is also capable of reading remote rasters that are available through HTTP, so if you wish to use your own layers, you could also put them somewhere and use their URL as the layer identifier. In that case, you just need to contact CRIA asking them to put the corresponding host name in the white list of remote raster sources.

Another service used by some of the components is called BioSTIF. BioSTIF is basically used to visualize points and rasters on a web interface. It also allows you to create masks and filter points. The default BioSTIF service being used by the components is hosted by the Cardiff University.

I hope you find ENM components useful to your research.

Subscribe to RSS feed for items in this pack feed Download Information Items (25)

  • Internal item

    Workflow: biostif_show_projections (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 12:31:18)

    moreExpand

  • Internal item

    Workflow: biostif_upload_points (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 11:11:08)

    moreExpand

  • Internal item

    Workflow: biostif_upload_raster (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 10:50:46)

    moreExpand

  • Internal item

    Workflow: configure_external_test (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 12:23:52)

    moreExpand

  • Internal item

    Workflow: convert_points_xml_to_csv (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-11-05 14:02:28)

    moreExpand

  • Internal item

    Workflow: create_model (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-10 17:33:09)

    moreExpand

  • Internal item

    Workflow: define_frequently_used_constants (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-11-10 19:16:24)

    moreExpand

  • Internal item

    File: Empty profile (Alex Hardisty)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-06 17:57:57)

    moreExpand

  • Internal item

    Workflow: evaluate_model (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-10 17:49:40)

    moreExpand

  • Internal item

    Workflow: extract_auc (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-10-09 15:32:28)

    moreExpand

  • Internal item

    Workflow: extract_confusion_matrix (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-10-13 17:35:21)

    moreExpand

  • Internal item

    Workflow: extract_roc_points (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-10-13 14:39:26)

    moreExpand

  • Internal item

    Workflow: get_available_algorithms (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-06 18:22:00)

    moreExpand

  • Internal item

    Workflow: get_available_layers (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-06 18:07:41)

    moreExpand

  • Internal item

    Workflow: loop_until_progress_complete (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-02-13 09:41:53)

    moreExpand

  • Internal item

    Workflow: parse_csv_points (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 11:41:36)

    moreExpand

  • Internal item

    Workflow: project_model (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 10:44:12)

    moreExpand

  • Internal item

    Workflow: sample_points (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-03-19 16:53:53)

    moreExpand

  • Internal item

    Workflow: select_algorithm_and_set_parameters (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-06 18:26:57)

    moreExpand

  • Internal item

    Workflow: select_layers (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-06 18:17:40)

    moreExpand

  • Internal item

    Workflow: select_matching_layers (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 11:08:22)

    moreExpand

  • Internal item

    Workflow: select_or_create_mask (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-10 16:51:23)

    moreExpand

  • Internal item

    Workflow: select_random_points_based_on_threshold (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2014-11-13 13:19:10)

    moreExpand

  • Internal item

    Workflow: show_test_results (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-24 12:35:48)

    moreExpand

  • Internal item

    Workflow: test_model (Renato De Giovanni)

    Added by Renato De Giovanni ... more than 1 year ago (2013-12-10 17:39:44)

    moreExpand



Information Relationships (0)

There are no relationships.



Information Download


25 items in this pack

Information License

All versions of this Pack are licensed under:

Information Tags (1)

Log in to add Tags

Information Tags from Items (2)

Information Shared with Groups (1)

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Favourited By (0)

No one

Information Statistics

180 viewings

36 downloads

[ see breakdown ]

 



Comments Comments (0)

No comments yet

Log in to make a comment


What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/packs/563


Alternative Formats

HTML
RDF
XML