BioVeL internal2012-05-15T09:54:59+00:00/groups/10132015-05-19T09:00:27+00:00Biodiversity eLaboratory shared Ecosystem modelling with Biome-BGCBrings together 5 workflows for ecosystem modelling and calculation of ecosystem service indicators. These workflows are developed around the Biome-BGC biogeochemical modelling software that simulates the storage and flux of water, carbon, and nitrogen between the ecosystem and the atmosphere, and within the components of the terrestrial ecosystems (Thornton, 2000). See descriptions of individual workflows for more details. The workflows in this pack have been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/ ) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359. urn:uuid:28b59169-bd52-4cd6-a259-8b8e5fb0c533Biodiversity eLaboratory2015-03-31T11:23:55+00:00Alan Williams shared Multiple selectionAn interaction page that allows multiple selections from a list of values. There is a single input port of depth one called selectionValues There is a single output port of depth one called answersurn:uuid:9d08a9a7-b074-46df-bd3b-041d565dfc05Alan Williams2014-12-05T18:53:11+00:00Bachirb shared MSA-PAD Genome Mode Multiple DNA Sequence Alignment Framework - Input Submission and email notificationBioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [ http://www.biovel.eu][1 ] [1]: http://www.biovel.eu ## 1 Description This workflow is used to submit the multiple alignment job. Once the computation is finished the user will receive an email notification indicating the obtained output address. The workflow at work translates DNA sequences following a user defined genetic code and one or more open reading frame/s. It devides the translated sequence at each stop codon into separate sequences. I …urn:uuid:f0306451-4ee0-408d-8851-4052b6d27858Bachirb2014-12-05T18:50:06+00:00Bachirb shared MSA-PAD Gene Mode: DNA Multiple Sequence Alignment Framework - Input Submission and email notificationBioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [ http://www.biovel.eu][1 ] [1]: http://www.biovel.eu ## 1 Description This workflow is used to submit the multiple alignment job. Once the computation is finished the user will receive an email notification indicating the obtained output address. The workflow at work translates DNA sequences following a user defined genetic code and one or more open reading frame/s. It devides the translated sequence at each stop codon into separate sequences. I …urn:uuid:b31af494-0c82-4094-beac-e7a8b30d4922Bachirb2014-12-05T18:49:53+00:00Bachirb shared MSA-PAD Gene Mode: DNA Multiple Sequence Alignment Framework - Input Submission and email notificationurn:uuid:bf7aba88-cdec-4387-a63a-90922cf0a39dBachirb2014-12-05T18:29:20+00:00Bachirb shared MsaPAD: Multiple Sequence Alignment - Input Submission and email notificationurn:uuid:bc52fbf7-5b30-4284-89e2-4bca300ccc10Bachirb2014-12-04T16:21:57+00:00Renato De Giovanni shared ENM resolution mix - single run versionSingle run version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates a random virtual niche. A random threshold within a given prevalence range is then used to separate suitable from unsuitable areas, from where random training and testing points are sampled. Training points are used to generate the models and independent testing points are used for external tests measuring …urn:uuid:aa70f726-b55a-449d-9b30-dd54b4196bf9Renato De Giovanni2014-12-04T16:21:16+00:00urn:uuid:19caad0a-9f96-4676-bbe8-1c93d715948eRenato De Giovanni2014-12-04T16:19:19+00:00Renato De Giovanni shared extract_roc_pointsExtracts the ROC points from a test result XML.urn:uuid:9999cb9d-cab3-4718-b7e0-7d4d3170fc31Renato De Giovanni2014-12-04T16:18:47+00:00Renato De Giovanni shared ENM resolution mix - multiple runs versionMultiple runs version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates a random virtual niche. A random threshold within a given prevalence range is then used to separate suitable from unsuitable areas, from where random training and testing points are sampled. Training points are used to generate the models and independent testing points are used for external tests measur …urn:uuid:c5fd463d-91e3-41fc-bb0a-dd7748dfb172Renato De Giovanni2014-12-04T16:14:20+00:00urn:uuid:3f79eefa-28b8-4ada-8144-f3bde51a5665Renato De Giovanni2014-12-04T16:13:47+00:00urn:uuid:d0f4a2b0-dd7c-4b5f-9c30-437fbb882f0cRenato De Giovanni