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3655?size=60x60 Nl Magnus Palmblad
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Blob Example results from the UniProt Protein Protein Net...

Created: 2015-12-04 14:50:06

Credits: User Magnus Palmblad User Yassene

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example results from the UniProt Protein Protein Network workflow (http://www.myexperiment.org/workflows/4778.html) on Apolipoprotein A-I (P02647). The purpose of the igraph graph is to check that the workflow ran OK. For further exploration and visualization of the network, one of the output files can be opened in Cytoscape or similar tool.

File type: PNG image

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71?size=60x60 Nl Katy Wolstencroft
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Blob Annotating Experimental Data

Created: 2015-12-03 08:31:02

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial about annotating experimental data with RightField

File type: PowerPoint 2007 presentation

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71?size=60x60 Nl Katy Wolstencroft
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Blob Geo File for Annotation

Created: 2015-12-03 08:23:05

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is an excel file to use in the RightField exercises in the BioSB Data Integration Course 2015

File type: application/excel

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71?size=60x60 Nl Katy Wolstencroft
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Blob Taverna Tutorial Data Integration NL 2015

Created: 2015-12-02 10:41:00 | Last updated: 2015-12-02 10:43:03

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial introduces you to using the Taverna workbench and shows you how you can use the Open PHACTS REST API to construct workflows over Open PHACTS services

File type: Adobe PDF

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4144?size=60x60 De Alexey Mints
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Blob PDF to BibTex

Created: 2015-10-13 15:11:36

Credits: User Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tries to create a good bibtex file from PDF

File type: text/x-python

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Avatar Gb Robert Muetzelfeldt
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Blob Miniworld model in Systo JSON format

Created: 2015-05-22 15:32:23

Credits: User Robert Muetzelfeldt

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Miniworld model in Systo JSON format 

File type: Trident (Package)

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4295?size=60x60 Tn WAEL KALLEL
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Blob RIEMANN

Created: 2015-05-14 12:08:11

Credits: User WAEL KALLEL

License: Creative Commons Attribution-Share Alike 3.0 Unported License

GRASSHOPPER MATH

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4295?size=60x60 Tn WAEL KALLEL
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Blob DRAKE EQUATION

Created: 2015-05-14 12:07:10

Credits: User WAEL KALLEL

License: Creative Commons Attribution-Share Alike 3.0 Unported License

GRASSHOPPER MATH

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4295?size=60x60 Tn WAEL KALLEL
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Blob Booleen

Created: 2015-05-14 06:38:54

Credits: User WAEL KALLEL

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Booleen workflow with Grasshopper Math

File type: JPEG image

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4260?size=60x60 Ua Igor Lutsenko
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Blob Development of a general structure of the technologi...

Created: 2015-05-13 06:07:39

Credits: User Igor Lutsenko

License: Creative Commons Attribution-Share Alike 3.0 Unported License

At present, technological subsystems are usually hard-coded to produce a consumer product with a certain performance, and efficiency, which is defined either by the factory settings, or determined by the technologist's view on the mode, suitable for this or that equipment.This is predetermined by a number of factors, however, features of the architecture of the technological line, which prevent the possibility to independently vary the feed of raw and energy products, as well as the lack ...

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4260?size=60x60 Ua Igor Lutsenko
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Blob Synthesis of the structure of the technological prod...

Created: 2015-05-13 06:01:12

Credits: User Igor Lutsenko

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Study of current controlled systems and scientific publications has shown that the architecture of controlled systems, related to the products conversion is based on the principle of austerity and, in general, does not provide the possibility of implementing a full parametric optimization.The paper proposes to develop a controlled conversion system from highly specialized systems, each of which performs only one function. The conversion system has the ability of independent conversion process...

File type: Adobe PDF

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4260?size=60x60 Ua Igor Lutsenko
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Blob Development of global efficiency criterion of target...

Created: 2015-05-13 05:56:35

Credits: User Igor Lutsenko

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Guaranteed maximization of financial returns from economic structures is only possible if all of its systems are focused on selecting target operations with maximum efficiency. Is it possible?Any system is created to enhance the value of output products of the system operation. Thus, two products: a consumer product that has value to the customer and the target product (value added), rewarding manufacturer of consumer value are formed at the output of the managed system.If the management syst...

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4260?size=60x60 Ua Igor Lutsenko
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Blob Determination of the value of the complex costs of t...

Created: 2015-05-13 05:43:03

Credits: User Igor Lutsenko

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Currently, the increase in financial returns from economic operations is constrained in view of the lack of a single efficiency criterion, which allows uniquely identify the business operation by their main feature - the possibility of obtaining the maximum value added (profit).One of the main scientific steps on the way to obtaining the formula of efficiency is developing the "resource intensity" indicator. The development of this indicator was based on the model of the deployed op...

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4260?size=60x60 Ua Igor Lutsenko
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Blob Identification of target system operations. 1. Deter...

Created: 2015-05-13 05:23:50 | Last updated: 2015-05-13 05:44:44

Credits: User Igor Lutsenko

License: Creative Commons Attribution-Share Alike 3.0 Unported License

It was found in the paper that the time frames of the studied system operation depend on the research objective. In cases when it comes to problems, related to the physical movement of the input and output products, limits of the study are defined by the time of the beginning of the movement of the first input product of the operation and ends with the time of issue of the last output product of the operation by the system. Time of completion of the physical movement of products is defined in...

File type: Adobe PDF

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3655?size=60x60 Nl Magnus Palmblad
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Blob Former countries

Created: 2015-05-05 12:43:01

Credits: User Magnus Palmblad User Arzu Tugce Guler

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File for mapping former countries to successor states using the ISO 3166 standards.

File type: Excel workbook

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3655?size=60x60 Nl Magnus Palmblad
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Blob ISO 3166-1 and ISO 3166-3

Created: 2015-05-05 12:39:15

Credits: User Magnus Palmblad

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The ISO 3166-1 and ISO 3166-3 country codes

File type: Excel workbook

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4185?size=60x60 Nl Eleni
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Blob converter_nanopublications

Created: 2015-04-03 21:08:40

Credits: User Eleni Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

this script is part of the nanopublication workflow from pack http://www.myexperiment.org/packs/486.html

File type: application/x-ruby

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4185?size=60x60 Nl Eleni
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Blob create nanopublications

Created: 2015-04-03 21:05:56

Credits: User Eleni Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This ruby script creates nanopublications for the results of the prioritized gene list from pack : http://www.myexperiment.org/packs/486.html 

File type: application/x-ruby

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1217?size=60x60 Gb Alan Williams
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Blob Multiple selection

Created: 2015-03-31 11:23:55 | Last updated: 2015-03-31 11:37:25

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

An interaction page that allows multiple selections from a list of values.There is a single input port of depth one called selectionValuesThere is a single output port of depth one called answers

File type: htm

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Avatar Richard Marchese Robinson
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Blob myExperiment.test

Created: 2015-03-20 19:45:13 | Last updated: 2015-03-20 20:15:02

Credits: User Richard Marchese Robinson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This has no value other than allowing me to test myExperiment.org functionality!

File type: ZIP archive

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4280?size=60x60 Gb HARESCHANDRA JAYANETHTHI
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Blob A Preliminary Study of Ichthyofauna of Kukulugala Fo...

Created: 2015-03-04 15:02:07 | Last updated: 2015-03-04 15:03:52

Credits: User HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

the report discuss about Ichthyofauna diversity of Kukulugala rain forest patch 

File type: Adobe PDF

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4280?size=60x60 Gb HARESCHANDRA JAYANETHTHI
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Blob A new record of endangered Jonklaas Loach Lepidoceph...

Created: 2015-03-04 14:57:16

Credits: User HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Loaches are small fishes that adapted for bottom dwelling life. The bodies are sub-cylindrical with flattened ventral  aspect. They all belong to family Cobitidae of super family Cobitoidea (Loaches) under the Order Cypriniformes. They  have a sub-orbital spine on their cheeks below the eyes. The body is covered with minute cycloid scales and they possess three or more pairs of short barbels (Nelson, 1976). They do not have air bladder as they always settle ...

File type: Adobe PDF

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4280?size=60x60 Gb HARESCHANDRA JAYANETHTHI
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Blob SOME OBSERVATIONS OF Cnemaspis podihuna DERANIYAGALA...

Created: 2015-03-04 14:50:51

Credits: User HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The dwarf day gecko Cnemaspis podihuna is the smallest gecko recorded in Sri Lanka, and it is considered endemic to the island. According to the IUCN (International Union for Conservation of Nature) Red List it is an endangered species. This small gecko has been previously recorded from fourteen areas of dry mixed forest and wet forest.here we record this species from new localities: Buddhangala, Geelone, Malayadikanda, and Nilgala. The information avai...

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4280?size=60x60 Gb HARESCHANDRA JAYANETHTHI
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Blob SOME OBSERVATIONS OF NESTING BEHAVIOR OF RUFOUS-BELL...

Created: 2015-03-04 14:47:35

Credits: User HARESCHANDRA JAYANETHTHI

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This eagle’s nest building was observed while the author was walking halfway through the mountain passing a Dothaluya tea plantation at around 9 in the morningThe rufous-bellied eagle’s characteristic behaviour was observed at Sabaragamuwa Province in Gamthuna village in Kegalla District. Located close to Kegalle City limits, the village consists of three sub-villages. Udugama is the village at the highest point, in the middle is Medagama an...

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3791?size=60x60 Gb David De Roure
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Blob The Future of Scholarly Communications UKSG proofed ...

Created: 2014-11-06 00:16:53

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The publisher's fulltext PDF is the final version of the paper. This is the Word version of the proof after revision, on which the published version was based, updated to include the figure and final page numbers.  

File type: Word 2007 document

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3791?size=60x60 Gb David De Roure
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Blob Four quadrant diagram

Created: 2014-11-05 23:58:21 | Last updated: 2014-11-06 00:37:54

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Powerpoint file for Figure 1.  This figure is based on an earlier diagram by Dave Robertson of University of Edinburgh which appeared in the EPSRC grant proposal EP/J017728/1 SOCIAM: The Theory and Practice of Social Machines

File type: PowerPoint 2007 presentation

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3791?size=60x60 Gb David De Roure
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Blob The Future of Scholarly Communications UKSG fulltext...

Created: 2014-11-05 23:50:39 | Last updated: 2014-11-05 23:59:51

Credits: User David De Roure

License: Creative Commons Attribution-Share Alike 3.0 Unported License

De Roure, D, The future of scholarly communications, Insights, 2014, 27(3), 233–238; DOI: http://dx.doi.org/10.1629/2048-7754.171 Please acknowledge Insights: the UKSG journal as the place of first publication. 

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4260?size=60x60 Ua Igor Lutsenko
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Blob Deploed model of extremal system operation for solvi...

Created: 2014-10-27 21:01:16 | Last updated: 2015-05-13 05:46:35

Credits: User Igor Lutsenko

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The reduced, simplified registration mathematical model of the system operation, obtained by scaling the registration signals of the basic model and determining the sum of the reduced, integrated flow rates by the input and output of the system under study was constructed. The studies of this traditional, for today model have shown the problem, associated with the existing approach in operations identification. As a result of using the agent model and system approach, it was found that regist...

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30?size=60x60 Nl Marco Roos
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Blob Concept Profile of phenotype Chorea

Created: 2014-10-20 08:34:10

Credits: User Marco Roos Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concept Profile generated from HPO term 'Chorea' via mapping to the corresponding UMLS phenotype concept.The profile contains ranked associations with Chorea conform mutual information content derived from co-occurrence in MedLine abstracts.Versions:HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings of the ISMB’2014 SIG meeting “BioLINK.” Retrieved from http://phenoday2014.bio-lark.org/pdf/...

File type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

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30?size=60x60 Nl Marco Roos
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Blob HTT-HPO concept profile match result

Created: 2014-10-20 08:26:32 | Last updated: 2014-10-20 08:35:28

Credits: User Marco Roos User Rajireturn Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example Concept Profile of the Human Phenotype named 'Chorea' also referred to by as Human Phenotype Ontology concept HP_0002072.This file contains a list of concepts from the Human Phenotype Ontology, ranked according to Concept Profile Matching with the profile of huntingtin, the protein whose aberrant form is the cause of Huntington's Disease.Versions:HPO-UMLS mapping: Winnenburg, R., & Bodenreider, O. (2014). Coverage of Phenotypes in Standard Terminologies. In Proceedings...

File type: Excel workbook

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1217?size=60x60 Gb Alan Williams
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Blob XPath service

Created: 2014-10-03 15:36:07

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use the XPath service in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob WoRMS and OBIS services

Created: 2014-10-03 15:35:11

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use WoRMS and OBIS services in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Working with BioVeL Portal

Created: 2014-10-03 15:34:08

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to work with the BioVeL portal

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Using R in Taverna

Created: 2014-10-03 15:33:06

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use R in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Tool service

Created: 2014-10-03 15:32:14

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a description of how to use the tool service in Taverna

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Using BiodiversityCatalogue

Created: 2014-10-03 15:31:21

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to use BiodiversityCatalogue

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Taverna introduction

Created: 2014-10-03 15:29:44

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation introducing Taverna

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1217?size=60x60 Gb Alan Williams
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Blob Simple workflow

Created: 2014-10-03 15:28:51

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about creating a simple workflow in Taverna

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1217?size=60x60 Gb Alan Williams
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Blob Nested workflows

Created: 2014-10-03 15:27:58

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about nested workflows within Taverna

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1217?size=60x60 Gb Alan Williams
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Blob Introduction to myGrid

Created: 2014-10-03 15:27:06

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation introducing myGrid

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1217?size=60x60 Gb Alan Williams
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Blob Installing Taverna

Created: 2014-10-03 15:26:12

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to install Taverna

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1217?size=60x60 Gb Alan Williams
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Blob Inputting data

Created: 2014-10-03 15:25:25

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to input data into Taverna workbench

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1217?size=60x60 Gb Alan Williams
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Blob help

Created: 2014-10-03 15:24:36

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing help information for Taverna Biodiversity

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1217?size=60x60 Gb Alan Williams
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Blob Embedding workflows in your website

Created: 2014-10-03 15:23:49

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about how to embed the running of workflows in your website, and examples.

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Components

Created: 2014-10-03 15:22:22

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation about Taverna components

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1217?size=60x60 Gb Alan Williams
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Blob Checking Taverna installation

Created: 2014-10-03 15:21:35

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to check your Taverna installation

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob Advanced Taverna

Created: 2014-10-03 15:20:26

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file that contains a presentation about Advanced Taverna features

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1217?size=60x60 Gb Alan Williams
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Blob forester_1037.jar

Created: 2014-10-03 11:27:41 | Last updated: 2014-10-03 12:33:14

License: GNU Lesser General Public License (LGPL) 2.1

forester is a collection of open source libraries of Java software for phylogenomics and evolutionary biology research. For example, the tree viewer Archaeopteryx is based on forester. The forester website is at https://sites.google.com/site/cmzmasek/home/software/foresterThe current developer version is available through Google code at: http://code.google.com/p/forester/Author: Christian Zmasek, Sanford-Burnham Medical Research Instituteforester is Cop...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob TRE file

Created: 2014-09-30 09:34:51

Credits: User Antonio Velez-Espino User Andres Araujo

Attributions: Workflow Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the time series of terminal run equivalents (TREs) of all ER indicator stocks.

File type: text/csv

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob TRE HR file

Created: 2014-09-30 09:32:41

Credits: User Antonio Velez-Espino User Andres Araujo

Attributions: Workflow Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the time series of terminal run equivalent (TRE) ocean harvest rates of ER indicator stocks.

File type: text/csv

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Term run file

Created: 2014-09-30 09:29:57 | Last updated: 2014-09-30 09:30:11

Credits: User Antonio Velez-Espino User Andres Araujo

Attributions: Workflow Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the time series of terminal run for each of the ER indicator stocks.

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Blob ER_Indicators file

Created: 2014-09-30 09:27:47

Credits: User Antonio Velez-Espino User Andres Araujo

Attributions: Workflow Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file shows the exploitation rate (ER) indicator stocks used to represent exploitation-rate time series with terminal-run time series of Chinook salmon aggregates.

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Blob Killer whale demography documentation

Created: 2014-09-26 12:19:25

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Andres Araujo User Jon Giddy User Francisco Quevedo

Attributions: Workflow Killer whale demography

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation contains the tutorial to run the Killer whale demography workflows. This tutorial explains the type of input data needed to run the workflow. The corresponding analysis use data from two distinct O. orca populations in Canada, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW). The Killer whale demography workflow performs the following analyses: •      Vital rates estimation and probability dis...

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Blob Resident killer whale-chinook salmon interactions an...

Created: 2014-09-26 12:09:28 | Last updated: 2014-09-26 12:11:12

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Andres Araujo User Jon Giddy User Francisco Quevedo

Attributions: Workflow Exploration of fishing scenarios Workflow Resident killer whale-chinook salmon interactions

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation contains the tutorial to run two related workflows. 1.    Resident killer whale-chinook salmon interactions workflow The Resident killer whale-chinook salmon interactions workflow provides an environment to create calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences in demographic rates be...

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4144?size=60x60 De Alexey Mints
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Blob FITS header printer

Created: 2014-09-23 15:01:02 | Last updated: 2014-11-27 08:26:31

Credits: User Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

usage: fitsheader.py [-h] [-f FILENAME] [-k KEYS] [-t TABLE] [--history]                     [--comments] [--data] [-o]optional arguments:  -h, --help            show this help message and exit  -f FILENAME, --filename FILENAME                        File to use  -k KEYS, --keys KEYS  Header keys to use (mask can be given)  -...

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Blob Sensitivity of resident killer whale population dyna...

Created: 2014-09-11 09:11:46 | Last updated: 2014-09-11 09:12:49

Credits: User Antonio Velez-Espino User Andres Araujo

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Sensitivity of resident killer whale population dynamics to Chinook salmon abundance.L. Antonio Vélez-Espino1,£, John K.B. Ford2, Charles K. Parken1, Graeme Ellis2, Eric Ward3, Larrie LaVoy4, Ken Balcomb5, M. Bradley Hanson3, Dawn P. Noren3, Tom Cooney4, Rishi Sharma6,7.(1) Salmon and Freshwater Ecosystems Division, Fisheries and Oceans Canada; (2) Marine Mammal Division, Fisheries and Oceans Canada; (3) Conservation Biology Division, Northwest Fisheries Science Center (NOAA); (4...

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Blob Comparative Demography and Viability of Northeastern...

Created: 2014-09-11 09:03:19

Credits: User Antonio Velez-Espino User Andres Araujo

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Comparative Demography and Viability of Northeastern Pacific Resident Killer Whale Populations at Risk.L.A. Vélez-Espino, J.K.B. Ford, H.A. Araujo, G. Ellis, C.K. Parken, and K.C. BalcombFisheries and Oceans CanadaScience Branch, Pacific RegionPacific Biological StationNanaimo, BCV9T 6N72014Canadian Technical Report ofFisheries and Aquatic Sciences 3084 Two distinct populations of resident killer whales (Orcinus orca) in the northeastern Pacific Ocean have been identified in Canad...

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Blob OWL Ontology Survey Data

Created: 2014-09-06 15:16:41 | Last updated: 2014-09-12 17:57:10

Credits: User Azlinayati

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the survey data for OWL Ontology on the Web survey.

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Blob Bonn 2014 Help links

Created: 2014-09-03 08:19:52 | Last updated: 2014-09-03 08:20:20

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Many useful links accurate Sept 2014

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Blob Bonn 2014 Example Fasta Ids Mac Format

Created: 2014-09-02 08:02:51

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Fasta files in MAC format. 

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Blob Bonn 2014 Fasta Example Values UNIX format

Created: 2014-09-02 07:57:46

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Fasta Example IDs in UNIX Format

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9?size=60x60 Gb Stian Soiland-Reyes
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Blob Bonn 2014 Agenda

Created: 2014-09-01 09:08:17 | Last updated: 2014-09-03 08:10:40

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Agenda Bonn “in silico experimentation” course 2014-09-01 / 2014-09-03Please sign up and join the myExperiment group: Bonn Workshop Sep 2014For each tutorial and presentation, there is an accompanying slideset in this group. For your convenience, this Agenda PDF has links to each of these as [T-xxx.pdf].  

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Blob Elasticity and Sensitivity of the Vital rates docume...

Created: 2014-08-29 14:49:44 | Last updated: 2014-08-29 14:50:15

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Elasticity and Sensitivity of the Vital rates

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow calculates the Elasticity and Sensitivity of population growth rate with respect to various vital rates. The goal in both cases is to determine which vital rate(s) has/have the most influence on population growth rate (λ).Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses.The sensitivity matrix: The sensitivity desc...

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Blob Orcinus orca (Killer whale) demography and populatio...

Created: 2014-08-29 12:21:35 | Last updated: 2014-08-29 16:23:18

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Jon Giddy

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name Normal 0 false false false EN-US X-NONE X-NONE ...

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Blob ChinookAbundance_FI_R file

Created: 2014-08-29 12:08:37

Credits: User Antonio Velez-Espino

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table showing the time series of Fishery Impacts of all stocks by time lag used in the analysis.

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Blob ChinookAbundance_Data_R file

Created: 2014-08-29 12:04:46 | Last updated: 2014-08-29 16:24:00

Credits: User Antonio Velez-Espino

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Table showing the time series of abundance (TR or OA) of all stocks and stock aggregates by time lag used in the analysis.

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Blob Chinook_Ab_Defs_FI_R file

Created: 2014-08-29 11:55:36

Credits: User Antonio Velez-Espino

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table used to define fishery impacts (FI) on Chinook abundance by stock aggregate, time lag (5YA: 5-year running average), and hypothesis (SR: Southern Resident Killer Whale; NR: Northern Resident Killer Whale) and abundance ID. FI represent ocean catch of specific Chinook stocks or stock aggregates. See below information about hypothesis.

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Blob Chinook_Ab_Definitions_R file

Created: 2014-08-29 11:53:56

Credits: User Antonio Velez-Espino

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table that contains Chinook abundance definitions by stock aggregate, abundance type (TR: Terminal Run; OA: Ocean Abundance), time lag (5YA: 5-year running average), and hypothesis (SR: Southern Resident Killer Whale; NR: Northern Resident Killer Whale) and abundance ID. See below information about hypothesis.

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Blob Vital Rates_combined

Created: 2014-08-29 11:51:09

Credits: User Antonio Velez-Espino

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

The stage-structured life cycle of resident killer whales with seven life stages:(1) calves; (Calf)(2) juveniles; (Juv)(3) young reproductive females; (F1)(4) old reproductive females; (F2)(5) post-reproductive females; (F3)(6) young mature males; and (M1)(7) old mature males (M2).Fi represent fertility; Gi represent stage transition probabilities, with female and male juvenile-to-adult transitions indicated as G2f and G2m, respectively; and, Pi represent the probability of surviving and rema...

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Blob Northern Resident Killer Whale (NRKW) demographic data

Created: 2014-08-29 11:46:14 | Last updated: 2014-08-29 16:25:25

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Northern Resident Killer Whale (NRKW) demographic data.The input data (a .csv-file) has to have the format of a table containing the Orcinus orca demographic data with the columns named: Year, Age, Count, Offspring and Cat1. Each year, the number of individuals per age and the number of offspring per age reproductive female category are counted (females ≥ 10 years old). IF A Female category does not have offspring equals to 0. For the called column, Cat1; Ages 1 to 9 belongs to Juv (Juveni...

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Blob Southern Resident Killer Whale (SRKW) demographic data

Created: 2014-08-29 11:43:47

Credits: User Antonio Velez-Espino

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License: Creative Commons Attribution-Share Alike 3.0 Unported License

Southern Resident Killer Whale (SRKW) demographic dataThe input data (a .csv-file) has to have the format of a table containing the Orcinus orca demographic data with the columns named: Year, Age, Count, Offspring and Cat1. Each year, the number of individuals per age and the number of offspring per age reproductive female category are counted (females ≥ 10 years old). IF A Female category does not have offspring equals to 0. For the called column, Cat1; Ages 1 to 9 belongs to Juv (Juvenil...

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Blob Example Fasta Ids CVS

Created: 2014-08-29 10:44:20

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a small csv file which has Fasta IDs in Column B rows 2 to 6

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Blob Variance matrix documentation

Created: 2014-08-28 13:53:09

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Variance matrix

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates the variance matrix from a list of matrices.

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Blob Calculate and Plot abundance over the years document...

Created: 2014-08-28 13:17:28

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Calculate and Plot abundance over the years

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow calculate and plot the survival based on two or more years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population.

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Blob Decomposed matrix of Gentiana pneumonanthe

Created: 2014-08-28 11:28:44

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file (decomposed matrix) is used in the documentation as example to run the Elsticity and Sensitivity of the Vital rates Workflow.

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Blob Bonn 2014 Example Fasta Ids Windows Format

Created: 2014-08-27 13:43:56 | Last updated: 2014-09-02 07:59:09

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a small list of Fasta IDs for testing workflows and tutorials.  

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Blob Demographic data Gentiana pneumonanthe 1987-1993

Created: 2014-08-22 12:01:38

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Calculate and Plot abundance over the years (http://www.myexperiment.org/packs/664.html)This table containing the demographic data on a series of individuals during 7 years, from 1987 to 1993 (6 periods: 1987-1988, 1988-1989 etc....

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Blob Log-log plots of variance vs. sensitivity and CV vs....

Created: 2014-08-21 09:16:10

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow creates log-log plots of both variance vs. sensitivity and CV vs. elasticity in matrix elements. Plots are based on Figure 2 in Pfister (1998).

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Blob Life Table Response Experiments Fixed design year ef...

Created: 2014-08-21 08:05:38

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Life Table Response Experiment year effect for multiple places

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Life Table Response Experiments Year Effect for Multiple Places workflow provides an environment to analyse two or more matrices (e.g., two or more matrices of different years from one place) at two or more different locations. The objective of this workflow is to determine the effects of the research years (2 or more) on λ. This workflow performs a fixed LTRE, o...

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Blob southern md

Created: 2014-08-17 20:26:57

Credits: User Jamie Wittenberg

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movie of southern md

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Blob hobie

Created: 2014-08-17 20:26:30

Credits: User Jamie Wittenberg

License: Creative Commons Attribution-Share Alike 3.0 Unported License

picture of hobie

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Blob Mean matrix documentation

Created: 2014-08-14 17:52:17 | Last updated: 2014-08-28 13:50:22

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Mean matrix

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates the mean matrix from a list of matrices.

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Blob Calculate the quasi-extinction probability documenta...

Created: 2014-08-14 12:05:06

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Calculate quasi-extinction threshold.

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates by simulation the quasi-extinction probability time cumulative distribution function for a structured population in an independently and identically distributed (iid) stochastic environment. This workflow is based on the popbio package (stoch.quasi.ext - Calculate quasi-extinction threshold, Stubben, Milligan and Nantel, 2013) based on the MATLAB cod...

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Blob Life Table Response Experiments Fixed design years e...

Created: 2014-08-14 08:44:30 | Last updated: 2014-08-14 08:45:27

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Life Table Response Experiment Year Effect in One Location or Place

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Life Table Response Experiments Effect of Years in One Place workflow provides an environment to analyse two or more matrices from different years in one location. The objective of this workflow is to determine the effects of the research years (2 or more) in one place on λ. This workflow performs a fixed LTRE, one way design (Caswell 2001).LTRE is a retrospectiv...

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Blob Life Table Response Experiments Fixed design Place e...

Created: 2014-08-14 08:03:58

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Life Table Response Experiment fixed design Place Effect

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Life Table Response Experiments place effect workflow provides an environment to analyse one or more matrices (e.g. matrices of different years from the same place) from two or more places. The objective of this workflow is to determine the effects of the research places or localities (2 or more) on λ. This workflow performs a fixed LTRE, one way design (Caswell ...

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3899?size=60x60 Se Sarah Bourlat
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Blob usability test file Sarah

Created: 2014-08-07 09:51:23 | Last updated: 2014-08-07 09:53:17

Credits: User Sarah Bourlat User Rekha Maryanne Louis

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

usability trial

File type: PowerPoint 2007 presentation

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4196?size=60x60 Biodiversity eLaboratory
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Blob Alexandrium minutum potential distribution in the Ba...

Created: 2014-08-04 15:24:08 | Last updated: 2015-02-16 11:52:32

Credits: User Biomobst User Sarah Bourlat

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The potential distribution  of Alexandrium minutum in the Baltic Sea

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Blob Alexandrium minutum potential distribution

Created: 2014-08-04 15:21:24 | Last updated: 2015-02-16 11:53:00

Credits: User Biomobst User Sarah Bourlat

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The potential distribution of Alexandrium minutum

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Blob Fucus vesiculosus current and 2050 difference

Created: 2014-08-04 11:35:16

Credits: User Sonja Leidenberger

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This PNG gives a low resolution image for the difference between the current and predicted 2050 niches for Fucus vesiculosus

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Blob Fucus vesiculosus 2050 distribution

Created: 2014-08-04 11:33:48 | Last updated: 2014-08-04 13:04:48

Credits: User Sonja Leidenberger

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This PNG gives a low resolution image of the niche predicted for Fucus vesiculosus in 2050

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Blob Fucus vesiculosus current distribution

Created: 2014-08-04 11:31:25 | Last updated: 2015-02-16 10:07:57

Credits: User Sonja Leidenberger

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This PNG gives a low-resolution picture of the predicted current niche of Fucus vesilosus

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Blob Fucus vesiculosus occurrences from GBIF

Created: 2014-08-04 11:24:58

Credits: User Sonja Leidenberger

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This spreadsheet indicates the source of occurrences of Fucus vesiculosus retrieved from GBIF.

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Blob Simulate stochastic growth from a sequence of matric...

Created: 2014-07-30 13:47:47

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Francisco Quevedo User Mikolaj Krzyzanowski User Gerard Oostermeijer

Attributions: Workflow Simulate stochastic growth from a sequence of matrices

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices.Outputs:Equal selection dataStochastic projectionUnequal selection dataTo know more detail...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Stage vectors, Survival and Growth rate curves (demo...

Created: 2014-07-25 12:41:06

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Stages vectors plots, Survival and Growth rate curves

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:Population projectionSurvival values calculations per stage per year and its respective plot;Growth rates (lambda) calculations per year and its respective plot;Stage Vectors calculations and their respective plots.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Transient dynamics documentation

Created: 2014-07-25 12:16:46

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

Attributions: Workflow Transient Dynamics.

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Transient dynamics or Calculate population growth rates by projection Workflow provides an environment to calculates the population growth rate and stable stage distribution by repeated projections of the equation n(t+1)=An(t) and to produce plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.Transient dynamic ana...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Net reproductive rate (Ro) documentation

Created: 2014-07-25 11:25:19

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Net reproductive rate (Ro)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Net reproductive rate (Ro) Workflow provides an environment to calculate the net reproductive rate (Ro). Ro is the mean number of offspring by which a new-born individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Generation Time (T) documentation

Created: 2014-07-25 11:22:18

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Generation time (T)

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Generation Time (T) Workflow provides an environment to calculate the generation time. The generation time is the time T required for the population to increase by a factor of Ro (net reproductive rate). In other words, T calculates how much time takes to a plant/animal to replace itself by a factor of Ro.

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Eigen analysis documentation

Created: 2014-07-25 11:18:44

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Eigen analysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Eigen analysis workflow provides an environment for the analysis of a stage-matrix and perform several analyses on it.The Eigen analysis results are a set of demographic statistics:Lambda or dominant eigenvalue (λ).The stable stage distribution (w).The sensitivity matrixThe Elasticity matrix.Reproductive value (v).The damping ratio (ρ)

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Damping ratio documentation

Created: 2014-07-25 11:07:01

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Damping ratio

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.The Damping ratio Workflow provides an environment to calculate the damping ratio of several matrices and plot them.The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the populati...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Matrix population models construction documentation

Created: 2014-07-25 11:02:01

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run a workflow) explains how to run a workflow that beolngs to the pack with the same name.The Creation of a stage matrix model Workflow provides an environment to construct a stage matrix model. This workflow create a stage matrix based on two years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population. The resulting is a stage matrix model.

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