USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5
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Transcript of USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 5
Using e-Infrastructures for Biodiversity Conservation
Gianpaolo Coro ISTI-CNR, Pisa, Italy
Module 5 - Outline
1. Aims and methods of the i-Marine e-Infrastructure
2. Community oriented applications
3. Data analytics
4. Tabular Data Manager
1. Aims and methods of the i-Marine e-Infrastructure
2. Community oriented applications
3. Data analytics
4. Tabular Data Manager
Supply a scientific network of • Models• Approaches• Computational facilities
To scientists that have limited access to hardware and software for data analytics
“It worked very well at the WKLIFE IV workshop and is likely to be used by ICES.”, Rainer Froese, senior scientist at the Helmholtz Center for Ocean Research, Kiel Germany.
“When looking at the performance maps […], CMSY was the most frequent best performer.”,FAO Report on Stock Assessment and Global Productivity in Fisheries, 2014
CMSY is available in iMarine on the Statistical Manager service
Given the catch statistics and (optionally) the biomass or CPUE history of a stock, CMSY estimates:
• Maximum Sustainable Yield
• Exploitation Rate• Current Biomass• Resilience• Productivity
Bayesian Catch-Maximum Sustainable Yield (CMSY), Froese & Coro 2014
herring
estimated resilience r
and productivity k
Usages:• Harvesting Control Rules (HCR)• Total Allowable Catch (TAC)• Health status monitoring• Stock Assessment
Training with iMarine
• Collecting and curating data for the Giant squid
• Producing maps using different Bayesian approaches and environmental features from iMarine
• Importing maps from reference literature approaches
• Comparing the results
1. Aims and methods of the i-Marine e-Infrastructure
2. Community oriented applications
3. Data analytics
4. Tabular Data Manager
Statistical Manager• Processes data using statistical
models• Integrates models from
communities• Hides algorithms complexity• Automatically generates the
interface• Uses Cloud computing
StatisticalManager
D4ScienceComputational
FacilitiesSharing
Setup and execution
Fisheries
CMSY: estimates Maximum Sustainable Yield from catch statistics LWR: transforms fish length into weight
CatchSeriesAnalysis: estimates the effect of piracy on catch trends
VTI: classifies vessels activities and estimates effort per 0.5 deg areas
Biodiversity
Plankton regime shift
Herring recovered after the fish ban
AquaMaps and ANN: calculates the potential and actual niche of a species
Clustering: detects common and rare species in marine areas
Trendylyzer: detects ecosystem changes and their effect on species trends
BiOnym: a flexible and powerful search engine in large taxonomic trees
Environment
MaxEntropy: finds the correlation between one phenomenon and N environmental variables
OccurrenceEnrichment: enriches presence points with environmental data
Rasterization: transforms vectorial datasets into raster datasets
XYZT - DataExtraction: extracts environmental data with uniform geographic projection
X
Open Platform Approach
External Computing
Facility
OGC WPS
Interface
People can contribute with:
• R scripts• Java programs• Linux programs• OGC-WPS services
Numbers
FishBase (US, CA, TW)GeomarNaturhistoriska riksmuseet: StartsidaAgrocampusAnonymous Individ-ualsINRAKing Abdullah Uni-versity of Science and TechnologyISTI
Users
2013 2014Avg Users per month 200 20100
Number of Algorithms 50 100
Number of contributing Organizations providing algorithms
2 CNR,
Geomar
7CNR,
Geomar,FIN,FAO,T2,IRD,
AgrocampusPublications 8 13Sum Impact
Factor 2.66 12.17
Statistical Manager related Wiki links:
Descriptions:http://gcube.wiki.gcube-system.org/gcube/index.php/Statistical_Manager
http://gcube.wiki.gcube-system.org/gcube/index.php/Statistical_Manager_Algorithms
Tutorials:http://gcube.wiki.gcube-system.org/gcube/index.php/Statistical_Manager_Tutorial
http://gcube.wiki.gcube-system.org/gcube/index.php/How_to_Interact_with_the_Statistical_Manager_by_client
http://gcube.wiki.gcube-system.org/gcube/index.php/How-to_Implement_Algorithms_for_the_Statistical_Manager
Experiments:http://wiki.i-marine.eu/index.php/MaxEnt
http://wiki.i-marine.eu/index.php/IOTC_Area_Predictive_analysis
http://wiki.i-marine.eu/index.php/ICES_SGVMS
1. Aims and methods of the i-Marine e-Infrastructure
2. Community oriented applications
3. Data analytics
4. Tabular Data Manager
Data Analytics
1. Prepare data 2. Analyse data
3. Recommend actions to decision makers
From several tools to One Online Platform
1. Aims and methods of the i-Marine e-Infrastructure
2. Community oriented applications
3. Data analytics
4. Tabular Data Manager
Tabular Data Manager
• Manipulates Big Tabular Datasets
• Prepares data for Analyses
• Makes data compliant with external Code Lists
• Visualizes, represents and inspects data
Advanced Processing1- TabMan imports datasets with tuna catch statistics
Yellowfin Skipjack
Advanced Processing2- Allows modifying columns
Advanced Processing3- Allows curating columns
b. Column splitting using regular expressions
c. Changing columns typesand Codelists compliancy
e. Denormalization:one column per row value
a. Duplicates deletion
d. Produce a new codelist
Advanced Processing4- Adding Geometries
Advanced Processing5- …and Csquare codes and FAO Ocean Areas codes
Advanced Processing6- Datasets can become interactive GIS maps published under standard formats
(WMS, WFS, WCS)
Advanced Processing7- Catch can be forecasted and analysed using an online R development environment
Advanced Processing8- Charts and analytics help discovering indicators
Online experiment: Tabular Data Manager
https://i-marine.d4science.org/group/tabulardatalab