DataMiner Algorithms

The complete list of algorithms supported by the DataMiner service is reported below.

ENSEMBLE_MODEL
Description	Implementation of an ensemble model approach to support advice and management in fisheries. Implementation on Thorpe et al. (2015). Evaluation and management implications of uncertainty in a multispecies size structured model of population and community responses to fishing. Methods in Ecology and Evolution, 6(1), 49-58.
SAMPLEONTABLE
Description	Algorithm that allows to perform a sample operation on a table
POINTS_TO_MAP
Description	A transducer algorithm to produce a GIS map of points from a set of points with x,y coordinates indications. A maximum of 259000 is allowed
SMARTSAMPLEONTABLE
Description	Algorithm that allows to perform a smart sample operation on a table
TIMEEXTRACTION
Description	An algorithm to extract a time series of values associated to a geospatial features repository (e.g. NETCDF, ASC, GeoTiff files etc. ). The algorithm analyses the time series and automatically searches for hidden periodicities. It produces one chart of the time series, one table containing the time series values and possibly the spectrogram.
HCAF_FILTER
Description	An algorithm producing a HCAF table on a selected Bounding Box (default identifies Indonesia)
FAO_OCEAN_AREA_COLUMN_CREATOR
Description	An algorithm that adds a column containing the FAO Ocean Area codes associated to longitude and latitude columns.
MOST_OBSERVED_TAXA
Description	An algorithm producing a bar chart for the most observed taxa in a certain years range (with respect to the OBIS database)
DBSCAN
Description	A clustering algorithm for real valued vectors that relies on the density-based spatial clustering of applications with noise (DBSCAN) algorithm. A maximum of 4000 points is allowed.
FIGIS_SDMX_DATA_CONVERTER
Description	This tool allows to convert easily a SDMX dataset into CSV, by callingthe rsdmx package for R
HCAF_INTERPOLATION
Description	Evaluates the climatic changes impact on species presence
ZEXTRACTION
Description	An algorithm to extract the Z values from a geospatial features repository (e.g. NETCDF, ASC, GeoTiff files etc. ). The algorithm analyses the repository and automatically extracts the Z values according to the resolution wanted by the user. It produces one chart of the Z values and one table containing the values.
FAO_OCEAN_AREA_COLUMN_CREATOR_FROM_QUADRANT
Description	An algorithm that adds a column containing the FAO Ocean Area codes associated to longitude, latitude and quadrant columns.
SGVM_INTERPOLATION
Description	An interpolation method relying on the implementation by the Study Group on VMS (SGVMS). The method uses two interpolation approached to simulate vessels points at a certain temporal resolution. The input is a file in TACSAT format uploaded on the Statistical Manager. The output is another TACSAT file containing interpolated points.The underlying R code has been extracted from the SGVM VMSTools framework. This algorithm comes after a feasibility study (http://goo.gl/risQre) which clarifies the features an e-Infrastructure adds to the original scripts. Limitation: the input will be processed up to 10000 vessels trajectory points. Credits: Hintzen, N. T., Bastardie, F., Beare, D., Piet, G. J., Ulrich, C., Deporte, N., Egekvist, J., et al. 2012. VMStools: Open-source software for the processing, analysis and visualisation of fisheries logbook and VMS data. Fisheries Research, 115-116: 31-43. Hintzen, N. T., Piet, G. J., and Brunel, T. 2010. Improved estimation of trawling tracks using cubic Hermite spline interpolation of position registration data. Fisheries Research, 101: 108-115. VMStools, available as an add-on package for R. Documentation available at https://code.google.com/p/vmstools/. Build versions of VMStools for Window, Mac, Linux available at https://docs.google.com/. Authors: Niels T. Hintzen, Doug Beare
AQUAMAPS_SUITABLE_2050
Description	Algorithm for Suitable 2050 Distribution by AquaMaps. A distribution algorithm that generates a table containing species distribution probabilities on half-degree cells according to the AquaMaps approach for suitable (potential) distributions for the 2050 scenario.
BIONYM_LOCAL
Description	A fast version of the algorithm implementing BiOnym, a flexible workflow approach to taxon name matching. The workflow allows to activate several taxa names matching algorithms and to get the list of possible transcriptions for a list of input raw species names with possible authorship indication.
SPECIES_OBSERVATION_MEOW_AREA_PER_YEAR
Description	Algorithm returning most observed species in a specific years range (data collected from OBIS database).
BIOCLIMATE_HCAF
Description	A transducer algorithm that generates an Half-degree Cells Authority File (HCAF) dataset for a certain time frame, with environmental parameters used by the AquaMaps approach. Evaluates the climatic changes impact on the variation of the ocean features contained in HCAF tables
MAPS_COMPARISON
Description	An algorithm for comparing two OGC/NetCDF maps in seamless way to the user. The algorithm assesses the similarities between two geospatial maps by comparing them in a point-to-point fashion. It accepts as input the two geospatial maps (via their UUIDs in the infrastructure spatial data repository - recoverable through the Geoexplorer portlet) and some parameters affecting the comparison such as the z-index, the time index, the comparison threshold. Note: in the case of WFS layers it makes comparisons on the last feature column.
ABSENCE_CELLS_FROM_AQUAMAPS
Description	An algorithm producing cells and features (HCAF) for a species containing absense points taken by an Aquamaps Distribution
DISCREPANCY_ANALYSIS
Description	An evaluator algorithm that compares two tables containing real valued vectors. It drives the comparison by relying on a geographical distance threshold and a threshold for K-Statistic.
PRESENCE_CELLS_GENERATION
Description	An algorithm producing cells and features (HCAF) for a species containing presence points
LWR
Description	An algorithm to estimate Length-Weight relationship parameters for marine species, using Bayesian methods. Runs an R procedure. Based on the Cube-law theory.
CMSY
Description	An algorithm to estimate the Maximum Sustainable Yield from a catch statistic. If also a Biomass trend is provided, MSY estimation is provided also with higher precision. The method has been developed by R. Froese, G. Coro, N. Demirel and K. Kleisner.
AQUAMAPS_NATIVE
Description	Algorithm for Native Distribution by AquaMaps. A distribution algorithm that generates a table containing species distribution probabilities on half-degree cells according to the AquaMaps approach for Native (Actual) distributions.
OCCURRENCES_MERGER
Description	A transducer algorithm that produces a duplicate-free table resulting from the union of two occurrence points tables where points equivalence is identified via user defined comparison thresholds. Works with up to 10000 points per table. Between two Ocurrence Sets, enrichs the Left Set with the elements of the Right Set that are not in the Left Set. Updates the elements of the Left Set with more recent elements in the Right Set. If one element in the Left Set corresponds to several recent elements in the Right Set, these will be all substituted to the element of the Left Set.
QUALITY_ANALYSIS
Description	An evaluator algorithm that assesses the effectiveness of a distribution model by computing the Receiver Operating Characteristics (ROC), the Area Under Curve (AUC) and the Accuracy of a model
BIONYM_BIODIV
Description	An algorithm implementing BiOnym oriented to Biodiversity Taxa Names Matching with a predefined and optimized workflow. This version applies in sequence the following Matchers: GSay (thr:0.6, maxRes:10), FuzzyMatcher (thr:0.6, maxRes:10), Levenshtein (thr:0.4, maxRes:10), Trigram (thr:0.4, maxRes:10). BiOnym is a flexible workflow approach to taxon name matching. The workflow allows to activate several taxa names matching algorithms and to get the list of possible transcriptions for a list of input raw species names with possible authorship indication.
LISTDBINFO
Description	Algorithm that allows to view information about one chosen resource of Database Type in the Infrastructure
EGIP_ENERGY_TRENDS
Description	An algorithm reporting the energy trends for the countries contributing to EGIP
LISTTABLES
Description	Algorithm that allows to view the table names of a chosen database
MOST_OBSERVED_SPECIES
Description	An algorithm producing a bar chart for the most observed species in a certain years range (with respect to the OBIS database)
RANDOMSAMPLEONTABLE
Description	Algorithm that allows to perform a sample operation on a table randomly
SPECIES_MAP_FROM_CSQUARES
Description	A transducer algorithm to produce a GIS map from a probability distribution associated to a set of csquare codes. A maximum of 259000 is allowed
AQUAMAPSNN
Description	The AquaMaps model trained using a Feed Forward Neural Network. This is a method to train a generic Feed Forward Artifical Neural Network to be used by the AquaMaps Neural Network algorithm. Produces a trained neural network in the form of a compiled file which can be used later.
BIOCLIMATE_HSPEC
Description	A transducer algorithm that generates a table containing an estimate of species distributions per half-degree cell (HSPEC) in time. Evaluates the climatic changes impact on species presence.
HSPEN
Description	The AquMaps HSPEN algorithm. A modeling algorithm that generates a table containing species envelops (HSPEN), i.e. models capturing species tolerance with respect to environmental parameters, to be used by the AquaMaps approach.
SPECIES_OBSERVATION_LME_AREA_PER_YEAR
Description	Algorithm returning most observed species in a specific years range (data collected from OBIS database).
FIGIS_SPATIAL_REALLOCATION_SIMPLIFIED
Description	The Spatial Reallocaton algorithm allows to estimate statistics for other areas from those where they were reported. The algorithm is based on spatial disaggregation technics and provides at now an area-weighted reallocation. This simplified algorithm is specifically targeting users from the FAO Fisheries and Aquaculture department, aims to facilitate its execution by doing abstraction of the intersections to provide.
OCCURRENCE_ENRICHMENT
Description	An algorithm performing occurrences enrichment. Takes as input one table containing occurrence points for a set of species and a list of environmental layer, taken either from the e-infrastructure GeoNetwork (through the GeoExplorer application) or from direct HTTP links. Produces one table reporting the set of environmental values associated to the occurrence points.
SPECIES_OBSERVATIONS_PER_AREA
Description	An algorithm producing a bar chart for the distribution of a species along a certain type of marine area (e.g. LME or MEOW)
OCCURRENCES_SUBTRACTION
Description	A transducer algorithm that produces a table resulting from the difference between two occurrence points tables where points equivalence is identified via user defined comparison thresholds. Works with up to 10000 points per table. Between two Ocurrence Sets, keeps the elements of the Left Set that are not similar to any element in the Right Set.
OCCURRENCES_DUPLICATES_DELETER
Description	A transducer algorithm that produces a duplicate free table of species occurrence points where duplicates have been identified via user defined comparison thresholds. Works with up to 100 000 points
SPECIES_MAP_FROM_POINTS
Description	A transducer algorithm to produce a GIS map from a probability distribution made upf of x,y coordinates and a certain resolution. A maximum of 259000 is allowed
GENERIC_CHARTS
Description	An algorithm producing generic charts of attributes vs. quantities. Charts are displayed per quantity column. Histograms, Scattering and Radar charts are produced for the top ten quantities. A gaussian distribution reports overall statistics for the quantities.
EGIP_ENERGY_YEAR_DISTRIBUTION
Description	An algorithm reporting the energy produced per year by the countries contributing to EGIP
XYEXTRACTOR
Description	An algorithm to extract values associated to an environmental feature repository (e.g. NETCDF, ASC, GeoTiff files etc. ). A grid of points at a certain resolution is specified by the user and values are associated to the points from the environmental repository. It accepts as one geospatial repository ID (via their UUIDs in the infrastructure spatial data repository - recoverable through the Geoexplorer portlet) or a direct link to a file and the specification about time and space. The algorithm produces one table containing the values associated to the selected bounding box.
FAOMSY
Description	An algorithm to be used by Fisheries managers for stock assessment. Estimates the Maximum Sustainable Yield (MSY) of a stock, based on a catch trend. The algorithm has been developed by the Resource Use and Conservation Division of the FAO Fisheries and Aquaculture Department (contact: Yimin Ye, yimin.ye@fao.org). It is applicable to a CSV file containing metadata and catch statistics for a set of marine species and produces MSY estimates for each species. The CSV must follow a FAO-defined format (e.g. http://goo.gl/g6YtVx). The output is made up of two (optional) files: one for sucessfully processed species and another one for species that could not be processed because data were not sufficient to estimate MSY.
GRID_CWP_TO_COORDINATES
Description	An algorithm that adds longitude, latitude and resolution columns analysing a column containing FAO Ocean Area codes (CWP format).
ZEXTRACTION_TABLE
Description	An algorithm to extract a time series of values associated to a table containing geospatial information. The algorithm analyses the time series and automatically searches for hidden periodicities. It produces one chart of the time series, one table containing the time series values and possibly the spectrogram.
SUBMITQUERY
Description	Algorithm that allows to submit a query
CSQUARES_TO_COORDINATES
Description	An algorithm that adds longitude, latitude and resolution columns analysing a column containing c-square codes.
GEO_CHART
Description	An algorithm producing a charts that displays quantities as colors of countries. The color indicates the sum of the values recorded in a country.
OCCURRENCES_MARINE_TERRESTRIAL
Description	A transducer algorithm that produces a table containing occurrence points by filtering them by type of area, i.e. by recognising whether they are marine or terrestrial. Works with up to 10000 points per table.
SPECIES_OBSERVATIONS_TREND_PER_YEAR
Description	An algorithm producing the trend of the observations for a certain species in a certain years range.
BIOCLIMATE_HSPEN
Description	A transducer algorithm that generates a table containing species envelops (HSPEN) in time, i.e. models capturing species tolerance with respect to environmental parameters, used by the AquaMaps approach. Evaluates the climatic changes impact on the variation of the salinity values in several ranges of a set of species envelopes
EGIP_ENERGY_AGGREGATED_DISTRIBUTION
Description	An algorithm reporting the aggregated energy in a time range produced by the countries contributing to EGIP
CSQUARE_COLUMN_CREATOR
Description	An algorithm that adds a column containing the CSquare codes associated to longitude and latitude columns.
TIME_SERIES_CHARTS
Description	An algorithm producing time series charts of attributes vs. quantities. Charts are displayed per quantity column and superposing quantities are summed.
HRS
Description	An evaluator algorithm that calculates the Habitat Representativeness Score, i.e. an indicator of the assessment of whether a specific survey coverage or another environmental features dataset, contains data that are representative of all available habitat variable combinations in an area.
FIGIS_SPATIAL_REALLOCATION_GENERIC
Description	The Spatial Reallocaton algorithm allows to estimate statistics for other areas from those where they were reported. The algorithm is based on spatial disaggregation technics and provides at now an area-weighted reallocation.
EGIP_ENERGY_COUNTRY_DISTRIBUTION
Description	An algorithm reporting the energy produced by the countries contributing to EGIP
TIMEEXTRACTION_TABLE
Description	An algorithm to extract a time series of values associated to a table containing geospatial information. The algorithm analyses the time series and automatically searches for hidden periodicities. It produces one chart of the time series, one table containing the time series values and possibly the spectrogram.
TIME_SERIES_ANALYSIS
Description	An algorithms applying signal processing to a non uniform time series. A maximum of 10000 distinct points in time is allowed to be processed. The process uniformly samples the series, then extracts hidden periodicities and signal properties. The sampling period is the shortest time difference between two points. Finally, by using Caterpillar-SSA the algorithm forecasts the Time Series. The output shows the detected periodicity, the forecasted signal and the spectrogram.
STEP_3___VPA_ICCAT_BFT_E_PROJECTION
Description	STEP 3: ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
MAX_ENT_NICHE_MODELLING
Description	A Maximum-Entropy model for species habitat modeling, based on the implementation by Shapire et al. v 3.3.3k, Princeton University, http://www.cs.princeton.edu/schapire/maxent/. In this adaptation for the D4Science infrastructure, the software accepts a table produced by the Species Product Discovery service and a set of environmental layers in various formats (NetCDF, WFS, WCS, ASC, GeoTiff) via direct links or GeoExplorer UUIDs. The user can also establish the bounding box and the spatial resolution (in decimal deg.) of the training and the projection. The application will adapt the layers to that resolution if this is higher than the native one.The output contains: a thumbnail map of the projected model, the ROC curve, the Omission/Commission chart, a table containing the raw assigned values, a threshold to transform the table into a 0-1 probability distribution, a report of the importance of the used layers in the model, ASCII representations of the input layers to check their alignment.Other processes can be later applied to the raw values to produce a GIS map (e.g. the Statistical Manager Points-to-Map process) and results can be shared. Demo video: http://goo.gl/TYYnTO and instructions http://wiki.i-marine.eu/index.php/MaxEnt
BIONYM
Description	An algorithm implementing BiOnym, a flexible workflow approach to taxon name matching. The workflow allows to activate several taxa names matching algorithms and to get the list of possible transcriptions for a list of input raw species names with possible authorship indication.
TIME_GEO_CHART
Description	An algorithm producing an animated gif displaying quantities as colors in time. The color indicates the sum of the values recorded in a country.
AQUAMAPS_NATIVE_2050
Description	Algorithm for Native 2050 Distribution by AquaMaps. A distribution algorithm that generates a table containing species distribution probabilities on half-degree cells according to the AquaMaps approach with native distribution estimated for 2050.
ESRI_GRID_EXTRACTION
Description	An algorithm to extract values associated to an environmental feature repository (e.g. NETCDF, ASC, GeoTiff files etc. ). A grid of points at a certain resolution is specified by the user and values are associated to the points from the environmental repository. It accepts as one geospatial repository ID (via their UUIDs in the infrastructure spatial data repository - recoverable through the Geoexplorer portlet) or a direct link to a file and the specification about time and space. The algorithm produces one ESRI GRID ASCII file containing the values associated to the selected bounding box.
TUNA_ATLAS_INDICATOR_1__SPECIES_BY_OCEAN_
Description	This visualization shows a time serie of Tuna Catches per species per ocean by using multiple interactive visualization libraries
ICHTHYOP_MODEL_MULTIPLE_RUNS
Description	This R code enables to extract multiple observed trajectories from data sources (FADs or Drifters) and to run (for each trajectory) an execution of Ichthyop driven by OSCAR data oin order to confront simulation with these observations. netCDF outputs are transformed into maps to be visualized with Qgis. Ichthyop is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics
AQUAMAPS_SUITABLE
Description	Algorithm for Suitable Distribution by AquaMaps. A distribution algorithm that generates a table containing species distribution probabilities on half-degree cells according to the AquaMaps approach for suitable (potential) distributions.
FIGIS_SPATIAL_REALLOCATION_SIMPLIFIED_TABLE
Description	The Spatial Reallocaton algorithm allows to estimate statistics for other areas from those where they were reported. The algorithm is based on spatial disaggregation technics and provides at now an area-weighted reallocation. This simplified algorithm is specifically targeting users from the FAO Fisheries and Aquaculture department, aims to facilitate its execution by doing abstraction of the intersections to provide.
FEED_FORWARD_A_N_N_DISTRIBUTION
Description	A Bayesian method using a Feed Forward Neural Network to simulate a function from the features space (R^n) to R. A modeling algorithm that relies on Neural Networks to simulate a real valued function. It accepts as input a table containing the training dataset and some parameters affecting the algorithm behaviour such as the number of neurons, the learning threshold and the maximum number of iterations.
POLYGONS_TO_MAP
Description	A transducer algorithm to produce a GIS map of filled polygons associated to x,y coordinates and a certain resolution. A maximum of 259000 is allowed
XYEXTRACTOR_TABLE
Description	An algorithm to extract values associated to a table containing geospatial features (e.g. Vessel Routes, Species distribution maps etc. ). A grid of points at a certain resolution is specified by the user and values are associated to the points from the environmental repository. It accepts as one geospatial table and the specification about time and space. The algorithm produces one table containing the values associated to the selected bounding box.
COMPUTE_FISHERIES_INDICATORS_FROM_OWN_FORMATTED_DATASET
Description	Compute some fisheries indicators (plots and maps) from a dataset that you have previously formatted and imported through the algorithm Import Fisheries Formatted Dataset. The codes to use for the filters in this algorithm must be the input dataset ones.
ICHTHYOP_MODEL_ONE_BY_ONE
Description	This R code packages some extraction to get observed trajectories from data sources (FADs or Drifters) and the execution of Ichthyop driven by OSCAR data to confront simulation with these observatios. netCDF outputs are transformed into maps to be visualized with Qgis. Ichthyop is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics
ICHTHYOP_MODEL_ONE_BY_ONE
Description	This R code packages some extraction to get observed trajectories from data sources (FADs or Drifters) and the execution of Ichthyop driven by OSCAR data to confront simulation with these observatios. netCDF outputs are transformed into maps to be visualized with Qgis. Ichthyop is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics
TAXONOMY_OBSERVATIONS_TREND_PER_YEAR
Description	Algorithm returning most observations taxonomy trend in a specific years range (with respect to the OBIS database)
OCCURRENCES_INTERSECTOR
Description	A transducer algorithm that produces a table of species occurrence points that are contained in both the two starting tables where points equivalence is identified via user defined comparison thresholds. Works with up to 10000 points per table. Between two ocurrence sets, it keeps the elements of the Right Set that are similar to elements in the Left Set.
FEED_FORWARD_ANN
Description	A method to train a generic Feed Forward Artifical Neural Network in order to simulate a function from the features space (R^n) to R. Uses the Back-propagation method. Produces a trained neural network in the form of a compiled file which can be used in the FEED FORWARD NEURAL NETWORK DISTRIBUTION algorithm.
GETTABLEDETAILS
Description	Algorithm that allows to view table details of a chosen database
LISTDBNAMES
Description	Algorithm that allows to view the available database resources names in the Infrastructure
LISTDBSCHEMA
Description	Algorithm that allows to view the schema names of a chosen database for which the type is Postgres
MPA_INTERSECT_V2
Description	An algorithm to compute areas of geomorphic features in an EEZ or ECOREGION area and in its intersecting Marine Protected Areas (MPAs)
ESTIMATE_MONTHLY_FISHING_EFFORT
Description	An algorithm that estimates fishing exploitation at 0.5 degrees resolution from activity-classified vessels trajectories. Produces a table with csquare codes, latitudes, longitudes and resolution and associated overall fishing hours in the time frame of the vessels activity. Requires each activity point to be classified as Fishing or other. This algorithm is based on the paper 'Deriving Fishing Monthly Effort and Caught Species' (Coro et al. 2013, in proc. of OCEANS - Bergen, 2013 MTS/IEEE). Example of input table (NAFO anonymised data): http://goo.gl/3auJkM
WEB_APP_PUBLISHER
Description	This algorithm publishes a zip file containing a Web site, based on html and javascript in the e-Infrastructure. It generates a public URL to the application that can be shared.
STAT_VAL
Description	statistical validation of BIPARTITE WEIGHTED network
CATCHES_AGGREGATED_FOLLOWING_A_SELECT_VARIABLE
Description	The outputs are temporal and spatial distribution of the catches aggregated gollowing a selected variable and given the filters applied by the user
GENETICALGORITHM
Description	Genetic Algorithm
CATCHES_BY_TYPE_OF_SCHOOL
Description	The output is a plot of the catches by type of school given the filters applied by the user
CATCHES_BY_GEAR_SIMPLIFIED_VERSION
Description	The output is a plot of the catches by gear given the filters applied by the user
TRAJECTORY_BUILDER
Description	A module to build trajectories from raw GPS observation using several constraints.
CCAMLR_EXPORTER_TOOL
Description	Functions to generates json data and graphs based on CCMLAR input data
STEP_1___VPA_ICCAT_BFT_E_RETROS
Description	STEP 1: ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
STEP_2__VPA_ICCAT_BFT_E_VISUALISATION
Description	ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
SIMULFISHKPIS
Description	Create simulation models for KPIs fish production in Aquaculture. Import data from SimulFish Growth database via URLs. Calculated KPIs are FCR, SFR, Mortality using Regression models generated by GAMs and MARs methodologies. Updated version on 30.08.2016
TUNA_ATLAS_DATA_ACCESS
Description	This R code enables users to adapt a SQL query to get data from Sardara database storing global
SHAPEFILE_PUBLISHER
Description	An algorithm to publish shapefiles under WMS and WFS standards in the e-Infrastructure. The produced WMS, WFS links are reported as output of this process. The map will be available in the VRE for consultation.
MPA_INTERSECT
Description	An algorithm to intersect MPA polygons with WFS spatial data layers
KMEANS
Description	A clustering algorithm for real valued vectors that relies on the k-means algorithm, i.e. a method aiming to partition n observations into k clusters in which each observation belongs to the cluster with the nearest mean, serving as a prototype of the cluster. A Maximum of 4000 points is allowed.
CATCHES_BY_SPECIES_SIMPLIFIED_VERSION
Description	The output is a plot of the catches by species given the filters applied by the user
QUICK_RANK_TRAIN_NO_VALIDATION
Description	QuickRank algorithm suite for training with no validation file
GLOBAL_CATCHES
Description	The output is a plot of the catches given the filters applied by the user
ECOPATH_WITH_ECOSIM
Description	Ecopath with Ecosim (EwE) is a free ecological/ecosystem modeling software suite. This algorithm implementation expects a model and a configuration file as inputs; the result of the analysis is returned as a zip archive. References: Christensen, V., & Walters, C. J. (2004). Ecopath with Ecosim: methods, capabilities and limitations. Ecological modelling, 172(2), 109-139.
ABSENCE_GENERATION_FROM_OBIS
Description	An algorithm to estimate absence records from survey data in OBIS. Based on the work in Coro, G., Magliozzi, C., Berghe, E. V., Bailly, N., Ellenbroek, A., & Pagano, P. (2016). Estimating absence locations of marine species from data of scientific surveys in OBIS. Ecological Modelling, 323, 61-76.
WHOLE_STEPS_VPA_ICCAT_BFT_E
Description	Whole Steps: ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
GENERIC_WORKER
Description	An algorithm that executes another other algorithm
RASTER_DATA_PUBLISHER
Description	This algorithm publishes a raster file as a maps or datasets in the e-Infrastructure. NetCDF-CF files are encouraged, as WMS and WCS maps will be produced using this format. For other types of files (GeoTiffs, ASC etc.) only the raw datasets will be published. The resulting map or dataset will be accessible via the VRE GeoExplorer by the VRE participants.
CATCHES_BY_GEARS
Description	The output is a plot of the catches by gears for tuna fisheries given the filters applied by the user
CATCHES_BY_FLAGS
Description	The output is a plot of the catches by flags given the filters applied by the user
STEP_4_VPA_ICCAT_BFT_E_REPORT
Description	ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
READWFS
Description	Read WFS requests and export attributes
PARALLELIZED_STEP1_VPA_ICCAT_BFT_E_RETROS
Description	STEP 1: ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
MAKE_ICHTHYOP_NETCDF_CF_COMPLIANT
Description	This code turns ichthyop netCDF into another netCDF whis is compliant with CF conventions and enables agreggation with NCML files
ICHTHYOP_NETCDF_OUTPUT_TO_SHAPEFILE
Description	This code turns trajectories of ichthyop model outputs delivered with netCDF into a shapefile
VPA_ICCAT_BFT_E_REPORT
Description	ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
XMEANS
Description	A clustering algorithm for occurrence points that relies on the X-Means algorithm, i.e. an extended version of the K-Means algorithm improved by an Improve-Structure part. A Maximum of 4000 points is allowed.
KNITR_COMPILER
Description	An algorithm to compile Knitr documents. Developed by IRD (reference Julien Bard, julien.barde@ird.fr)
SEADATANET_INTERPOLATOR
Description	A connector for the SeaDataNet infrastructure. This algorithms invokes the Data-Interpolating Variational Analysis (DIVA) SeaDataNet service to interpolate spatial data. The model uses GEBCO bathymetry data and requires an estimate of the maximum spatial span of the correlation between points and the signal-to-noise ratio, among the other parameters. It can interpolate up to 10,000 points randomly taken from the input table. As output, it produces a NetCDF file with a uniform grid of values. This powerful interpolation model is described in Troupin et al. 2012, 'Generation of analysis and consistent error fields using the Data Interpolating Variational Analysis (Diva)', Ocean Modelling, 52-53, 90-101.
LOF
Description	Local Outlier Factor (LOF). A clustering algorithm for real valued vectors that relies on Local Outlier Factor algorithm, i.e. an algorithm for finding anomalous data points by measuring the local deviation of a given data point with respect to its neighbours. A Maximum of 4000 points is allowed.
ESTIMATE_FISHING_ACTIVITY
Description	An algorithm that estimates activity hours (fishing or other) from vessels trajectories, adds bathymetry information to the table and classifies (point-by-point) fishing activity of the involved vessels according to two algorithms: one based on speed (activity_class_speed output column) and the other based on speed and bathymetry (activity_class_speed_bath output column). The algorithm produces new columns containing this information. This algorithm is based on the paper 'Deriving Fishing Monthly Effort and Caught Species' (Coro et al. 2013, in proc. of OCEANS - Bergen, 2013 MTS/IEEE). Example of input table (NAFO anonymised data): http://goo.gl/3auJkM
QUICK_RANK_TRAIN
Description	QuickRank algorithm suite for training
CATCHES_BY_FLAGS_SIMPLIFIED_VERSION
Description	The output is a plot of the catches by flags given the filters applied by the user
IMPORT_FISHERIES_FORMATTED_DATASET___QUICK_IMPORT
Description	Import into the global database a dataframe that has previously been formatted to the standard database format. After the import you will be able to compute the fisheries indicators (e.g. the algorithm Compute fisheries indicators from own formatted dataset) using your data.
QUICK_RANK_TEST
Description	QuickRank algorithm suite for test
PROJECTIONS_REPORT_VPA_ICCAT_BFT_E
Description	Projections_report: ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD
CATCHES_BY_SPECIES
Description	The output is a plot of the catches by species given the filters applied by the user