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Table 2 Workflows for biodiversity science (Additional file 3)

From: BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Workflow (family) Capability/purpose (i.e., what is it for?)
incl. persistent identifier (purl) to locate the workflow and references to scientific studies that have exploited it
Data refinement The data refinement workflow (DRW) is for preparing taxonomically accurate species lists and observational data sets for use in scientific analyses such as: species distribution analysis, species richness and diversity studies, and analyses of community structure
purl: http://purl.ox.ac.uk/workflow/myexp-2874.13
Portal: https://portal.biovel.eu/workflows/641
Scientific studies: [33, 34]
Ecological niche modelling (ENM) The generic ENM workflow creates, tests, and projects ecological niche models (ENM), choosing from a wide range of algorithms, environmental layers and geographical masks
purl: http://purl.ox.ac.uk/workflow/myexp-3355.20
Portal: https://portal.biovel.eu/workflows/440
The BioClim workflow retrieves environmentally unique points from a species occurrence file under a given set of environmental layers, and calculates the range of the environmental variables (min–max) for a given species
purl: http://purl.ox.ac.uk/workflow/myexp-3725.2
Portal: https://portal.biovel.eu/workflows/443
Scientific studies: [33, 35, 36]
ENM statistical difference (ESW) Statistical post-processing of results from ecological niche modelling
ESW DIFF workflow computes extent, direction and intensity of change in species potential distribution through computation of the differences between two models, including change in the centre point of the distribution
purl: http://purl.ox.ac.uk/workflow/myexp-3959.2
Portal: https://portal.biovel.eu/workflows/442
ESW STACK workflow computes extent, intensity, and accumulated potential species distribution by computing the average sum from multiple models
purl: http://purl.ox.ac.uk/workflow/myexp-3856.3
Portal: https://portal.biovel.eu/workflows/70
Scientific studies: [33, 36]
Population modelling Matrix population model construction and analysis workflows provide a complete environment for creating a stage-matrix with no density dependence, and then to perform several analyses on it. Each of the workflows in the collection is also available separately. The expanded version of this table, available as Additional information contains a link
purl: http://purl.ox.ac.uk/researchobj/myexp-483
Portal: https://portal.biovel.eu/workflows/596
Integral projection models workflow provides an environment to create and test an integral projection model and to perform several analyses on that
purl: http://purl.ox.ac.uk/researchobj/myexp-482
Portal: https://portal.biovel.eu/workflows/599
Scientific studies: no publication yet
Ecosystem modelling Based around the Biome-BGC biogeochemical model, a collection of five workflows for calibrating and using Biome-BGC for modelling ecosystems and calculating a range of ecosystem service indicators. The Biome-BGC projects database and management system provides a user interface for setting of model parameters, for support sharing and reusing of datasets and parameter settings
purl: http://purl.ox.ac.uk/researchobj/myexp-687
Portal: https://portal.biovel.eu/workflows/81
https://portal.biovel.eu/workflows/289
https://portal.biovel.eu/workflows/300
https://portal.biovel.eu/workflows/48
https://portal.biovel.eu/workflows/507
Scientific studies: [3740]
Metagenomics Microbial metagenomic trait calculation and statistical analysis (MMT) workflow calculates key ecological traits of bacterial communities as observed by high throughput metagenomic DNA sequencing. Typical use is in the analysis of environmental sequencing information from natural and disturbed habitats as a routine part of monitoring programs
purl: http://purl.ox.ac.uk/workflow/myexp-4489.3
Portal: access on request
(BioMaS) Bioinformatic analysis of Metagenomic ampliconS is a bioinformatic pipeline supporting biomolecular researchers to carry out taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data arrangement to final taxonomic identification. This workflow is typically used in meta-barcoding high-throughput-sequencing experiments
url: https://www.biodiversitycatalogue.org/services/71
Scientific studies: [4143]
Phylogenetics Bayesian phylogenetic inference workflows are for performing phylogenetic inference for systematics and diversity research. Bayesian methods guide selection of the evolutionary model and a post hoc validation of the inference is also made. Phylogenetic partitioning of the diversity across samples allows study of mutual information between phylogeny and environmental variables
purl: http://purl.ox.ac.uk/researchobj/myexp-370
Portal: https://portal.biovel.eu/workflows/466
https://portal.biovel.eu/workflows/549
https://portal.biovel.eu/workflows/550
https://portal.biovel.eu/workflows/525
PDP workflow, using PhyloH for partitioning environmental sequencing data using both categorical and phylogenetic information
purl: http://purl.ox.ac.uk/workflow/myexp-3570.5
Portal: https://portal.biovel.eu/workflows/434
https://portal.biovel.eu/workflows/71
MSA-PAD workflow performs a multiple DNA sequence alignment coding for multiple/single protein domains invoking two alignment modes: gene and genome
Gene mode purl: http://purl.ox.ac.uk/workflow/myexp-4549.1
Portal: https://portal.biovel.eu/workflows/712 (access on request)
Genome mode purl: http://purl.ox.ac.uk/workflow/myexp-4551.1
Portal: https://portal.biovel.eu/workflows/713 (access on request)
SUPERSMART (self-updating platform for estimating rates of speciation and migration, ages and relationships of taxa) is a pipeline analytical environment for large-scale phylogenetic data mining, taxonomic name resolution, tree inference and fossil-based tree calibration
url: https://www.biodiversitycatalogue.org/services/78
Scientific studies: [4447]