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 |
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 |
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 |
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 |
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 |
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 |