SAHM for VisTrails: Software for Assisted Habitat Modeling

From a 2014 USGS fact sheet announcing a twice-yearly training course.

The software

VisTrails is an open-source system for managing scientific workflows that combines workflow management with scientific visualisation. Developers can extend it by writing custom modules for its bundled packages.

The Invasive Species Science Branch of the USGS Fort Collins Science Center and the Department of the Interior's North Central Climate Science Center built one such module: the Software for Assisted Habitat Modeling (SAHM). SAHM speeds up habitat modelling and keeps a record of the input data, the steps before and after processing, and the modelling options used to build an ecological response model — for example, a map of where a species is likely to occur.

Using SAHM with VisTrails for species distribution modelling has four main advantages:

1. the whole modelling process is formalised and traceably recorded;
2. collaboration is easier within a common modelling framework;
3. a user-friendly graphical interface manages input files, model runs and output;
4. it can be extended with further modelling routines and tools.

A SAHM workflow in VisTrails, from input data through preprocessing and correlative models to output. USGS.

The course

To meet growing interest, the Fort Collins Science Center offered a SAHM:VisTrails training course twice a year, combining lectures, hands-on work and discussion.

Participants would:

• learn how the SAHM:VisTrails package works and how to use it;
• get an overview of the statistical packages SAHM includes;
• work through an example species distribution dataset.

Afterwards they would be ready to apply the package to their own data and join its user community.

The course was held at the Center's Resource for Advanced Modeling, 2150 Centre Avenue, Building C, Fort Collins, Colorado — a collaborative space where resource managers meet USGS scientists to build predictive ecological models, equipped with networked laptops and a 24-monitor "VisWall." Sessions were scheduled for September 9–10 and March 24–25, September 8–9 and March 22–23, and September 6–7.

More information

• SAHM software (USGS Fort Collins Science Center)
• VisTrails
• Morisette, J.T., and others, 2013, "VisTrails SAHM—Visualization and workflow management for species habitat modeling," Ecography 36(2): 129–135.

Sources

• Holcombe, T., 2014, SAHM:VisTrails (Software for Assisted Habitat Modeling for VisTrails)—Training course: U.S. Geological Survey Fact Sheet 2014–3007. https://pubs.usgs.gov/publication/fs20143007