Software

Data

Data Formats

Standard Identifiers

Websites with data

Olympus

Olympus is a linux-based supercomputer intended to be a workspace for model development and running experiments. It is configured with several programming languages, compilers, and popular development tools (listed below) for general modeling work. Olympus is also configured to run 4 disease transmission models, and hosts synthetic ecosystems for many countries.

Olympus is provided as a free resource to members of the MIDAS network. To sign up for an account on Olympus, please visit http://epimodels.org.

For more information on Olympus, please read this PowerPoint presentation or watch the video

Software available on Olympus

A list of the programming languages, compilers, development tools, and disease transmission models that are available on Olympus is shown below. A wiki describing how to use Olympus is available at https://git.isg.pitt.edu/hpc/olympus/wikis/home.

If you require software on Olympus that is not listed below, please contact remarks@psc.edu.

System Software

Tools

Statistical analysis
Image manipulation
Genetic sequence

Disease Transmission Models

These entries are cross-references of disease transmission models listed on the 'Content' page.

Modeling Platforms

Workflows on Olympus

These scripts and all the programs they invoke are staged on the Olympus cluster. Follow the instructions below to execute a workflow on your Olympus account. Alternatively, you can copy and edit the script before running on Olympus.

Obtaining a Synthetic Population in Synthia Format

The LSDTM script requests the name of the synthetic population ('Synthia' or 'SPEW') and the location. It creates a runnable instance of pFRED for that location.




About

The primary purpose of the MIDAS Digital Commons (MDC) is to support infectious disease epidemiologists who are developing computational models of biological phenomena. The scope of the MDC is primarily defined by the past and present research of the MIDAS research network as reflected in its 1000+ publications (listed and linked to in reverse chronologic order here).

At present, the MDC consists of (1) a collection of digital objects in the domain of infectious disease epidemiology (2) a compute platform for running experiments, and (3) a search function that makes the digital objects findable.

The digital objects include software, datasets, and data formats.

The compute platform hosts programming languages and other software tools and some of the digital objects (e.g., disease transmission models and synthetic ecosystems). The locally hosted digital objects are labelled AOC (Available on the Olympus Cluster). Other digital objects are hosted remotely (i.e., they are virtual w.r.t. this digital commons).

We intend that all digital objects conform to FAIR (Findable, Accessible, Interoperable, Reusable) guidelines. To make datasets interoperable, we represent them whenever possible in Apollo-XSD syntax and label them as being AE (Apollo-Encoded) in the MDC.

FAIR-o-meter

We track conformance to FAIR guidelines here.

Ontology

The Apollo-SV ontology represents our conceptualization of infectious disease epidemiology. You can find it here.

Web service

A programmatic interface to the MIDAS Digital Commons is available in the form of a RESTful Web service. The Web service (1) returns a list of the DOIs in MDC, (2) returns an object's metadata when presented with a DOI, and (3) returns data when presented with a DOI and a distribution identifier (there are one our more distributions of a dataset in the metadata) of a dataset. The MDC Web service is documented using the Swagger software library which describes the endpoint URLs, HTTP methods, required parameters, optional parameters, response syntaxes and input forms to test the API directly from a web browser. The Web service documentation is available here.

Submission Guidelines

If you have any digital objects that you'd like to submit to the commons, please contact Mike Wagner via email at mmw1@pitt.edu.

Funding

The MIDAS Digital Commons is funded by the National Institutes of Health (NIGMS) program for Models of Infectious Disease Agent Study (MIDAS) grant U24GM110707.

Disclaimer

By using the MIDAS Digital Commons you agree that no warranties of any kind are made by the University of Pittsburgh (University) with respect to the data provided in the MIDAS Digital Commons or any use thereof, and the University hereby disclaim the implied warranties of merchantability, fitness for a particular purpose and non-infringement. The University shall not be liable for any claims, losses or damages of any kind arising from the data provided in the MIDAS Digital Commons or any use thereof.

Please direct comments and questions to our development team.