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Multilocus ANTIgenic Simulator

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The Multilocus ANTIgenic Simulator (MANTIS) is a software package for the R statistical environment, designed and developed by this research group. MANTIS offers a wide range of functions to simulate and analyse epidemiological time-series, generated under the biological assumptions of the strain theory of host-pathogen systems by Gupta et al. (Science, 1998).

MANTIS’s main goal is to serve as a free academic software tool. It aims to reduce the existing gap between mathematical approaches and population biology research. We argue for this tool’s place and usefulness in educational programmes such as epidemiology and ecology courses, by supporting students in their exploration of host-pathogen systems in which host immunity may play a significant role. With this in mind, the package was developed to be user-friendly, not only wrapping the use of complex ODE systems into single-function calls, but also including a variety of functions for easy time-series visualization and exportation. The open source nature of MANTIS further provides a valuable opportunity for researchers with advanced programming skills to expand and tweak its capabilities for their own research goals.

Timeseries

MANTIS is available (see below) under the GNU GPL license.

MANTIS's open access research article is published on BMC Bioinformatics (2015).

For any query please contact José Lourenço or find us on twitter!

News:

Nov/2015: MANTIS V3.0 (cryptonym: red egg) is out, see below for associated resources.

Nov/2015: MANTIS V3.0 (cryptonym: red egg) is in preparation for release by the end of this month. Updates will include several new functionalities to experiment on seasonality and altered strain phenotypes. 

May/2015: MANTIS V1.0 (cryptonym: green egg) research article published. Open access PDF can be found here.

May/2015: MANTIS V2.0 (cryptonym: blue egg) package and manual update for bug fixes and added functionality based on new concepts of antigenic dynamics. Description and examples of new functions made available in a dedicated PDF file.

Apr/2015: MANTIS V1.0 (cryptonym: green egg) research article accepted on BMC bioinformatics (soon to be available on this page).

Apr/2015: MANTIS V1.0 (cryptonym: green egg) code examples that replicate the figures on MANTIS's article have been added to the website.

Jan/2015:MANTIS V1.0 (cryptonym: green egg) package made available. Website launch. Research article submitted to BMC bioinformatics (under review).

The Package (current version):

MANTIS V3.0 (cryptonym: red egg) [release date Nov/2015]

Requirements: R 3.2 or higher; Rcpp 0.11.2 or higher; GNU GCC 4.8.2 or higher (MacOS, Linux); Rtools (Windows).

Manual: download PDF

Source package: download tar.gz

Description and examples of new functionalities: download PDF.

Installation guidelines for Windows and MacOS: download PDF.

Educational resource: 3rd year tutorial I (Department of Zoology, University of Oxford), download PDF.

Educational resource: poster presented at Epidemics5 conference, download PDF.

Previous (discontinued) versions:

MANTIS V2.0 (cryptonym: blue egg) [release date May/2015]

MANTIS V1.0 (cryptonym: green egg)[release date Jan/2015]

Code examples for article's figures: download PDF