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Easyworm: an open-source software tool to determine the mechanical properties of worm-like chains

Guillaume Lamour123*, Julius B Kirkegaard4, Hongbin Li3, Tuomas PJ Knowles4 and Jörg Gsponer13

Author Affiliations

1 Centre for High-Throughput Biology, University of British Colombia, Vancouver, BC V6T 1Z4, Canada

2 Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada

3 Department of Biochemistry & Molecular Biology, University of British Colombia, Vancouver, BC V6T 2A1, Canada

4 Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK

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Source Code for Biology and Medicine 2014, 9:16  doi:10.1186/1751-0473-9-16

Published: 10 July 2014

Abstract

Background

A growing spectrum of applications for natural and synthetic polymers, whether in industry or for biomedical research, demands for fast and universally applicable tools to determine the mechanical properties of very diverse polymers. To date, determining these properties is the privilege of a limited circle of biophysicists and engineers with appropriate technical skills.

Findings

Easyworm is a user-friendly software suite coded in MATLAB that simplifies the image analysis of individual polymeric chains and the extraction of the mechanical properties of these chains. Easyworm contains a comprehensive set of tools that, amongst others, allow the persistence length of single chains and the Young’s modulus of elasticity to be calculated in multiple ways from images of polymers obtained by a variety of techniques (e.g. atomic force microscopy, electron, contrast-phase, or epifluorescence microscopy).

Conclusions

Easyworm thus provides a simple and efficient tool for specialists and non-specialists alike to solve a common problem in (bio)polymer science. Stand-alone executables and shell scripts are provided along with source code for further development.

Keywords:
Matlab; GUI; Polymer; Worm-like chain model; Persistence length; Young’s modulus; AFM