MADpatterns

Description

MADpatterns is a tool to Model and Analyze 1D patterns using the software MATLAB, that was developed in the lab of Prof. Nancy Kleckner at Harvard University http://projects.iq.harvard.edu/kleckner_lab

Key Features

1. Quantitatively model 1D patterning events based on the Beam-Film model for crack formation
2. Automate analysis of 1D patterns

Installation

Download program, unzip the folder, open MATLAB and add the unzipped folder to the file path.

Usage

For a detailed user guide and information on the relevance of this program to the study of meiotic recombination events, please read our manuscript currently available on bioRxiv and soon to be available in Methods in Molecular Biology.

DOI: http://dx.doi.org/10.1101/083808

Update

A new function has been added to the program to model the effect of a reduced number of active precursors (Parameter Y). For more information on this parameter, please read our new paper:

Wang et al. (2017). Inefficient Crossover Maturation Underlies Elevated Aneuploidy in Human Female Meiosis. Cell; 168: 977 - 989. http://dx.doi.org/10.1016/j.cell.2017.02.002

In order to incorporate this new function into the program, the format of the input table for simulating 1D patterns according to the Beam-Film model has been updated. The appropriate format of this table can be found in the updated example input table (simulation_parameters.csv) that is included with the program

Citing MADpatterns

To cite the program, please use the following reference:

White M.A., Wang S., Zhang L., and Kleckner N. (2016). Quantitative modeling and automated anlaysis of meiotic recombination. bioRxiv 083808

In addition, each version of the program will be assigned its own DOI via Zenodo. The DOI of the most recent release can be found on the left-hand side of this page.

Get Help and Contribute

We hope that MADpatterns will become a useful resource for the meiotic recombination community, and beyond. Users can contribute to the program (e.g. suggest new features) and report issues using the project's GitHub page. MADpatterns.

Credits

This program was developed by Martin White in the lab of Prof. Nancy Kleckner with help from Liangran Zhang. A significant fraction of this program is either directly taken or derived from a previous program developed by Liangran Zhang, Nancy Kleckner and John Hutchinson:

Kleckner et al. (2004). A mechanical basis for chromosome function. Proc. Natl. Acad. Sci. USA; 101: 12592 - 12597

Zhang et al. (2014). Crossover patterning by the Beam-Film model: analysis and implications. PLoS Genetics; 10: e1004042

Zhang et al. (2014). Topoisomerase II mediates meiotic crossover interference. Nature; 511: 551-556.

This version of the program is available for download here:https://app.box.com/s/hv91q2nrtq0cp9n8iy9m

License

MIT License

Copyright (c) 2016 Martin Andrew White

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.