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Modelling of a region of the fly genome

Example of using IMP to model a region of the Fly genome https://integrativemodeling.org/systems/

tickVerified to work with the latest stable IMP release (2.9.0). The files are also available at GitHub.
Additional software needed to use these files: IMP scipy numpy argparse install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp scipy numpy argparse

(argparse is only needed if you are using Python 2.6)

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp python/scipy python/numpy python/argparse
Tags chromatin drosophila melanogaster model TADs

These scripts are extracted from TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions, to illustrate the use of IMP to model a genomic region with 5 Topologically Associating Domains (TADs) from the fly genome.

Directories:

Running the IMP scripts for the fly genome:

To run the modeling script, just change into its directory and run it from the command line, e.g.

A prebuild optimal imp parameters it's already included in the data directory to speed up the test which should take around 2 hours in a single cpu. If you wish to test the optimization and the modeling just delete the configuration file or change the extension to something else than .tsv. The whole computation should take around 40 hours in a single cpu.

The results will be produced in the outputs directory as described above.

Information

Author(s): François Serra, Davide Baù, David Castillo, Guillaume Filion, Marc A. Marti-Renom

Date: October 1st, 2016

Last known good IMP version: build info build info

Testable: Yes.

Parallelizeable: Yes

Citation: