Spring Model

Spring model is a webservice for modelling chromatin domains using direct information about contacts derived from experiments like Hi-C or ChIA-PET. It is employs polymer physics and molecular mechanics using OpenMM library. Please visit manual, and tutorial pages for more info.

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New request

General

Title:	Up to 255 characters	Example 1 Example 2	Example 3
Initial structure type:	line circle self-avoiding random walk pure random walk baseball	Stiffness:		Values between 0 and 100 are suitable for most cases.
		Spherical container:		Diameter of container in σ (bead diameter) units. Leave empty for modelling without this constraint.
		Refinement:		May significantly extend computation time.
		Excluded volume:		Check to include ev term

Model coordinates

Number of beads:	The limits are: 5 - 2000
Restraints:

or

Genomic coordinates

Region:		Genomic region in format chrN:xxx-yyy
Resolution:		Values between 1000 - 100 000 are usually reasonable and strongly depend on size of modelling region
Interactions:	BEDPE format

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