Multi-Chromosome Constrained Self-Avoiding Chromatin
1- Code requires installation of cmake and boost and eigen3 libraries.
2- After libraries are installed, make sure to change the paths in CMakeLists.txt file.
3- Create a folder called build in the directory where you have the code
cd build cmake .. make
Above should compile the code. Hopefully no error.
4- to test, I have a test configuration file in the folder. You can run it as
../build/bin/chromatin.sis.coarse -conf <<.ini file>> -prefix AA
../build/bin/chromatin.sis.coarse = executable created after building the code <<.ini file>> = configuration file needed to point to the input files AA = prefix for the output chain files.
This helps to iterate over when creating multiple chains.
Brief explanation of the <<.ini>> file
out_path = output path persistence_length = length of each unit in A (e.g. 30 nm chromatin fiber will have 30, each 10nm is a kb long) ) collision_length = 300 (in A, this is the diameter of each bead) nucleus_sphere_diameter = 5200 (nucleus diameter in A) number_nodes = number of beads in the chain (i.e., the total length of the chain is number of nodes x 3 kb) number_of_chains = number of chromosome chain_length_i = number of nodes in the ith chromosome number_sample_points = divides the sampling sphere around a monomer to 640 distrete points
When referencing this code, please cite:
(1) Gamze Gursoy, Yun Xu, and Jie Liang. "Spatial organization of budding yeast genome from landmark constraints and predicting biological chromatin interactions from Chromosome Conformation Capture Data", PLOS Comp. Bio., 2017:13(7):e1005658
(2) Gamze Gursoy, Yun Xu and Jie Liang. "Computational predictions of structures of multichromosomes of budding yeast", Conf Proc IEEE Eng Med Biol Soc., 2014