File	Date	Author	Commit
doc	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
README	2014-10-09	Andrea Pinna	[29fd45] Initial commit
acyclic_random_network.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
assortativity.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
check_settings.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
date_string.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
degree_assignment.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
display_et.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
eq_simplified_model.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
exp_in_pow_out_network.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
exponential_distribution.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
find_gamma.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
generate_Zs.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
generate_parameters.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
generate_perturbation_parameters.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
generate_perturbation_parameters_kd.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
generate_perturbation_parameters_ko.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
generate_perturbation_parameters_oe.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
generate_phenotype_nodes.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
generate_single_Z.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
intersect_wr.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
ismember_wr.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
isnnint.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
isposint.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
isprobability.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
modular_network.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
modularity.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
module_sizes.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
network_components.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
network_condensation.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
network_generation.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
parameters_generation.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
paths_generation.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
plot_correlation_distributions.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
plot_gene_expression_distribution.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
plot_heritability_distribution.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
plot_node_degree_distributions.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
plot_output_figures.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
plot_parameter_distributions.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
power_law_distribution.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_edge_list.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_gene_expression.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_genetic_map.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_genotype_information.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_genotype_matrix.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_module_list.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_output_files.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
print_pajek_network_file.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_perturbation_list.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_phenotype_matrix.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
print_simulation_summary.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
print_topological_properties.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
random_in_power_out_network.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
random_network.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
read_edge_list.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
read_gene_marker_map.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
read_genetic_map.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
remove_diag.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
setdiff_wr.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
sign_assignment.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
smallworld_network.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
steady_states_computation.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
sysgensim.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
sysgensim_gui.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
truncated_randn.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit
union_wr.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
unique_wr.m	2015-03-05	pinno	[288ae4] Update to SysGenSIM 1.2
uu_network.m	2014-10-09	Andrea Pinna	[29fd45] Initial commit

Read Me

REQUIREMENTS
------------

To run SysGenSIM you need Mathworks MATLAB® ( 
http://www.mathworks.com/products/matlab/ ) version 7.9 (R2009b) or 
later, with Bioinformatics and Statistics toolboxes.

INSTALL
-------

To install SysGenSIM just unpack the archive, then add the SysGenSIM 
directory to your MATLAB search path. One possibility is to add to your 
startup.m file the following line:

addpath('PATH/TO/SysGenSIM');

where PATH/TO/SysGenSIM is the path to the SysGenSIM directory. For info 
about startup.m and other ways to add the directory to your search path, 
please consult the MATLAB documentation.

RUNNING THE GRAPHICAL USER INTERFACE
------------------------------------

In MATLAB execute the main script:

>> sysgensim_gui

REFERENCES
----------

If you use SysGenSIM for a scientific work, we kindly ask you to cite 
this paper:

A. Pinna, N. Soranzo, I. Hoeschele, A. de la Fuente
"Simulating system genetics data with SysGenSIM"
Bioinformatics 27(17), pp. 2459-2462, 2011

CONTACTS
--------

See doc/AUTHORS file.