What's new in SysGenSIM 1.2
Mar 25, 2015
- Updated the toolbox (due to issues with RandStream, unique, union, setdiff, intersect, ismember) to run with the most recent versions of MATLAB.
- Beautified the function date_string.m
- Set to "output" the name of the default folder to save output files and figures (instead of "Output Files")
New in SysGenSIM 1.1.1 (May 24, 2014)
- Regenerated the manual with mw-render
New in SysGenSIM 1.1 (May 24, 2014)
- Updated the GUI into a 6-panel interface
- Added the possibility to simulate experimental perturbations, e.g. single-gene knock-out, knock-down and over-expression experiments
- Added the functions to generate the perturbation parameters
- Added the "perturbation list" amongst the available output files
- Updated the function print_simulation_summary.m to take into account the experimental perturbations
New in SysGenSIM 1.0.3 (May 24, 2014)
- Fix paths of saved files on Windows
- Save settings, parameters and random number generator state to file before simulating experiments, so that a run can be exactly replicated
New in SysGenSIM 1.0.2 (May 24, 2014)
- Correct load of Gene network or Gene+Phenotype network through the GUI
- Correct load of a previously saved network in read_edge_list.m
New in SysGenSIM 1.0.1 (May 24, 2014)
- Corrected a bug in truncated_randn.m which was incorrectly checking lower and upper bounds
- Updated the reference for SysGenSIM paper in README, final version officially published in Bioinformatics
- Updated doc/TODO
New in SysGenSIM 1.0.0 (Jul 18, 2011)
- Updated the reference for SysGenSIM paper in README, now officially published in Bioinformatics!
- Added "small-world" to the available network topologies in the GUI smallworld_network() function now expects as second parameter the average degree instead of the average outdegree. Moreover, the requested degree is now approximated instead of being rounded
- Simplified integer check in isposint.m and isnnint.m
- Add some input checks to functions: acyclic_random_network.m, random_network.m, smallworld_network.m, truncated_randn.m
- Added help text to functions: acyclic_random_network.m, random_network.m, smallworld_network.m.
New in SysGenSIM 0.2.2 (Jul 18, 2011)
- Added new function read_gene_marker_map.m
- Fixed small inconsistencies and bugs in some functions
- Moved AUTHORS, Changelog, COPYING and TODO files to the doc/ subdirectory
- The manual is now included in the package in the doc/ subdirectory
New in SysGenSIM 0.2.1 (Jul 18, 2011)
- Fixed few small bugs when selecting 0 phenotypes.
New in SysGenSIM 0.2 (Jul 18, 2011)
- Add a vertical scrollbar to the main window
- Use new find_gamma.m instead of fminsearch with gamma_obj_function.m
- Don't require the MATLAB Optimization Toolbox
- Correct bug "??? Error using ==> fprintf - Function is not defined for sparse inputs." on MATLAB R2010a and later
- Added AUTHORS, Changelog, COPYING (license), README and TODO files
- Added license header to every file
- Removed unused functions close_biographs.m , check_network.m, exp_in_pow_out_modular_network.m, gamma_obj_function.m, hierarchically_modular_network.m, modular_random_network.m,
- random_module_size.m, remove_self_loops.m, settings.m,
- unconnected_modules_identification.m