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sysgensim-users — General discussion list about SysGenSIM
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From: Priya A. <gal...@ya...> - 2019-04-03 08:15:20
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Hi,I have started using sysgensim to simulate expression data and have some queries in specifying the genetic parameters. I used the default value specified for each parameter and generated expression values. Otherwise, when do I change these parameter values? For example, there are 2 outliers in the expression value of one gene. So do I have to change the value of SD in transcriptional variance and degradation variance and simulate till the expression values of this gene across all the subjects are within the same range? How do I decide on setting the mean and SD values for cooperativity coefficient, transcriptional and degradation variance?. Please guide me on this issue. In the genotype matrix file, genes are given either values 0 or 1. Does 0 mean, it is a minor allele and 1 mean it is a major allele?. As upper and lower bound values for Z are given, value between the lower bound and upper bound becomes 1 and value lower than lower bound becomes 0? Thank youRegardsPriya |
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From: Priya A. <gal...@ya...> - 2019-03-20 12:10:00
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Hello,I am trying to simulate gene expression using sysgensim. When I load my network with 3 genes, I get the following error: Error using sparse.Sparse matrix sizes must be non-negative integers less than MAXSIZE as defined by COMPUTER. My network has only 3 nodes and I am facing memory issues. Though I can create a random network with more than 3 nodes. How do I fix this issue? Thank youRegardsPriya |
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From: Andrea P. <and...@cr...> - 2015-03-05 14:39:54
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Dear SysGenSIM users, SysGenSIM has been finally updated to run on the most recent MATLAB releases! Changelog: - 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") Enjoy! Andrea Pinna |
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From: Nicola S. <so...@cr...> - 2013-01-17 14:25:29
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Dear SysGenSIM users, a new release of SysGenSIM has been released with a revamped user interface and the possibility to simulate experimental perturbations. This is the Changelog: - 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 Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2012-05-23 16:16:46
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Dear SysGenSIM users, a new release of SysGenSIM has been released with a bug fix and a minor new feature. This is the Changelog: - 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 Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2012-05-08 14:51:00
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Dear SysGenSIM users, a new release of SysGenSIM has been released with minor bug fixes. This is the Changelog: - Correct load of Gene network or Gene+Phenotype network through the GUI - Correct load of a previously saved network in read_edge_list.m Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2012-04-26 16:44:10
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Dear SysGenSIM users, a new release of SysGenSIM has been released with minor bug fixes. This is the Changelog: - 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 Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2011-09-12 14:16:46
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Dear SysGenSIM users, Andrea and me have just refreshed the look of the SysGenSIM webpage, take a look at http://sysgensim.sourceforge.net/ Let us know if you like it or if you have problems, we are open to any suggestion for improvement. Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2011-09-06 09:54:01
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Alle giovedì 14 luglio 2011, Nicola Soranzo ha scritto: > Dear SysGenSIM users, > the first official stable release of SysGenSIM has been released with minor > new features to celebrate paper acceptance! > > This is the Changelog: > - Updated the reference for SysGenSIM paper in README, now officially > published in Bioinformatics! The SysGenSIM paper reference for the in-print version is: A. Pinna, N. Soranzo, I. Hoeschele, A. de la Fuente "Simulating system genetics data with SysGenSIM" Bioinformatics 27(17), pp. 2459-2462, 2011 Kind regards -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2011-07-14 15:09:22
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Dear SysGenSIM users, the first official stable release of SysGenSIM has been released with minor new features to celebrate paper acceptance! This is the Changelog: - 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 Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2011-06-17 09:03:52
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Dear SysGenSIM users, a new release of SysGenSIM has been released with small bug fixes. This is the Changelog: - 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 PDF manual is now included in the package in the doc/ subdirectory Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2011-06-03 09:53:46
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Dear SysGenSIM users, a new release of SysGenSIM has been released with small bug fixes. This is the Changelog: - Fixed few small bugs when selecting 0 phenotypes. Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2011-06-01 13:56:23
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Dear SysGenSIM users, a new release of SysGenSIM has been released with important bug fixes and other small changes. This is the Changelog: - 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 Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
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From: Nicola S. <so...@cr...> - 2011-05-18 14:49:27
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Opening post for the new SysGenSIM mailing list. Enjoy! -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ |
