Package: cxsystem2
CxSystem2, A Flexible Cortical Simulation FrameworkWarning: CxSystem2 BUI is developed for using in a local environment and should not be installed on a publicly accessible server unless extra security measures are added on top of itTable of ContentsSynopsisInstallationWindowsLinux/MacDevelopmentInterfacesBrowser User Interface (BUI)Command Line Interface (CLI)DocumentationCitationSupportTeamLicenseSynopsisCxSystem is a cerebral cortex simulation framework, which operates on personal computers. We have tested the simulation software with a simplified version of a comprehensive cortical microcircuit model [1], which is available as configuration file.The CxSystem aims at easy testing and buildup of diverse models at single cell resolution.  Implemented on the top of the Python-basedBrian2 simulator, CxSystem supports the main goal of Brian, i.e. minimizing development time, by providing the user with a simplified interface.The preliminary version of this software has been developed at Aalto University 2012-2015 [2], and the full version at the Hospital District of Helsinki and Uusimaa and University of Helsinki 2013-2017. The software is distributed under the terms of the GNU General Public License, Copyright 2017 Vafa Andalibi, Henri Hokkanen and Simo Vanni.InstallationWe highly recommend installingCxSystem2on a virtual environment. Use the following commands to install a Python3 virtual environment and install CxSystem:WindowsMake sure you have python 3.5 or above. To create activate avenvin windows at~/CX2(you can deactivate the environment with the commanddeactivateand reactivate later by running the second command):C:\>python--version
Python3.7.4
C:\>python3-mvenv%userprofile%\CX2
C:\>%userprofile%\CX2\Scripts\activate(CX2)C:\>pipinstall--upgradesetuptools(CX2)C:\>pipinstall-Ucxsystem2Moreover, to use the C++ standalone device on Windows, install theVisual C++ Build Tools 2015.Linux/MacMake sure you have python 3.5 or above. To create activate avenvin Linux/Mac at~/CX2(you can deactivate the environment with the commanddeactivateand reactivate later by running the second command):$python--version
Python3.7.4
$python3-mvenv~/CX2
$source~/CX2/bin/activate(CX2)$pipinstall--upgradesetuptools(CX2)$pipinstall-Ucxsystem2DevelopmentTo developCxSystem2, after cloning the repository install it with the following commands:(CX2)$gitclonehttps://github.com/VisualNeuroscience-UH/CxSystem2(CX2)$cdCxSystem2(CX2)$pipinstall--upgradesetuptools(CX2)$pipinstall-rrequirements.txt(CX2)$pipinstall-U-e.With this method any change to the code will be reflected on the package immediately.InterfacesCxSystem2comes with two interfaces:Browser User Interface (BUI)CxSystem's BUI is built to provide users with an interactive environment for changing the parameters for simulations.Command Line Interface (CLI)Beside the BUI, Some of the main functionalities of theCxSystem2are available in terminal, including the BUI itself. All of the following commands have built-in documentations available with-hor--helpflags:cxsystem2This command (all in lower letters and case sensitive) can be used to run a simulation locally using anatomy and physiology configuration files.cxserverThis command will run theCxSystem2BUI django server.cxconfigCxSystem2 supportscsvandjsonfor importing/exporting configuration files. To convert the configuration files, use thecxconfigand pass the path to the configuration file path as its argument. This command recognizes the file type and convert it to the alternative extension.cxclusterUsecxclusterto download the results from the cluster.cxclustertakes in one argument which is the path to the metadata file saved as a result of cluster-run submission. For convenience, at the end of a cluster-run job submission,CxSystem2prints the command that should be run to retrieve the result.cxvisualizeThis command can be used to visualize the result of the simulation usingvisimplvisualizer. ViSimpl binaries are available at the Modeling and Virtual Reality Groupdownload pageat  Universidad Rey Juan Carlos and Universidad Politécnica de Madrid. This command can also be used to generate a pdf of rasterplots from a set of simulations.DocumentationYou can access the documentation of the CxSystem2 atcxsystem2.readthedocs.io.CitationIf you use CxSystem2 for your work, we kindly ask you to cite any of our related articles:Andalibi, V., Hokkanen, H., Vanni, S., Controlling complexity of cerebral cortex simulations—I: CxSystem, a flexible cortical simulation framework, 2019, Neural computationHokkanen, H., Andalibi, V., Vanni, S., Controlling complexity of cerebral cortex simulations—II: Streamlined microcircuits, 2019, Neural computationSupportYou are encouraged to useGithub's Issuesto report bugs, or request enhancements or new features.TeamVafa AndalibiHenri HokkanenSimo VanniLicenseGPL-3-ClauseCopyright 2019 ©HUS Helsinki University Hospital.[1] Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Sanchez, C. A., … Schürmann, F. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell, 163(2), 456–492.http://doi.org/10.1016/j.cell.2015.09.029[2]Heikkinen, H., Sharifian, F., Vigário, R., & Vanni, S. (2015). Feedback to distal dendrites links fMRI signals to neural receptive fields in a spiking network model of the visual cortex. Journal of Neurophysiology, 114(1), 57–69.http://doi.org/10.1152/jn.00169.2015