From mattioni at ebi.ac.uk Wed Apr 30 00:09:37 2008 From: mattioni at ebi.ac.uk (Michele Mattioni) Date: Wed, 30 Apr 2008 00:09:37 +0100 Subject: [neuroConstruct] source code of NeuroConstructor Message-ID: <290ea1b00804291609p3beb0d82ieb21e8b5b7dde5c0@mail.gmail.com> Hi list, how can I download the code of NeuroConstructor? I tried to run the quick tutorial but I can not run the simulation from Neuroconstruct but I'm not able to do it. I've got the error attached. When I tried to run the genesis simulation it worked. Do you have any suggestion? Regards, Michele -------------- next part -------------- 00:01:30.543> GeneratedNetworkConnections: Finished saving data to file: /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/simulations/Sim_30/NetworkConnections.dat 00:01:30.543> GeneratedElecInputs : Saving 1 inputs to file: /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/simulations/Sim_30/ElectricalInputs.dat 00:01:30.544> GeneratedElecInputs : File: /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/simulations/Sim_30/ElectricalInputs.dat doesn't exist. 00:01:30.544> GeneratedElecInputs : Finished saving data to file: /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/simulations/Sim_30/ElectricalInputs.dat 00:01:30.545> CellGroupsInfo : Request for Cell Type in group: SampleCellGroup 00:01:30.546> GenesisSettings : Looking for text for location: Type -1, Before Cells created 00:01:30.547> GenesisSettings : Found: 00:01:30.547> GenesisSettings : Looking for text for location: Type 5, Before Final reset 00:01:30.547> GenesisSettings : Found: 00:01:30.548> GenesisSettings : Looking for text for location: Type 10, After Final reset 00:01:30.548> GenesisSettings : Found: null 00:01:30.549> GenesisSettings : Looking for text for location: Type 15, After simulation run 00:01:30.549> GenesisSettings : Found: null 00:01:30.549> SequenceGenerator : Num in sequence: 1 00:01:30.550> SequenceGenerator : Num in sequence: 1 00:01:30.550> SequenceGenerator : Num in sequence: 1 00:01:30.556> GenesisFileManager : Assuming *nix environment... 00:01:30.557> GenesisFileManager : Assume we're using Gnome 00:01:31.181> GenesisFileManager : Going to execute command: --title=GENESIS_simulation___Sim_30 --working-directory=/home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/generatedGENESIS -x /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/generatedGENESIS/runsim.sh 00:01:31.198> GenesisFileManager : *** ERROR*** : Error running the command: --title=GENESIS_simulation___Sim_30 --working-directory=/home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/generatedGENESIS -x /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/generatedGENESIS/runsim.sh 00:01:31.199> MainFrame : *** ERROR*** : User being informed of error 00:01:31.199> MainFrame : *** ERROR*** : Error executing the GENESIS file: /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/generatedGENESIS/Ex1-Simple.g 00:01:31.201> MainFrame : *** ERROR*** : ucl.physiol.neuroconstruct.genesis.GenesisException: Error executing the GENESIS file: /home/mattions/Work/progs/neuroConstruct_1.0.4.1/examples/Ex1-Simple/generatedGENESIS/Ex1-Simple.g 00:01:31.202> MainFrame : *** ERROR*** : at ucl.physiol.neuroconstruct.genesis.GenesisFileManager.runGenesisFile(GenesisFileManager.java:2731) 00:01:31.202> MainFrame : *** ERROR*** : at ucl.physiol.neuroconstruct.gui.MainFrame.doRunGenesis(MainFrame.java:5812) 00:01:31.202> MainFrame : *** ERROR*** : at ucl.physiol.neuroconstruct.gui.MainFrame.jButtonGenesisRun_actionPerformed(MainFrame.java:10737) 00:01:31.203> MainFrame : *** ERROR*** : at ucl.physiol.neuroconstruct.gui.MainFrame$23.actionPerformed(MainFrame.java:1111) 00:01:31.203> MainFrame : *** ERROR*** : at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012) 00:01:31.203> MainFrame : *** ERROR*** : at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335) 00:01:31.204> MainFrame : *** ERROR*** : at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404) 00:01:31.204> MainFrame : *** ERROR*** : at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) 00:01:31.204> MainFrame : *** ERROR*** : at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:253) 00:01:31.205> MainFrame : *** ERROR*** : at java.awt.Component.processMouseEvent(Component.java:6101) 00:01:31.205> MainFrame : *** ERROR*** : at javax.swing.JComponent.processMouseEvent(JComponent.java:3276) 00:01:31.205> MainFrame : *** ERROR*** : at java.awt.Component.processEvent(Component.java:5866) 00:01:31.206> MainFrame : *** ERROR*** : at java.awt.Container.processEvent(Container.java:2105) 00:01:31.206> MainFrame : *** ERROR*** : at java.awt.Component.dispatchEventImpl(Component.java:4462) 00:01:31.207> MainFrame : *** ERROR*** : at java.awt.Container.dispatchEventImpl(Container.java:2163) 00:01:31.207> MainFrame : *** ERROR*** : at java.awt.Component.dispatchEvent(Component.java:4288) 00:01:31.207> MainFrame : *** ERROR*** : at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4461) 00:01:31.208> MainFrame : *** ERROR*** : at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4125) 00:01:31.208> MainFrame : *** ERROR*** : at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4055) 00:01:31.208> MainFrame : *** ERROR*** : at java.awt.Container.dispatchEventImpl(Container.java:2149) 00:01:31.209> MainFrame : *** ERROR*** : at java.awt.Window.dispatchEventImpl(Window.java:2478) 00:01:31.209> MainFrame : *** ERROR*** : at java.awt.Component.dispatchEvent(Component.java:4288) 00:01:31.209> MainFrame : *** ERROR*** : at java.awt.EventQueue.dispatchEvent(EventQueue.java:604) 00:01:31.210> MainFrame : *** ERROR*** : at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275) 00:01:31.210> MainFrame : *** ERROR*** : at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200) 00:01:31.211> MainFrame : *** ERROR*** : at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190) 00:01:31.211> MainFrame : *** ERROR*** : at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185) 00:01:31.212> MainFrame : *** ERROR*** : at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177) 00:01:31.212> MainFrame : *** ERROR*** : at java.awt.EventDispatchThread.run(EventDispatchThread.java:138) 00:01:31.212> MainFrame : *** ERROR*** : Caused by: java.io.IOException: Cannot run program "--title=GENESIS_simulation___Sim_30": java.io.IOException: error=2, No such file or directory 00:01:31.213> MainFrame : *** ERROR*** : at java.lang.ProcessBuilder.start(ProcessBuilder.java:474) 00:01:31.213> MainFrame : *** ERROR*** : at java.lang.Runtime.exec(Runtime.java:610) 00:01:31.213> MainFrame : *** ERROR*** : at java.lang.Runtime.exec(Runtime.java:448) 00:01:31.214> MainFrame : *** ERROR*** : at java.lang.Runtime.exec(Runtime.java:345) 00:01:31.214> MainFrame : *** ERROR*** : at ucl.physiol.neuroconstruct.genesis.GenesisFileManager.runGenesisFile(GenesisFileManager.java:2723) 00:01:31.215> MainFrame : *** ERROR*** : ... 28 more 00:01:31.215> MainFrame : *** ERROR*** : Caused by: java.io.IOException: java.io.IOException: error=2, No such file or directory 00:01:31.215> MainFrame : *** ERROR*** : at java.lang.UNIXProcess.(UNIXProcess.java:164) 00:01:31.216> MainFrame : *** ERROR*** : at java.lang.ProcessImpl.start(ProcessImpl.java:81) 00:01:31.216> MainFrame : *** ERROR*** : at java.lang.ProcessBuilder.start(ProcessBuilder.java:467) 00:01:31.216> MainFrame : *** ERROR*** : ... 32 more From p.gleeson at ucl.ac.uk Wed Apr 30 10:34:26 2008 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Wed, 30 Apr 2008 10:34:26 +0100 Subject: [neuroConstruct] source code of NeuroConstructor In-Reply-To: <290ea1b00804291609p3beb0d82ieb21e8b5b7dde5c0@mail.gmail.com> References: <290ea1b00804291609p3beb0d82ieb21e8b5b7dde5c0@mail.gmail.com> Message-ID: <48183D22.9000607@ucl.ac.uk> An HTML attachment was scrubbed... URL: From mattions at gmail.com Wed Apr 30 12:51:03 2008 From: mattions at gmail.com (Michele Mattioni) Date: Wed, 30 Apr 2008 12:51:03 +0100 Subject: [neuroConstruct] source code of NeuroConstructor In-Reply-To: <48183D22.9000607@ucl.ac.uk> References: <290ea1b00804291609p3beb0d82ieb21e8b5b7dde5c0@mail.gmail.com> <48183D22.9000607@ucl.ac.uk> Message-ID: <290ea1b00804300451h4ca506b3q30af81facc9f9d87@mail.gmail.com> On Wed, Apr 30, 2008 at 10:34 AM, Padraig Gleeson wrote: > > Hi, > > neuroConstruct isn't currently open source, but going fully open is a key > part of funding request we're making at the moment. We've also got a new > developer starting next month who'll be looking at cleaning up the code > already and making it more modular so that others can extra functionality > more easily. > Ah ok. I've understood the code was already available. thanks. > The problem below can be fixed by either specifying "gnome-terminal -x" or > "konsole" (for Gnome or KDE desktops respectively) at Settings -> General > Properties -> Command line. The comment below that text field is a bit > misleading, but will be fixed in a new update planned for the next few days. > I've tried with the -x option but it doesn't work. I've tested this also directly from the gnome-teminal but it seems the terminal doesn't execute the command It seems it is a gnome-terminal bug With the xterm everything work as expected and it is possible to run the simulation. BTW: It's really a nice tool. Cheers, Michele. From p.gleeson at ucl.ac.uk Wed Apr 30 14:26:01 2008 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Wed, 30 Apr 2008 14:26:01 +0100 Subject: [neuroConstruct] source code of NeuroConstructor In-Reply-To: <290ea1b00804300451h4ca506b3q30af81facc9f9d87@mail.gmail.com> References: <290ea1b00804291609p3beb0d82ieb21e8b5b7dde5c0@mail.gmail.com> <48183D22.9000607@ucl.ac.uk> <290ea1b00804300451h4ca506b3q30af81facc9f9d87@mail.gmail.com> Message-ID: <48187369.7030305@ucl.ac.uk> An HTML attachment was scrubbed... URL: