From astakhov at ncmir.ucsd.edu Tue Dec 9 18:24:33 2008 From: astakhov at ncmir.ucsd.edu (astakhov) Date: Tue, 09 Dec 2008 10:24:33 -0800 Subject: [neuroConstruct] neuroConstruct_API Message-ID: <493EB7E1.8020806@ncmir.ucsd.edu> Hello. I am using neuroConstruct GUI to generate Neuron script for the simmulation. It is a very nice tool. But I should go through GUI dosen times when I do incremental modification of some paramiters. Is it possible to do "Export Network", NEURON ->"Generate code" and "Create hoc simmulation" from command line ? That would provide let us to automate the process of Neuron script generation and save a lot of time May be there is an API for neuroConstruct .jar (or source code) available ? I would very appreciate any advice. Best regards, Vadim Astakhov Data Integration Team Leader for Biomedical Informatics Research Network University of California San Diego From p.gleeson at ucl.ac.uk Wed Dec 10 10:53:41 2008 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Wed, 10 Dec 2008 10:53:41 +0000 Subject: [neuroConstruct] neuroConstruct v1.2.0 release Message-ID: <493F9FB5.3090601@ucl.ac.uk> An HTML attachment was scrubbed... URL: From p.gleeson at ucl.ac.uk Wed Dec 10 10:54:40 2008 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Wed, 10 Dec 2008 10:54:40 +0000 Subject: [neuroConstruct] neuroConstruct_API In-Reply-To: <493EB7E1.8020806@ncmir.ucsd.edu> References: <493EB7E1.8020806@ncmir.ucsd.edu> Message-ID: <493F9FF0.6050609@ucl.ac.uk> Hi, The best solution is to use the scripting interface (based on Jython, a Java based implementation of Python). The latest release (see previous mail) has some updated examples of this. The most appropriate file is pythonnC/Ex5_MultiSimGenerate.py, which can be run with nC.bat -python. This runs multiple simulations changing a single parameter each time (though any changes can be made to the project between runs). I can send on a more detailed API for the commands which can be called in scripts (basically the same structure as the corresponding Java methods). The source code will be put online in the next few weeks when I get a new SVN server set up and figure out about licences. Regards, Padraig astakhov wrote: > Hello. > > I am using neuroConstruct GUI to generate Neuron script for the > simmulation. It is a very nice tool. > > But I should go through GUI dosen times when I do incremental > modification of some paramiters. > > Is it possible to do "Export Network", NEURON ->"Generate code" and > "Create hoc simmulation" from command line ? > > That would provide let us to automate the process of Neuron script > generation and save a lot of time > > May be there is an API for neuroConstruct .jar (or source code) > available ? > > I would very appreciate any advice. > > Best regards, > > Vadim Astakhov > > Data Integration Team Leader for > > Biomedical Informatics Research Network > > > University of California San Diego > > From astakhov at ncmir.ucsd.edu Wed Dec 10 19:55:27 2008 From: astakhov at ncmir.ucsd.edu (astakhov) Date: Wed, 10 Dec 2008 11:55:27 -0800 Subject: [neuroConstruct] neuroConstruct_API In-Reply-To: <493F9FF0.6050609@ucl.ac.uk> References: <493EB7E1.8020806@ncmir.ucsd.edu> <493F9FF0.6050609@ucl.ac.uk> Message-ID: <49401EAF.4060700@ncmir.ucsd.edu> Dear Padraig. Thank your for comments. (I was using version 1.1.2) I just updated it with 1.2.0 and looking this pythonnC/ It is great. I see that I can load project, change it and save as NeuroML. But what if my neurons was already saved in NeuroML. I do not need to add them manually in the script. Can I add them to the project from NeuroML file. May be just load it some how to the existing project and then save the modified project ? Does it make sense ? Do you have such Python script ? Then it would be easy to use Ex5_MultiSimGenerate.py to generate NEURON simmulation script for the new project. Thanks again for your comments. Best Regards, *Vadim Astakhov Data Integration Team Leader for Biomedical Informatics Research Network University of California San Diego * > Hi, > > The best solution is to use the scripting interface (based on Jython, > a Java based implementation of Python). The latest release (see > previous mail) has some updated examples of this. The most appropriate > file is pythonnC/Ex5_MultiSimGenerate.py, which can be run with nC.bat > -python. This runs multiple simulations changing a single parameter > each time (though any changes can be made to the project between > runs). I can send on a more detailed API for the commands which can be > called in scripts (basically the same structure as the corresponding > Java methods). The source code will be put online in the next few > weeks when I get a new SVN server set up and figure out about licences. > > Regards, > Padraig > > > > astakhov wrote: > >> Hello. >> >> I am using neuroConstruct GUI to generate Neuron script for the >> simmulation. It is a very nice tool. >> >> But I should go through GUI dosen times when I do incremental >> modification of some paramiters. >> >> Is it possible to do "Export Network", NEURON ->"Generate code" and >> "Create hoc simmulation" from command line ? >> >> That would provide let us to automate the process of Neuron script >> generation and save a lot of time >> >> May be there is an API for neuroConstruct .jar (or source code) >> available ? >> >> I would very appreciate any advice. >> >> Best regards, >> >> Vadim Astakhov >> >> Data Integration Team Leader for >> >> Biomedical Informatics Research Network >> >> >> University of California San Diego >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.gleeson at ucl.ac.uk Thu Dec 11 18:24:21 2008 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Thu, 11 Dec 2008 18:24:21 +0000 Subject: [neuroConstruct] neuroConstruct_API In-Reply-To: <49401EAF.4060700@ncmir.ucsd.edu> References: <493EB7E1.8020806@ncmir.ucsd.edu> <493F9FF0.6050609@ucl.ac.uk> <49401EAF.4060700@ncmir.ucsd.edu> Message-ID: <49415AD5.8030208@ucl.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ex6_LoadCells.py Type: application/x-python Size: 2072 bytes Desc: not available URL: