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New Izhikevich neuron model; nest_names and synapse dynamics
by Nina Doorn 15 Nov '21

15 Nov '21

Good afternoon, I have adapted the current nest izhikevich neuron model in C++ to obtain a more general izhikevich neuron where more parameters can be set (for example voltage shifts and the membrane capacitance), and the b-parameter can change over time according to some condition, such that also thalamic neurons can be simulated. The new extension module works very well (with much thanks to all earlier help regarding installing extension modules). So hopefully people can eventually, with this model, obtain all the kinds of neurons that Izhikevich describes. As soon as everything is cleaned up and finished, I will upload the code to github. However, before I do that, I have two questions: 1. For the new parameters I added to the existing izhikevich model, I could only use parameter names that are in nest::names. However, for generality and to make it easy to use, I thought it would be better to use the same symbols that Izhikevich uses to describe his model. That way, people can easily replicate all the different types of neurons that Izhikevich describes. He uses these parameters: [image: image.png] Is it possible to include these parameters in the neuron model? Or is it better to just replace them with other parameter names that are already in the nest_names file? 2. The current izhikevich neuron model doesn't model realistic synapses. The membrane potential just jumps on each spike arrival. I would like to include different post-synaptic dynamics with different and preferably multiple timescales (like the beta_multisynapse). Someone mentioned before that a lot of the synaptic dynamics can be defined outside the neuron. So can I use beta synapses with the izhikevich neuron as it is now? Or should I somehow include these dynamics in the C++ file of my new module? I hope the questions are clear. Please let me know if I should provide any additional information. Thanks in advance and have a very nice weekend! Kind regards, Nina

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Installing an extension module in tvb-nest docker
by Nina Doorn 11 Nov '21

11 Nov '21

Dear experts, To develop a spiking neuronal network model of the thalamus, I want to adapt the Izhikevich neuron model to account for the behavior of thalamocortical neurons. Before I do this, I wanted to test if it was possible to install an extension module in my setup. Therefore I followed these steps: https://nest-extension-module.readthedocs.io/en/latest/extension_modules.ht… to install this example nest-extension-module: https://github.com/nest/nest-extension-module . I am working with the tvb-multiscale docker container ( https://github.com/the-virtual-brain/tvb-multiscale/tree/master/tvb_multisc…) in VScode on windows. I've been working with this succesfully and easily managed to make thalamus models with the available aeIF neuron model of NEST. I'm using a python 3.7.3 interpreter and NEST 3. I've succesfully "made" the module with: > docker@84fabd16af99:~/mmb$ cmake > -Dwith-nest=/home/docker/env/neurosci/nest_build/bin/nest-config > ../nest-extension-module-master It gives me the message: > You can now build and install 'mymodule' using > make > make install > The library file libmymodule.so will be installed to > /home/docker/env/neurosci/nest_build/lib/nest/ > Help files will be installed to > /home/docker/env/neurosci/nest_build/share/doc/nest > The module can be loaded into NEST using > nest.Install('mymodule') (in PyNEST) > (mymodule) Install (in SLI > -- Configuring done > -- Generating done > -- Build files have been written to: /home/docker/mmb However, when I try to "make". I get a bunch of errors that I have added at the end of this email. My colleague tried to install exactly the same module in exactly the same way on his linux machine and it worked perfectly. But somehow for me, I get these weird errors that I haven't been able to resolve so far. Does anyone have an idea what the problem might be? It would be greatly appreciated. If you need any additional information please let me know. Thank you in advance and have a nice day! Kind regards, Nina Doorn Error message: docker@84fabd16af99:~/mmb$ make Scanning dependencies of target mymodule_module [ 10%] Building CXX object src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:92:1: error: expected class-name before ‘{’ token { ^ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:115:21: error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’ using nest::Node::handle; ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:116:21: error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’ using nest::Node::handles_test_event; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:121:14: error: ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&, nest::port, nest::synindex, bool)’ marked ‘override’, but does not override nest::port send_test_event( nest::Node&, nest::port, nest::synindex, bool ) override; ^~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:129:8: error: ‘void mynest::pif_psc_alpha::handle(nest::SpikeEvent&)’ marked ‘override’, but does not override void handle( nest::SpikeEvent& ) override; //! accept spikes ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:130:8: error: ‘void mynest::pif_psc_alpha::handle(nest::CurrentEvent&)’ marked ‘override’, but does not override void handle( nest::CurrentEvent& ) override; //! accept input current ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:131:8: error: ‘void mynest::pif_psc_alpha::handle(nest::DataLoggingRequest&)’ marked ‘override’, but does not override void handle( nest::DataLoggingRequest& ) override; //! allow recording with multimeter ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:133:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::SpikeEvent&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:134:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::CurrentEvent&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:135:14: error: ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&, nest::port)’ marked ‘override’, but does not override nest::port handles_test_event( nest::DataLoggingRequest&, nest::port ) override; ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:138:8: error: ‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’ marked ‘override’, but does not override void get_status( DictionaryDatum& ) const override; ^~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:139:8: error: ‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’ marked ‘override’, but does not override void set_status( const DictionaryDatum& ) override; ^~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:143:8: error: ‘void mynest::pif_psc_alpha::init_buffers_()’ marked ‘override’, but does not override void init_buffers_() override; ^~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:146:8: error: ‘void mynest::pif_psc_alpha::calibrate()’ marked ‘override’, but does not override void calibrate() override; ^~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:149:8: error: ‘void mynest::pif_psc_alpha::update(const nest::Time&, long int, long int)’ marked ‘override’, but does not override void update( nest::Time const&, const long, const long ) override; ^~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&, nest::port, nest::synindex, bool)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:324:23: error: no matching function for call to ‘nest::SpikeEvent::set_sender(mynest::pif_psc_alpha&)’ e.set_sender( *this ); ^ In file included from /home/docker/env/neurosci/nest_build/include/nest/connector_model.h:34, from /home/docker/env/neurosci/nest_build/include/nest/common_synapse_properties.h:27, from /home/docker/env/neurosci/nest_build/include/nest/connection.h:27, from /home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27, from /home/docker/nest-extension-module-master/src/mymodule.cpp:29: /home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note: candidate: ‘void nest::Event::set_sender(nest::Node&)’ Event::set_sender( Node& s ) ^~~~~ /home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note: no known conversion for argument 1 from ‘mynest::pif_psc_alpha’ to ‘nest::Node&’ In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘nest::port mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&, nest::port)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53: error: ‘get_name’ was not declared in this scope throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53: note: suggested alternative: ‘get_V_m_’ throw nest::UnknownReceptorType( receptor_type, get_name() ); ^~~~~~~~ get_V_m_ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:380:3: error: ‘ArchivingNode’ has not been declared ArchivingNode::get_status( d ); ^~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member function ‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’: /home/docker/nest-extension-module-master/src/pif_psc_alpha.h:397:3: error: ‘ArchivingNode’ has not been declared ArchivingNode::set_status( d ); ^~~~~~~~~~~~~ In file included from /home/docker/env/neurosci/nest_build/include/nest/connection_manager_impl.h:33, from /home/docker/nest-extension-module-master/src/mymodule.cpp:38: /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h: In instantiation of ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const DictionaryDatum&) const [with ConnBuilderType = mynest::StepPatternBuilder; nest::NodeCollectionPTR = std::shared_ptr<nest::NodeCollection>; DictionaryDatum = lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>]’: /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:67:3: required from here /home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:72:12: error: no matching function for call to ‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR&, nest::NodeCollectionPTR&, const DictionaryDatum&, const DictionaryDatum&)’ return new ConnBuilderType( sources, targets, conn_spec, syn_spec ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:31: /home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&)’ StepPatternBuilder( const nest::NodeCollectionPTR sources, ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3: note: no known conversion for argument 4 from ‘const DictionaryDatum’ {aka ‘const lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>’} to ‘const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&’ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(const mynest::StepPatternBuilder&)’ class StepPatternBuilder : public nest::ConnBuilder ^~~~~~~~~~~~~~~~~~ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate expects 1 argument, 4 provided /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(mynest::StepPatternBuilder&&)’ /home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7: note: candidate expects 1 argument, 4 provided In file included from /home/docker/env/neurosci/nest_build/include/nest/model_manager.h:31, from /home/docker/env/neurosci/nest_build/include/nest/kernel_manager.h:31, from /home/docker/env/neurosci/nest_build/include/nest/connector_base_impl.h:26, from /home/docker/env/neurosci/nest_build/include/nest/connection.h:29, from /home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27, from /home/docker/nest-extension-module-master/src/mymodule.cpp:29: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::has_proxies() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:174:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:176:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘has_proxies’ return proto_.has_proxies(); ~~~~~~~^~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::one_node_per_process() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:181:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:183:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘one_node_per_process’ return proto_.one_node_per_process(); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘bool nest::GenericModel<ElementT>::is_off_grid() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:188:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:190:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘is_off_grid’ return proto_.is_off_grid(); ~~~~~~~^~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::calibrate_time(const nest::TimeConverter&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:195:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:197:10: error: ‘class mynest::pif_psc_alpha’ has no member named ‘calibrate_time’; did you mean ‘calibrate’? proto_.calibrate_time( tc ); ~~~~~~~^~~~~~~~~~~~~~ calibrate /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::GapJunctionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:209:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( ge ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( ge ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::InstantaneousRateConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:216:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( re ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( re ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::DiffusionConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:223:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( de ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( de ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::sends_secondary_event(nest::DelayedRateConnectionEvent&) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:230:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘sends_secondary_event’; did you mean ‘send_test_event’? return proto_.sends_secondary_event( re ); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ send_test_event /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:43: error: return-statement with a value, in function returning ‘void’ [-fpermissive] return proto_.sends_secondary_event( re ); ^ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘nest::SignalType nest::GenericModel<ElementT>::sends_signal() const [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:237:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:239:17: error: ‘const class mynest::pif_psc_alpha’ has no member named ‘sends_signal’ return proto_.sends_signal(); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘const nest::Node& nest::GenericModel<ElementT>::get_prototype() const [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:267:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:269:10: error: invalid initialization of reference of type ‘const nest::Node&’ from expression of type ‘const mynest::pif_psc_alpha’ return proto_; ^~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘void nest::GenericModel<ElementT>::set_model_id(int) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:274:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:276:10: error: ‘class mynest::pif_psc_alpha’ has no member named ‘set_model_id’ proto_.set_model_id( i ); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘int nest::GenericModel<ElementT>::get_model_id() [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:281:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:283:17: error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_model_id’ return proto_.get_model_id(); ~~~~~~~^~~~~~~~~~~~ /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘DictionaryDatum nest::GenericModel<ElementT>::get_status_() [with ElementT = mynest::pif_psc_alpha; DictionaryDatum = lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:251:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:253:30: error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_status_base’; did you mean ‘get_status’? DictionaryDatum d = proto_.get_status_base(); ~~~~~~~^~~~~~~~~~~~~~~ get_status /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In instantiation of ‘nest::Node* nest::GenericModel<ElementT>::allocate_(void*) [with ElementT = mynest::pif_psc_alpha]’: /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:159:1: required from here /home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:161:9: error: cannot convert ‘mynest::pif_psc_alpha*’ to ‘nest::Node*’ in initialization Node* n = new ( adr ) ElementT( proto_ ); ^ make[2]: *** [src/CMakeFiles/mymodule_module.dir/build.make:63: src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:125: src/CMakeFiles/mymodule_module.dir/all] Error 2 make: *** [Makefile:152: all] Error 2

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Using NEST in Spyder/anaconda
by Julien Ballbé 10 Nov '21

10 Nov '21

Dear Sir, Dear Madam, I am currently trying to install NEST in order to be able to use it within an IDE, like Spyder. For the moment I am only able to do the following: open Terminal python3 import nest This works when I use it in the terminal of the computer, but when I open Spyder and execute the following: import nest neuron=nest.Create("iaf_psc_alpha") neuron.get() I get the following error message in the IPython console: runfile('/Users/julienballbe/NEST/untitled0.py', wdir='/Users/julienballbe/NEST') Traceback (most recent call last): File "/Users/julienballbe/NEST/untitled0.py", line 11, in <module> neuron=nest.Create("iaf_psc_alpha") AttributeError: module 'nest' has no attribute 'Create' I am using a Macbook pro M1Max, MacOS 12.0, Spyder 5.1.5, Python 3.9.7. I followed the instruction for building nest on your website ( https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht…) and used your recommendation for M1 macs ( https://nest-simulator.readthedocs.io/en/latest/installation/conda_tips.html ). I build Nest following your instruction, the only error I got was when I ran : (nest-simulator-dev) julienballbe@pclnrs241 NEST % make installcheck NEST Testsuite Results ---------------------------------------------------------------------- Phase Tests Skipped Failures Errors Time ---------------------------------------------------------------------- 01 basetests 6 0 0 0 2.0 02 selftests 8 0 0 0 1.0 03 unittests 179 0 0 0 47.0 04 regressiontests 94 2 0 0 55.0 07 pynesttests 93 0 0 93 2.0 07 pynesttests nc 0 0 0 0 0.0 08 cpptests 30 0 0 0 0.0 ---------------------------------------------------------------------- Total 410 2 0 93 107.0 ---------------------------------------------------------------------- THE NEST TESTSUITE DISCOVERED PROBLEMS The following tests failed | .share.nest.testsuite.pytests.test_NodeCollection | .share.nest.testsuite.pytests.test_aeif_lsodar | .share.nest.testsuite.pytests.test_changing_tic_base | .share.nest.testsuite.pytests.test_clopath_synapse | .share.nest.testsuite.pytests.test_connect_all_to_all | .share.nest.testsuite.pytests.test_connect_array_fixed_indegree | .share.nest.testsuite.pytests.test_connect_array_fixed_outdegree | .share.nest.testsuite.pytests.test_connect_arrays | .share.nest.testsuite.pytests.test_connect_conngen | .share.nest.testsuite.pytests.test_connect_fixed_indegree | .share.nest.testsuite.pytests.test_connect_fixed_outdegree | .share.nest.testsuite.pytests.test_connect_fixed_total_number | .share.nest.testsuite.pytests.test_connect_one_to_one | .share.nest.testsuite.pytests.test_connect_pairwise_bernoulli | .share.nest.testsuite.pytests.test_connect_symmetric_pairwise_bernoulli | .share.nest.testsuite.pytests.test_create | .share.nest.testsuite.pytests.test_current_recording_generators | .share.nest.testsuite.pytests.test_erfc_neuron | .share.nest.testsuite.pytests.test_errors | .share.nest.testsuite.pytests.test_events | .share.nest.testsuite.pytests.test_facetshw_stdp | .share.nest.testsuite.pytests.test_get_set | .share.nest.testsuite.pytests.test_getconnections | .share.nest.testsuite.pytests.test_getnodes | .share.nest.testsuite.pytests.test_glif_cond | .share.nest.testsuite.pytests.test_glif_psc | .share.nest.testsuite.pytests.test_helper_functions | .share.nest.testsuite.pytests.test_jonke_synapse | .share.nest.testsuite.pytests.test_json | .share.nest.testsuite.pytests.test_labeled_synapses | .share.nest.testsuite.pytests.test_mc_neuron | .share.nest.testsuite.pytests.test_multiple_synapses | .share.nest.testsuite.pytests.test_nodeParametrization | .share.nest.testsuite.pytests.test_onetooneconnect | .share.nest.testsuite.pytests.test_parameter | .share.nest.testsuite.pytests.test_parrot_neuron | .share.nest.testsuite.pytests.test_parrot_neuron_ps | .share.nest.testsuite.pytests.test_poisson_generator_rate_change | .share.nest.testsuite.pytests.test_pp_psc_delta | .share.nest.testsuite.pytests.test_pp_psc_delta_stdp | .share.nest.testsuite.pytests.test_quantal_stp_synapse | .share.nest.testsuite.pytests.test_random123 | .share.nest.testsuite.pytests.test_random_parameter | .share.nest.testsuite.pytests.test_rate_copy_model | .share.nest.testsuite.pytests.test_rate_instantaneous_and_delayed | .share.nest.testsuite.pytests.test_rate_neuron | .share.nest.testsuite.pytests.test_rate_neuron_communication | .share.nest.testsuite.pytests.test_recording_backend_ascii | .share.nest.testsuite.pytests.test_recording_backend_memory | .share.nest.testsuite.pytests.test_recording_backends | .share.nest.testsuite.pytests.test_refractory | .share.nest.testsuite.pytests.test_regression_issue-1034 | .share.nest.testsuite.pytests.test_regression_issue-1409 | .share.nest.testsuite.pytests.test_regression_issue-2069 | .share.nest.testsuite.pytests.test_regression_issue-2125 | .share.nest.testsuite.pytests.test_siegert_neuron | .share.nest.testsuite.pytests.test_split_simulation | .share.nest.testsuite.pytests.test_stack | .share.nest.testsuite.pytests.test_status | .share.nest.testsuite.pytests.test_stdp_multiplicity | .share.nest.testsuite.pytests.test_stdp_nn_synapses | .share.nest.testsuite.pytests.test_stdp_synapse | .share.nest.testsuite.pytests.test_stdp_triplet_synapse | .share.nest.testsuite.pytests.test_step_rate_generator | .share.nest.testsuite.pytests.test_synapsecollection | .share.nest.testsuite.pytests.test_threads | .share.nest.testsuite.pytests.test_tsodyks2_synapse | .share.nest.testsuite.pytests.test_urbanczik_synapse | .share.nest.testsuite.pytests.test_visualization | .share.nest.testsuite.pytests.test_vogels_sprekeler_synapse | .share.nest.testsuite.pytests.test_weight_recorder | .share.nest.testsuite.pytests.test_weights_as_lists | .share.nest.testsuite.pytests.test_sp.test_conn_builder | .share.nest.testsuite.pytests.test_sp.test_disconnect | .share.nest.testsuite.pytests.test_sp.test_disconnect_multiple | .share.nest.testsuite.pytests.test_sp.test_enable_multithread | .share.nest.testsuite.pytests.test_sp.test_growth_curves | .share.nest.testsuite.pytests.test_sp.test_sp_manager | .share.nest.testsuite.pytests.test_sp.test_synaptic_elements | .share.nest.testsuite.pytests.test_sp.test_update_synaptic_elements | .share.nest.testsuite.pytests.test_spatial.test_SynapseCollection_distance | .share.nest.testsuite.pytests.test_spatial.test_basics | .share.nest.testsuite.pytests.test_spatial.test_connect_layers | .share.nest.testsuite.pytests.test_spatial.test_connect_sliced | .share.nest.testsuite.pytests.test_spatial.test_connection_with_elliptical_mask | .share.nest.testsuite.pytests.test_spatial.test_create_spatial | .share.nest.testsuite.pytests.test_spatial.test_dumping | .share.nest.testsuite.pytests.test_spatial.test_layerNodeCollection | .share.nest.testsuite.pytests.test_spatial.test_layer_GetStatus_SetStatus | .share.nest.testsuite.pytests.test_spatial.test_plotting | .share.nest.testsuite.pytests.test_spatial.test_rotated_rect_mask | .share.nest.testsuite.pytests.test_spatial.test_selection_function_and_elliptical_mask | .share.nest.testsuite.pytests.test_spatial.test_spatial_distributions Please report test failures by creating an issue at https://github.com/nest/nest_simulator/issues ---------------------------------------------------------------------- make[3]: *** [CMakeFiles/installcheck] Error 1 make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2 make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2 make: *** [installcheck] Error 2 Can you please help me with this? I stay at your disposal for any further information. Thank you for your help, Best feelings, Julien Ballbé -- *Julien BALLBÉ Y SABATÉ* *Étudiant en thèse - PhD student* *Neurophysiology of Visual Computation* Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35

2 1

population specific structural plasticity switch
by Aadhar Sharma 10 Nov '21

10 Nov '21

2 2

NeuronUnit interface to NEST Adexp model.
by Russell J. Jarvis 10 Nov '21

10 Nov '21

Hi there NEST community, I am trying to build an interface between [NEST reduced cell models (Izhikevich/AdExp) and NeuronUnit](https://github.com/russelljjarvis/NESTNeuronUnit). For example here is one such [interface](https://github.com/russelljjarvis/NESTNeuronUnit/blob/master/nes… ) I find that if I run a single current injection experiment using the interface I get an expected number of spikes, but if I keep re-using the same interface in more and more experiments I get the same or similar number of spikes even with different current injection values. Its as if the initial conditions of the model are not re-setting properly. I wonder if there are any ideas of things I could check. This [simple file works okay](https://github.com/russelljjarvis/NESTNeuronUnit/blob/master/test_int…, but it only has one simulation run. Russell Jarvis (he,him) PhD Neuroscience [Personal Website](https://russelljjarvis.github.io/home/) I acknowledge the Dja Dja Wurrung and Taungurung Owners and Custodians of the lands on which I live and work and pay my respect to Elders past, present and future. phone: 61444576301 email: russelljarvis(a)protonmail.com Sent with [ProtonMail](https://protonmail.com/) Secure Email.

2 3

Get details of source and target from Connection list
by Maryada Maryada 09 Nov '21

09 Nov '21

Dear NEST users, In the past version, for debugging purposes I used to get information of my source and target using the GetStatus function. However, with NEST 3.0, I couldn't find a way to do so, mainly because I have to pass either a SynpaseCollection or NeuronCollection as a function argument to GetStatus. Is it possible to fetch node collection from neuron id? Or any easier way to get source and target properties. I referred document at link https://nest-simulator.readthedocs.io/en/v3.1/guides/connection_management.… I have attached the python file for the same. -- Thanks, *Maryada*

2 3

install nest-2.20.0
by Alberto 08 Nov '21

08 Nov '21

Dear experts, I'd like to install the Nest version 2.20.0 instead of the last 3.1. Is it still available for download? Thanks Alberto

4 8

Get details of source and target from Connection list
by Maryada Maryada 08 Nov '21

08 Nov '21

Dear NEST users, In the past version, for debugging purposes, I used to get information of my source and target using the GetStatus function. However, with NEST 3.0, I couldn't find a way to do so, mainly because I have to pass either a SynpaseCollection or NeuronCollection as a function argument to GetStatus. Is it possible to fetch node collection from neuron id? Or any easier way to get the source and target properties. I referred document at link https://nest-simulator.readthedocs.io/en/v3.1/guides/connection_management.… I have attached the python file for the same. -- Thanks and Regards *Maryada*

1 0

Open NEST Developer Video Conference Monday 8 November 2021 11:30 CET (UTC+1)
by Dennis Terhorst 08 Nov '21

08 Nov '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 8 November, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-11-08-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

1 0

Requesting for workflow and analysis
by D S Jaswanth 04 Nov '21

04 Nov '21

Sir /madam I'm jaswanth , pursuing my master's degree in biochemistry @reva university Were I'm very much interested working with brain modelling by using neuroinformatical tools as part of my research project I request that please give me workflow for Analysing dataset and codes for analysis of dataset finally what types of datasets can be used for brain modelling by nest I hope for your consideration and guidance Thanks and regards

2 3

NEST on macOS 12 Monterey
by Hans Ekkehard Plesser 04 Nov '21

04 Nov '21

Dear NEST Users, I would just like to let you know that I have successfully built, installed and tested NEST on macOS 12.0.1 (Monterey) on Apple Silicon, following the standard procedure for the Mac. Both Apple Clang 13.0 and G++ 11 work. Note that there have been some reports that upgrading to macOS Monterey can very thoroughly lock your machine, especially Intel-based machines (https://arstechnica.com/gadgets/2021/11/why-macos-updates-might-brick-your-…), so you may want to wait with upgrading until this is solved. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Head, Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

1 0

Re: Adapt custom models from NEST 2.16 to NEST 3.
by Agnes Korcsak-Gorzo 28 Oct '21

28 Oct '21

Dear all, the request below from 20.10.2021 was successfully resolved. Best regards, Agnes """" Hello everyone, I want to adapt two custom models called "global_volume_transmitter" and "dopa_connection" from NEST 2.16 to NEST 3.1. The .cpp and .h files are attached to this email. Is it possible to have the models adapted to NEST 3.1? How could this be done? I hope someone can help me with that. Best regards, Daniel Todt """

1 0

nest installment in Docker nestsim/nest container
by Nina Doorn 25 Oct '21

25 Oct '21

Dear experts, I have a question about using nest on docker/vscode on my windows PC. I hope this is the right place to ask since I couldn't answer my question using the troubleshooting session. I am using docker to use pyNEST on my windows computer. I have successfully installed NEST using the instructions mentioned here for installing on docker: https://nest-simulator.readthedocs.io/en/v2.20.1/installation/index.html. If I am in the container, I have python version 3.8.10. If I run python and then try to "import nest" it says there is no module named nest. Importing other python packages works perfectly in this way. But indeed, when I look at all the installed packages using pip list, there is no package called "nest". There is, however "nest-desktop 3.0.3" there. So I guess nest is not installed. However, I also don't know how to install it. If I use pip install nest, another package called nest is installed that is not the nest simulator (according to: #754 <https://github.com/nest/nest-simulator/issues/754>). Also, I don't know whether this problem is related or totally unrelated but it might give some insight: when I am in VScode in the nestsim/nest container and I click on python: select interpreter, nothing happens, I cannot select a python interpreter/no window opens. So maybe there is something wrong with the python installations or the used path? I hope the problem is clear. I've been trying different things for days so I would greatly appreciate any help you can offer me! Thanks in advance and have a nice day! Kind regards, Nina Doorn

4 8

Open NEST Developer Video Conference Monday 11 October 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 25 Oct '21

25 Oct '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 25 October, 11.30-12.30 CEST (UTC+2). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-10-25-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

1 0

HBP CodeJam#12
by Dennis Terhorst 21 Oct '21

21 Oct '21

Dear all, next month there will be another HBP CodeJam [1] coming up on Nov 23rd-26th and we think this might be an interesting occasion to meet and bring everyone up to the new possibilities now becoming available. The setup of models has become a lot simpler for example using NEST 3's object attribute access, and many models just need minor changes to make use of the powerful new syntax. Additionally the EBRAINS infrastructure has recently released very useful features that allow to combine different tools across the platform. While the CodeJam is mainly advertised for service providers, it would be extremely helpful to have interested power users in the discussion to get direct feed-back for which features to specially prioritize. As far as I know the event is open to anyone with an EBRAINS account for which you can quickly register [2]. We can set up discussion slots also for discussing your use-case, questions or comments, and the event is also suited to work on real code and boost your project. If you are interested for example to have a look into migrating your model to NEST 3, or if you have a particular topic you would like to discuss with NEST developers, or see what is possible on EBRAINS now, please register for the event and let me know! I'll try to gather the most productive set of people for those discussions. (In case you create a new EBRAINS account for this CodeJam let me know, so I can have your account linked to the workshop – need to check…) Looking forward! Best, Dennis [1]: https://www.humanbrainproject.eu/en/follow-hbp/events/ebrainshbp-codejam-co… [2]: https://ebrains.eu/register -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de ---------------------------------------------------------------------- Forschungszentrum Juelich GmbH, 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ----------------------------------------------------------------------

1 0

Connection management for huge network
by kusch lionel 20 Oct '21

20 Oct '21

Dear all, In my working group, we are working on the creation of the spiking neural network of human CA1 (4.8 million neurons). We are using a specific function for defining the connection between the neurons. This function gives us 30 billion pairwise connections. We would like to know what the most efficient for the creating the network in NEST 3 using this pairwise connectivity. Thank you in advance for your answer, Kusch Lionel

3 4

Adapt custom models from NEST 2.16 to NEST 3.1
by Daniel Todt 20 Oct '21

20 Oct '21

Hello everyone, I want to adapt two custom models called "global_volume_transmitter" and "dopa_connection" from NEST 2.16 to NEST 3.1. The .cpp and .h files are attached to this email. Is it possible to have the models adapted to NEST 3.1? How could this be done? I hope someone can help me with that. Best regards, Daniel Todt -- Daniel Todt HPC in Neuroscience Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich GmbH Tel.: +49 2461 61 85277 E-Mail: d.todt(a)fz-juelich.de ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

Dennis Asked
by Chris Huyck 12 Oct '21

12 Oct '21

I've recently downloaded a new version of NEST, and I'm trying to make a new synaptic model, but am breaking down in building their default MyModule model. The process onhttps://nest.github.io/nest-simulator/extension_modules<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnest.gith…> says to run bootstrap.sh, but I can't find a bootstrap.sh. Do you have a version you could send me? If not, who can I contact for help (and how)? -Chris

2 1

Open NEST Developer Video Conference Monday 11 October 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 11 Oct '21

11 Oct '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 11 October, 11.30-12.30 CEST (UTC+2). Today we again have two possible topics for the in-depth discussion that you may be interested in: * Plasticity models via NESTML, and * NEST wheels (Python package mechanism). As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-10-11-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

1 0

Open NEST Developer Video Conference Monday 27 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 27 Sep '21

27 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 27 September, 11.30-12.30 CEST (UTC+2). As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-09-27-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

1 0

NEST 3.1 is there!
by Dennis Terhorst 15 Sep '21

15 Sep '21

2 1

Open NEST Developer Video Conference Monday 13 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 13 Sep '21

13 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 13 September, 11.30-12.30 CEST (UTC+2). Today we have two topics for the in-depth discussion that you may be interested in. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion * Failing assertions #2101 <https://github.com/nest/nest-simulator/issues/2101> * Naming of modules (see nest-connplotter:#2 <https://github.com/nest/nest-connplotter/pull/2>) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-09-13-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you're in. In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. - Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800 - Using the SIP protocol:97938800@vc.dfn.de - By telephone: +49-30-200-97938800 For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4

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NEST 3.0: Plot weight matrices example ERROR
by Ing Jyh Tsang 31 Aug '21

31 Aug '21

I think there is an error in https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m… * min(E_neurons)and min(I_neurons) should be replace to * min(E_neurons.tolist()) and min(I_neurons.tolist())or some other way to get the right values Suggestion: The file plot_weight_matrices.py just contain a def plot_weight_matrices(E_neurons, I_neurons). If it had a complete code to create nodes, assign weights then plot the weight matrixes, the error could have been caught automatically (CI/CD)? Best, Inton

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Problems after ubuntu installed nest-3.0 built on Aug 24 2021
by Ing Jyh Tsang 31 Aug '21

31 Aug '21

Hi, After my ubuntu upgraded nest. Whenever I run a program it does not seems to identify the nest module. For example, running the twoneuron.py example gives: Traceback (most recent call last): File "twoneurons.py", line 43, in <module> import nest.voltage_trace ModuleNotFoundError: No module named 'nest.voltage_trace' Please solution for this? I tried remove and reinstalling and did not work. I did not try building it. Thanks, Inton

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AttributeError: module 'nest' has no attribute 'SetKernelStatus'
by Alberto 31 Aug '21

31 Aug '21

Hi, suddenly, I am starting having this error. I have both PyNN and Nest installed. If it's more related to the PyNN community, I will forward this message to them, but at this moment I don't know if it's more related to Nest or PyNN side. Maybe some of you have met a similar issue. >>> import pyNN.nest as sim Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/__init__.py", line 18, in <module> from . import simulator File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 261, in <module> state = _State() # a Singleton, so only a single instance ever exists File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 58, in __init__ self.spike_precision = "off_grid" File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 114, in _set_spike_precision nest.SetKernelStatus({'off_grid_spiking': True}) AttributeError: module 'nest' has no attribute 'SetKernelStatus' Thanks, Alberto

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