Software WG taskforce: simulator selection resource<br>Consolidated notes from meetings

# Software WG taskforce: simulator selection resource<br>Consolidated notes from meetings ## Resource links ### Meeting notes * [Meeting 1: 2022-11-02](https://hackmd.io/@sanjayankur31/B1thUbeSo) * [Meeting 2: 2022-11-16](https://hackmd.io/8GCjcf2hSvy8iWjzgrdNHg) * [Meeting 3: 2022-11-30](https://hackmd.io/yS2m5vftR_CkUsVsS-zyOA) * [Meeting 4: 2023-01-11](https://hackmd.io/@mstimberg/SJ5LcV2cj) * [Meeting 5: 2023-01-25](https://hackmd.io/@mstimberg/rkN-yS6ji) * [Meeting 6: 2023-08-02](https://hackmd.io/@mstimberg/S1PxWQZ6j) * [Meeting 7: 2023-22-02](https://hackmd.io/@mstimberg/r1w_pqXAs) * [Meeting 8: 2023-03-08](https://hackmd.io/@mstimberg/SkaUQ181n) * [Meeting 9: 2023-03-22](https://hackmd.io/@mstimberg/BkECWB_gn) * [Meeting 10: 2023-04-05](https://hackmd.io/@mstimberg/Bkvkvyjb2) * [Meeting 11: 2023-04-19](https://hackmd.io/@mstimberg/SkqazEpz3) * [Meeting 12: 2023-05-03](https://hackmd.io/@mstimberg/B1R6f2JN3) * [Meeting 13: 2023-05-31](https://hackmd.io/@mstimberg/HJ5_en4Ih) * [Meeting 14: 2023-06-14](https://hackmd.io/@mstimberg/HJ_ht4PDn) * [Meeting 15: 2023-06-28](https://hackmd.io/@mstimberg/SJI_FiY_2) * [Meeting 16: 2023-07-12](https://hackmd.io/@mstimberg/BJMUZX3Fh) * [Meeting 17: 2023-09-13](https://hackmd.io/@mstimberg/BJA1wl1kp) * [Meeting 18: 2023-09-27](https://hackmd.io/@mstimberg/Bk8Q_Ybgp) * [Meeting 19: 2023-10-11](https://hackmd.io/@mstimberg/HkgnzGVW6) * [Meeting 20: 2023-10-25](https://hackmd.io/@mstimberg/ByTnoHIzp) * [Meeting 21: 2023-12-06](https://hackmd.io/@mstimberg/SJz9WJCST) * [Meeting 22: 2023-12-20](https://hackmd.io/@mstimberg/S1gXwSevT) * [Meeting 23: 2024-01-17](https://hackmd.io/@mstimberg/ByYsCf4ta) * [Meeting 24: 2024-02-14](https://hackmd.io/@mstimberg/SyV-WsLqa) * [Meeting 25: 2024-02-28](https://hackmd.io/@mstimberg/Bys-5ih3p) * [Meeting 26: 2024-03-13](https://hackmd.io/@mstimberg/HJBcPzk0p) * [Meeting 27: 2024-05-22](https://hackmd.io/@mstimberg/H1_BYms7R) * [Meeting 28: 2024-06-05](https://hackmd.io/@mstimberg/H1RrAipEA) * [Meeting 29: 2024-07-31](https://hackmd.io/s/BJo4TcwtC) * [Meeting 30: 2024-10-09](https://hackmd.io/@mstimberg/SJxxAMAQk1l) * [Meeting 31: 2024-11-06](https://hackmd.io/@mstimberg/H1mGqLIx1e) * [Meeting 32: 2024-12-04](https://hackmd.io/@mstimberg/S1wUN26mJe) * [Meeting 33: 2025-01-15](https://hackmd.io/@mstimberg/Syvr1ZBPkx) * [Meeting 34: 2025-01-29](https://hackmd.io/@mstimberg/HyKNGFv_Jg) * [Meeting 35: 2025-02-27](https://hackmd.io/@mstimberg/HkwZxDs51x) * [Meeting 36: 2025-03-12](https://hackmd.io/@mstimberg/S1SUz0CiJl) * [Meeting 37: 2025-03-26](https://hackmd.io/@mstimberg/SJ3y2OZTkx) * [Meeting 38: 2025-04-09](https://hackmd.io/@mstimberg/Hy1mqnmAyg) * [Meeting 39: 2025-05-07](https://hackmd.io/@mstimberg/Hkgin5suexl) * [Meeting 40: 2025-05-21](https://hackmd.io/@mstimberg/BkvckXo-eg) * [Meeting 41: 2025-06-04](https://hackmd.io/@mstimberg/rkhVjipzxx) * [Meeting 42: 2025-06-18](https://hackmd.io/@mstimberg/r1_l5xe4ex) * [Meeting 43: 2025-07-09](https://hackmd.io/@mstimberg/HyLcfRXree) * [Meeting 44: 2025-09-10](https://hackmd.io/@mstimberg/ry6MvkJoel) ### Related discussions * Initial discussion on GitHub: https://github.com/OCNS/SoftwareWG/issues/61 ### Existing lists of simulators * https://github.com/asoplata/open-computational-neuroscience-resources#simulation-software * https://compneuroweb.com/sftwr.html#modeling ### Model databases - [ModelDB](https://senselab.med.yale.edu/modeldb/) - [Open source brain](https://www.opensourcebrain.org/projects) - [List of data bases by the Fedora Project](https://docs.fedoraproject.org/en-US/neurofedora/related-links/#_neuroscience_databases) ### Review papers about model types - [Modeling Single-Neuron Dynamics and Computations](https://www.science.org/doi/full/10.1126/science.1127240) - [Theory and Simulation in Neuroscience](https://www.science.org/doi/full/10.1126/science.1227356) ## Criteria for tool inclusion/exclusion ### General agreement * Must be FOSS and accessible without required registration or similar * Accept tools that rely on proprietary software (MATLAB, CUDA, …), if the tool itself is FOSS * Should be installable/working (also see status metadata below) * Must have some point of contact (email, GitHub issues, forum, …) * Must have free and freely accessible documentation (enough to use it, there could be additional non-free material like books or courses) * neuroscience-specific tool (or main/major use case), not general chemical/physical simulator – use best judgement, we can always include additional tools if authors/users claim that they are relevant ### Still needs discussion * Do we need to make a difference between "frontend tools" like PyNN, BMTK, NetPyNE, and simulators? What about things like MUSIC? ## Meta data/annotations ### General agreement * some general structured information: website and other links, os support, interface language * Some kind of explanation for metadata/tags needed (e.g. glossary, examples, [model hierarchy](https://docs.arbor-sim.org/en/latest/ecosystem/index.html#simulators), …) * Describe things from user-perspective first (e.g. programming language is the language of the interface, not of the backend) ### Still needs discussion * Only free-form tags or additional pre-defined meta data (model type, scale, description language support, …)? * maintenance development status, Unknown/Unmaintained/Archived, functional/maintained, active dev? For example: * active dev: regular releases or commits (at least one commit within last month, one release in last year). * maintained: occasional bug fixes (at least one in past year) * unknown: unknown ;) ## Annotated list of simulators :::info NEW: **[YAML version of this list](https://github.com/OCNS/simselect/blob/main/simtools/simtools.yaml)** ::: - Arbor (brent) - website: arbor-sim.org - biological-level: detailed neurons, single cells, large networks - network-level: - tags: multicompartment, hpc, gpu, python, c++, large-scale, neuroml, neurolucida, swc, nmodl - floss license: BSD - installable: lin/win/macos - Point of contact: Gitter https://gitter.im/arbor-sim/community, Matrix: #arbor-sim_community:gitter.im, Github https://github.com/arbor-sim/arbor/, email contact@arbor-sim.org - user docs: docs.arbor-sim.org - status: maintained - inclusion: yes :) - Arbor GUI (brent) - website: https://github.com/arbor-sim/gui/ - level: detailed neurons, single cells - tags: multicompartment, hpc, gpu, python, c++, large-scale, gui, - floss license: BSD - installable: lin/win/macos - Point of contact: Gitter https://gitter.im/arbor-sim/gui, Github https://github.com/arbor-sim/gui/issues, Matrix: #arbor-sim_community:gitter.im - user docs: https://github.com/arbor-sim/gui/ - status: maintained - inclusion: yes - Brian (Marcel) - website: [https://briansimulator.org/](https://briansimulator.org/) - tags: python, single-compartment models, channel-based models, integrate-and-fire models, basic multi-compartmental models, custom models, differential equations, spiking networks, networks, physical units, code generation, OpenMP, multi-threading, single machine, simulation - interface language: python - license: CeCILL 2.1 license - installable: linux/macOS/windows - Point of contact: [discourse](https://brian.discourse.group/), github issues - user docs: [https://brian2.readthedocs.io/en/stable/](https://brian2.readthedocs.io/en/stable/) - status: maintained and actively developed - inclusion: yes - BrainDynamics Tool box - website: https://bdtoolbox.teachable.com/ - tags: dynamical systems, matlab, ode - floss license: BSD but requires Matlab (Octave explicitly noted to not be supported) - installable: lin/win/macos (Matlab!) - PoC: e-mail - user docs: a free beginner level course, and chapter 1 of handbook is free; paid course and full handbook needs to be purchased - inclusion: yes - BMTK (brent) - website: https://alleninstitute.github.io/bmtk/ , https://alleninstitute.github.io/bmtk/index.html#base-installation - level: multi-compartment biophysically detailed networks, to point-neuron models, to filter-based models, and even population-level firing rate models. - tags: detailed neurons, single cells, networks, sonata - floss license: BSD - installable: Lin/win/macos (Python, but may require other tools: NEST/dipde etc. so may depend on individual tools in the stack) - PoC: issues/PRs - user docs: https://alleninstitute.github.io/bmtk/ - inclusion: yes - Nest (Ankur) - website: https://nest-simulator.org - tags: python, c++, gui, large-scale - license: GPLv2 - installable: lin/win/macos - PoC: GitHub, mailing list, e-mail - user docs: https://nest-simulator.org - status: maintained - inclusion: yes - biological scale: point neurons, HH type with one compartment, "neurons with few compartments" - network scale: single cell, small scale, meso scale networks, large scale networks - large scale implemented by: MPI - interface languages: Python, SLI, C++(?) - model coverage: built-in models, extensible - file formats in: ? - file formats out: ? - Neuron (and CoreNEURON) (Ankur) - website: https://neuron.yale.edu/neuron/ - tags: python, gpu, c/c++, gui, compartment, - license: BSD - installable: lin/win/macos - point of contact: GitHub, forum - user docs: [CoreNeuron](https://nrn.readthedocs.io/en/latest/coreneuron/index.html) [Neuron](https://nrn.readthedocs.io/en/8.2.1/) - status: maintained - inclusion: yes - biological scale: sub-cellular, reaction-diffusion, point neurons, HH type with single, HH type with multiple compartments - network scale: single cell, small scale networks, meso scale networks, large scale networks - large scale implemented by: MPI (user friendly term: supercomputing/cluster/multi-node support? ) - interface languages: Python, HOC, NMODL - model coverage: built-in models, extensible - file formats in: ? - LFPy (brent) - website: https://lfpy.readthedocs.io/en/latest/ - tags: python, local field potentials, multicompartment neurons - license: GNU General Public License (GPL) - installable: OS Independent - point of contact: ? (maybe github issues) - user docs: https://lfpy.readthedocs.io/en/latest/ - status: maintained - inclusion: ? - other: based on NEURON simulator - NetPyNE (Ankur) - website: http://www.netpyne.org/ - tags: python, - license: MIT License - installable: OS Independent (python package) - point of contact: - user docs: http://www.netpyne.org/about.html - status: stable, maintained, actively developed - inclusion: yes - biological scale: reaction-diffusion, point neurons, HH type with single and multiple compartments - network scale: single cell, small scale networks, meso scale networks, large scale networks - large scale implemented by: MPI, batch processing, NSG support (I think) - interface languages: Python, GUI - model coverage: built-in models, extensible - file formats: ? - comment: sits on top of based on NEURON simulator, but does lots of other handy things (like the UI and EEG calculation etc.) - PyNN (Ankur) - website: http://neuralensemble.org/PyNN/ - tags: python, - license: CeCILL - installable: lin/macos - point of contact: GitHub, [NeuralEnsemble group](groups.google.com/group/neuralensemble) - user docs: http://neuralensemble.org/docs/PyNN/ - inclusion: yes - status: stable, maintained, actively developed - biological scale: point neurons, HH type with single and multiple compartments, (not sure if it supports NEURON's RxD) - network scale: single scale, small scale networks, meso scale networks - large scale implemented by: MPI? (not sure if it supports Brian/NEST/NEURON etc through MPI), Neuromorphic hardware - interface language: Python - model coverage: built-in models, extensible - file formats: ? - comment sits on top of multiple simulator backends, but one does not have to explicitly interact with the backends, so this should be included - Genesis - wesite: http://www.genesis-sim.org/ - tags: single neuron, large network, Python, GUI - license: GPLv2 - installable: lin/win - user docs: http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual.html - POC: none - status: unmaintained (last update 2019) - inclusion: ? - MOOSE - website: https://moose.ncbs.res.in/ - tags: Python, GUI, C++ - license: GPLv3 - installable: Linux and MacOSX - point of contact: mailing list, - user docs: https://moose.ncbs.res.in/readthedocs/index.html - tutorials and examples: https://github.com/BhallaLab/moose-examples - status: maintaned (last commit 2020) - inclusion: - other: NeuroML reader available - TheVirtualBrain (TVB) - website: https://www.thevirtualbrain.org/ - tags: python, large-scale, whole-brain - license: Baycrest - installable: lin/win/macos - point of contact: GitHub, email - user docs: https://docs.thevirtualbrain.org/ - status: actively developed - inclusion: hopefully yes! - NeuroRD - website: https://krasnow1.gmu.edu/CENlab/software.html - status: maintained - license: GPLv2 - tags: reaction-diffusion, java - installable: platform independent (Java) - PoC: GitHub - user docs: tutorials, publications and published models (also on ModelDB) - inclusion: yes - Smoldyn - website: https://www.smoldyn.org/ - status: maintained - license: LGPL + GPLv3 + public domain - tags: reaction-diffusion, biochemistry, Python - installable: Linux/Mac/Windows - PoC: e-mail - user docs: on website - inclusion: yes - Steps - website: https://steps.sourceforge.net/STEPS/default.php - status: maintained - license: GPLv2 - tags: reaction-diffusion, Python - installable: Linux/Mac/Windows (but not sure if explicitly mentioned) - PoC: GitHub discussions, e-mail - user docs: [on website](https://steps.sourceforge.net/manual/manual_index.html) - inclusion: yes - MUSIC (MUlti-SImulation Coordinator) - website: https://github.com/INCF/MUSIC - tags: large-scale, c++, python, multi-simulation - license: GPL-3.0 - installabel: lin/ - point of contact: GitHub - user docs: [pdf file](https://raw.githubusercontent.com/wiki/INCF/MUSIC/files/music-manual.pdf) - status: last update 11 months ago - inclusion: ? - NeuroML (Ankur) - website: https://neuroml.org - tags: standard, LEMS, multi-scale, ecosystem, multi-simulator - license: GPL - installable: linux/windows/mac (java + python, with C++ and matlab bindings also available) - PoC: Github, mailing list, e-mail - user docs: https://docs.neuroml.org - status: maintained - inclusion: yes: similar to PyNN, sits on top of simulation engines, but users do not have to interact with the simulation engines themselves - biological scale: sub-cellular, point neuron, HH with single and multiple compartments - network scale: single cell, small scale networks, meso scale networks, large scale networks - large scale implemented by: MPI (NetPyNE) - interface language: Python, XML(!), GUI (neuroConstruct, exports from NEURON/NetPyNE etc.), Java API, C++ API, MatLab (via Java API) - model coverage: built-in models, extensible - file formats: ? - Brain dynamics toolbox - website: http://bdtoolbox.org/about/ - status: maintained - license: BSD - tags: MATLAB, non-linear dynamical systems, gui, large-scale, theoretical - installable: win/macos - PoC: not specified - user docs: need to purchase the handbook, the first chapter is free [here](https://github.com/bdtoolbox-org/bdtoolbox/releases/download/2022b/HandbookSample2022.pdf) - note: requires MATLAB + purchasing the handbook, not sure if needed to be excluded - inclusion: ? - c302 - website: https://www.opensourcebrain.org/projects/c302 - status: maintained (last commit 8 months ago) - tags: multi-scale, single & multi-compartment, python, docker - installable: Linux/Mac/Windows (but not sure if explicitly mentioned) - PoC: not specified - user docs: no docs, just the link to the website: https://www.opensourcebrain.org/projects/c302 - note: uses libNeuroML, jNeuroML & pyNeuroML - inclusion: ? - MiMiC - website: https://mimic-project.org/en/latest/ - status: active development - tags: multi-scale, python - installable: lin/macos - PoC: not specified - user docs: https://mimic-project.org/en/latest/ - note: introduced in the Simulate with EBRAINS event - inclusion: ? - ReMoto (Eliane) - website: http://remoto.leb.usp.br - tags: realistic network modeling, gui, multi-scale, single neuron/neural networks, neuromuscle simulation, java - license: website - installable: linux/windows/mac - PoC: e-mail - user docs: on website - status: active development - inclusion: ? - Brain Scaffold Builder (brent) - website: https://bsb.readthedocs.io - tags: multiparadigm neural modelling, code-free configuration , parallelized workflow - license: GPL3 - installable: linux/windows/macos - PoC: https://github.com/dbbs-lab/bsb/issues/ - user docs: https://bsb.readthedocs.io - status: active - inclusion: ? - BluePyOpt - website: https://bluepyopt.readthedocs.io - tags: multiparadigm neural modelling, code-free configuration , parallelized workflow - license: Mixed GPL, LGPL, BSD - installable: linux/windows/macos - PoC: https://github.com/BlueBrain/BluePyOpt/issues - user docs: https://bluepyopt.readthedocs.io - status: active - inclusion: ? - nrn-patch (brent) - website: https://github.com/helveg/patch - tags: user friendly, python, compartment, neuron-wrapper - license: MIT - installable: linux/windows/macos - PoC: https://github.com/helveg/patch/issues - user docs: - - status: ? - inclusion: ? - DiPDE (Marcel) - website: [https://alleninstitute.github.io/dipde/index.html](https://alleninstitute.github.io/dipde/index.html) - tags: python, population models, population density equations, firing-rate model, non-spiking model, simulation, single machine - interface language: python - license: GPL-3.0 - installable: OS Independent (pure python package) - PoC: github issues - user docs: https://alleninstitute.github.io/dipde/ - status: maintained, but no active development - inclusion: yes (I guess) - Geppeto - website: https://alleninstitute.github.io/dipde/index.html - tags: web-based platform, visualization, simulation, cell, whole-brain - license: MIT - installable: none, ran on website - PoC: github, email - user docs: http://docs.geppetto.org/en/latest/#contact-us - status: inactive (last update 2018) - inclusion: - NeuronC (Marcel) - website: [http://retina.anatomy.upenn.edu/~rob/neuronc.html](http://retina.anatomy.upenn.edu/~rob/neuronc.html) - tags: neural circuits, simulations, cable equation, channel-based models, compartments, c++ - interface language: neuronC or C++ - license: not specified - installable: lin/macos (win via lin env>) - PoC: email - user docs: [http://retina.anatomy.upenn.edu/~rob/ncmanindex.html](http://retina.anatomy.upenn.edu/~rob/ncmanindex.html) - status: maintained (last update 2020) - inclusion: rather no - Nodus - website: http://nodus.uclouvain.be/ - tags: java, multimodal, intermodal, transportation network modeling, standalone app, GUI - license: GPL3 - installable: lin/macos/win/no pip - PoC: github, email - user docs: http://nodus.uclouvain.be/ - status: active - inclusion: - SNNAP - website: https://med.uth.edu/nba/snnap/ (this link is broken on Jim's website) - tags: Java, standalone app, single neuron/neural networks simulation, multi-compartment, GUI - license: none - installable: essentially everywhere - PoC: none - user docs: https://med.uth.edu/nba/snnap/snnap-tutorials/ videos; https://med.uth.edu/nba/snnap/snnap-models-and-examples/ models & examples; https://med.uth.edu/nba/wp-content/uploads/sites/29/2021/11/snnap_8_tutorial_v2019.pdf manual - status: inactive (last update 2003, revised 2019) - inclusion: ### Excluded tools | Tool excluded | Why excluded? | Comment | | ------------- | ------------- | --------| | Abstracted Protein Simulator | out of scope | protein simulator, not quite in our research domain | | BioNetGen | out of scope | general purpose biochemical mechanism simulator | | Copasi | out of scope | general purpose chemical pathway simulator | | E-cell | out of scope | general purpose cell simulator | | EONS | unmaintained?, free but requires login to download, unclear if FOSS | login link doesn't work for me | | Meredys | link from Jim's page doesn't work | GitHub search didn't return anything either | | Modigliani | unmaintained | a repo on [GitHub](https://github.com/rouzbeh/Modigliani) has the last commit from 2018, website link from Jim's page returns nginx test page | | psics | unmaintained? | last changelog entry [from 2011](http://www.psics.org/about/log.html), link to forum also does not work | | Brain Lab | limited scope, proprietary(?), unmaintained | teaching resource, not really a simulator ; limited to ipad/iphone ; website link from Jim's page doesn't open for me, so limited info available | | [Conical](https://strout.net/conical/package/doc/note-release.html) | unmaintained | last release, page update from 1996 | | [insilico](https://github.com/insilico-lib/insilico) | out of scope, unmaintained | biology simulation; link from Jim's page to doc is broken; last update 8 years ago | | [maxsim](http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/Maxsim/Spec.html) | unmaintained, no info | links to a one-page website that doesn't provide enough info; proposed in 1996 | | [NANS](https://vlsi.eecs.harvard.edu/research/nans.html) | unmaintained; no info | requires asking a person to share source code; no docs or examples) | | [MIEN](https://sourceforge.net/projects/mien/) | unmaintained, out of scope | provides tools for development, searching, editing, execution, and visualization of biophysical models; no documentation; last update 2013 | | [Surf-Hippo](http://surf-hippo.neurophysics.eu/manuals-and-publications.html) | unmaintained | last update 2003, doesn't have docs; written in LISP | | [XPP](https://compneuroweb.com/sftwr.html#modeling) |out of scope | biophysical modelling ### Unsure tools table | Tool| Comment | |-----|---------| | [CalC](https://web.njit.edu/~matveev/calc.html)| Intracellular Ca dynamics, but not necessarily neuronal specific | | [Mcell](https://mcell.org/) | general cell micro-physiology simulator: in scope or not? | | [VCell](https://vcell.org/why-vcell)| general cell simulator: in scope or not? | | [c302](https://github.com/openworm/c302/) | isn't really a simulator, looks like scripts to generate NeuroML models for C. elegans (can double check with Padraig) | | [PyDSTool](https://pydstool.github.io/PyDSTool/ProjectOverview.html) | mainly focuses on analysis and description of geometric structures |

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