From 4e3754f312cd4a38ac2df07cbafb20da00c81359 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Thu, 5 Dec 2024 13:30:54 +0000 Subject: [PATCH 1/4] Modeldb updates & osb gh repos --- libraries/client/cached_info/modeldb.json | 458 ++++++++++++++++++++++ libraries/client/cached_info/osb_gh.json | 34 +- 2 files changed, 475 insertions(+), 17 deletions(-) diff --git a/libraries/client/cached_info/modeldb.json b/libraries/client/cached_info/modeldb.json index 8d34aa5b..45155c25 100644 --- a/libraries/client/cached_info/modeldb.json +++ b/libraries/client/cached_info/modeldb.json @@ -227374,6 +227374,94 @@ "ver_date": "2024-06-09T16:57:10.818448", "ver_number": 4 }, + "2016218": { + "_citation_text": "", + "_implementers_text": "Medlock, Laura [laura.medlock at mail.utoronto.ca]", + "class_id": 19, + "created": "2024-02-01T18:12:19.122917+00:00", + "currents": { + "attr_id": 27, + "value": [] + }, + "expmotivation": "", + "gene": { + "attr_id": 476, + "value": [] + }, + "id": 2016218, + "implemented_by": { + "attr_id": 299, + "value": [ + { + "object_id": 263070, + "object_name": "Medlock, Laura [laura.medlock at mail.utoronto.ca]" + } + ] + }, + "license": "MIT", + "model_concept": { + "attr_id": 113, + "value": [ + { + "object_id": 245798, + "object_name": "Touch" + } + ] + }, + "model_paper": { + "value": [ + { + "object_id": 2018013, + "object_name": "Medlock L et al. 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The resulting model parameters highlight key mechanistic differences across the RA spectrum; specifically, the integration window of different RAs transitions from wide to narrow as tuning preferences across the population move from low to high frequencies...\"" + }, + "public_submitter_email": { + "attr_id": 309, + "value": "laura.medlock@mail.utoronto.ca" + }, + "receptors": { + "attr_id": 26, + "value": [] + }, + "region": { + "attr_id": 471, + "value": [] + }, + "ver_date": "2024-10-21T17:00:27.170705", + "ver_number": 2 + }, "2016219": { "_citation_text": "Aziz, A., Patil, B.K., Lakshmikanth, K., Sreeharsha, P.S., Mukhopadhay, A. and Chakravarthy, V.S., 2022. Modeling Hippocampal Spatial Cells in Rodents navigating in 3D environments. bioRxiv, pp.2022-06.", "_implementers_text": "", @@ -227777,6 +227865,102 @@ "ver_date": "2024-02-23T22:54:09.426301+00:00", "ver_number": 1 }, + "2016662": { + "_citation_text": "", + "_implementers_text": "Nooshin Abdollahi", + "class_id": 19, + "created": "2024-03-22T00:29:28.713417+00:00", + "currents": { + "attr_id": 27, + "value": [ + { + "object_id": 116966, + "object_name": "I_K,Na" + } + ] + }, + "expmotivation": "", + "gene": { + "attr_id": 476, + "value": [] + }, + "id": 2016662, + "implemented_by": { + "attr_id": 299, + "value": [ + { + "object_id": 2015408, + "object_name": "Abdollahi, Nooshin [nooshin.abdollahi at mail.utoronto.ca]" + } + ] + }, + "license": "other", + "model_concept": { + "attr_id": 113, + "value": [] + }, + "model_paper": { + "value": [] + }, + "model_type": { + "attr_id": 112, + "value": [ + { + "object_id": 3538, + "object_name": "Axon" + } + ] + }, + "modeling_application": { + "attr_id": 114, + "value": [ + { + "object_id": 1882, + "object_name": "NEURON" + }, + { + "object_id": 195884, + "object_name": "NetPyNE" + }, + { + "object_id": 114646, + "object_name": "Python" + } + ] + }, + "name": "Impact of extracellular current flow on action potential propagation in myelinated axons", + "neurons": { + "attr_id": 25, + "value": [] + }, + "neurotransmitters": { + "attr_id": 28, + "value": [] + }, + "notes": { + "attr_id": 24, + "value": "Impact of extracellular current flow on action potential propagation in myelinated axons" + }, + "public_submitter_email": { + "attr_id": 309, + "value": "nooshin.abdollahi@mail.utoronto.ca" + }, + "receptors": { + "attr_id": 26, + "value": [] + }, + "region": { + "attr_id": 471, + "value": [ + { + "object_id": 115954, + "object_name": "Spinal motoneuron" + } + ] + }, + "ver_date": "2024-09-18T19:41:28.444407", + "ver_number": 2 + }, "2016663": { "_citation_text": "https://doi.org/10.7554/eLife.90960.1", "_implementers_text": "", @@ -228378,6 +228562,38 @@ "ver_date": "2024-06-10T03:15:23.700265", "ver_number": 3 }, + "2017005": { + "_citation_text": "https://doi.org/10.7554/eLife.90624.2", + "_implementers_text": "", + "class_id": 19, + "created": "2024-05-30T00:13:45.940304+00:00", + "expmotivation": "", + "id": 2017005, + "license": "GPL", + "model_paper": { + "value": [] + }, + "model_type": { + "attr_id": 112, + "value": [ + { + "object_id": 267344, + "object_name": "Spiking neural network" + } + ] + }, + "name": "Reverse Engineering MN Pool (Chardon et al, 2023)", + "notes": { + "attr_id": 24, + "value": "In this study, we develop new reverse engineering (RE) techniques to identify the organization of the synaptic inputs generating firing patterns of populations of neurons. We tested these techniques in silico to allow rigorous evaluation of their effectiveness, using remarkably extensive parameter searches enabled by massively-parallel computation on supercomputers. We chose spinal motoneurons as our target neural system, since motoneurons process all motor commands and have well established input-output properties. One set of simulated motoneurons was driven by 300,000+ simulated combinations of excitatory, inhibitory, and neuromodulatory inputs. Our goal was to determine if these firing patterns had sufficient information to allow RE identification of the input combinations. Like other neural systems, the motoneuron input-output system is likely non-unique. This non-uniqueness could potentially limit this RE approach, as many input combinations can produce similar outputs. However, our simulations revealed that firing patterns contained sufficient information to sharply restrict the solution space. Thus, our RE approach successfully generated estimates of the actual simulated patterns of excitation, inhibition, and neuromodulation, with variances accounted for ranging from 75% to 90%. It was striking that nonlinearities induced in firing patterns by the neuromodulation inputs did not impede RE, but instead generated distinctive features in firing patterns that aided RE. These simulations demonstrate the potential of this form of RE analysis. It is likely that the ever-increasing capacity of supercomputers will allow increasingly accurate RE of neuron inputs from their firing patterns from many neural systems." + }, + "public_submitter_email": { + "attr_id": 309, + "value": "m-chardon@northwestern.edu" + }, + "ver_date": "2024-05-30T00:13:45.940304+00:00", + "ver_number": 1 + }, "2017006": { "_citation_text": "Feng B, Zhu Y, La JH, Wills ZP, Gebhart GF. Experimental and computational evidence for an essential role of NaV1.6 in spike initiation at stretch-sensitive colorectal afferent endings. J Neurophysiol. 2015 Apr 1;113(7):2618-34. doi: 10.1152/jn.00717.2014. Epub 2015 Feb 4. PMID: 25652923; PMCID: PMC4416596.", "_implementers_text": "", @@ -228935,5 +229151,247 @@ }, "ver_date": "2024-07-11T00:53:26.046401", "ver_number": 2 + }, + "2018009": { + "_citation_text": "Effects of synapse location, delay and background stochastic activity on synchronising hippocampal CA1 neurons. Chaos, Solitons and fractals X, 2024", + "_implementers_text": "Alessandro Fiasconaro; Michele Migliore", + "class_id": 19, + "created": "2024-10-19T15:42:04.633568+00:00", + "currents": { + "attr_id": 27, + "value": [ + { + "object_id": 146507, + "object_name": "Ca pump" + }, + { + "object_id": 247, + "object_name": "I A" + }, + { + "object_id": 255, + "object_name": "I CAN" + }, + { + "object_id": 2396, + "object_name": "I Calcium" + }, + { + "object_id": 248, + "object_name": "I K" + }, + { + "object_id": 253, + "object_name": "I K,Ca" + }, + { + "object_id": 243, + "object_name": "I L high threshold" + }, + { + "object_id": 250, + "object_name": "I M" + }, + { + "object_id": 242, + "object_name": "I Na,t" + }, + { + "object_id": 245, + "object_name": "I T low threshold" + }, + { + "object_id": 251, + "object_name": "I h" + }, + { + "object_id": 143445, + "object_name": "I_KD" + } + ] + }, + "expmotivation": "", + "gene": { + "attr_id": 476, + "value": [] + }, + "id": 2018009, + "implemented_by": { + "attr_id": 299, + "value": [ + { + "object_id": 2018010, + "object_name": "Fiasconaro, Alessandro" + }, + { + "object_id": 33737, + "object_name": "Migliore, Michele [Michele.Migliore at Yale.edu]" + } + ] + }, + "license": "GPL", + "model_concept": { + "attr_id": 113, + "value": [ + { + "object_id": 3649, + "object_name": "Action Potentials" + }, + { + "object_id": 3641, + "object_name": "Detailed Neuronal Models" + }, + { + "object_id": 49304, + "object_name": "Methods" + } + ] + }, + "model_paper": { + "value": [] + }, + "model_type": { + "attr_id": 112, + "value": [ + { + "object_id": 3537, + "object_name": "Neuron or other electrically excitable cell" + } + ] + }, + "modeling_application": { + "attr_id": 114, + "value": [ + { + "object_id": 1882, + "object_name": "NEURON" + } + ] + }, + "name": "Synchronization in a realistic model of CA1 pyramidal neurons (Fiasconaro and Migliore 2024)", + "neurons": { + "attr_id": 25, + "value": [ + { + "object_id": 258, + "object_name": "Hippocampus CA1 pyramidal GLU cell" + } + ] + }, + "neurotransmitters": { + "attr_id": 28, + "value": [] + }, + "notes": { + "attr_id": 24, + "value": "We study the synchronisation of neurons in a realistic model under the Hodgkin-Huxley dynamics. 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"pushed_at": "2024-11-26T13:20:51Z", + "pushed_at": "2024-12-02T16:50:50Z", "releases_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/releases{/id}", - "size": 2228, + "size": 2281, "ssh_url": "git@github.com:OpenSourceBrain/SBMLShowcase.git", "stargazers_count": 1, "stargazers_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/stargazers", @@ -215171,7 +215171,7 @@ }, "private": false, "pulls_url": "https://api.github.com/repos/OpenSourceBrain/osb-model-validation/pulls{/number}", - "pushed_at": "2024-11-26T11:18:07Z", + "pushed_at": "2024-11-26T15:20:44Z", "releases_url": "https://api.github.com/repos/OpenSourceBrain/osb-model-validation/releases{/id}", "size": 843, "ssh_url": "git@github.com:OpenSourceBrain/osb-model-validation.git", From ff9bbe5ee273ece016c91396eed0f6c90d214f0b Mon Sep 17 00:00:00 2001 From: pgleeson Date: Thu, 5 Dec 2024 13:44:59 +0000 Subject: [PATCH 2/4] Add neuromlsbmlshowcase test project --- libraries/client/cached_info/projects_v1.json | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/libraries/client/cached_info/projects_v1.json b/libraries/client/cached_info/projects_v1.json index 52627b08..59520b4b 100644 --- a/libraries/client/cached_info/projects_v1.json +++ b/libraries/client/cached_info/projects_v1.json @@ -2225,6 +2225,30 @@ "main_branch": "master", "name": "NeuroMLlite Showcase" }, + "neuromlsbmlshowcase": { + "Brian support": "-1", + "Category": "Showcase", + "Curation level": "2", + "Endorsement": "1", + "Family": "Other", + "GENESIS 2 support": "-1", + "GitHub repository": "https://github.com/OpenSourceBrain/NeuroMLSBMLShowcase.git", + "MOOSE support": "0", + "NEST support": "-1", + "NeuroML v1.x support": "0", + "NeuroML v2.x support": "2", + "NeuroML version": "v2.x", + "PSICS support": "-1", + "PyNN support": "-1", + "Spine classification": "None", + "Status info": "In progress", + "Tags": "SBML", + "description": "github:README.md", + "id": 295, + "identifier": "neuromlsbmlshowcase", + "main_branch": "main", + "name": "NeuroMLSBMLShowcase" + }, "neuromorpho": { "Brain region": "Other", "Brian support": "-1", From c95a0bc89b90efb74897de13a82951bc0e9539f5 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Thu, 5 Dec 2024 13:58:50 +0000 Subject: [PATCH 3/4] Picking up osb gh changes --- libraries/client/cached_info/osb_gh.json | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/libraries/client/cached_info/osb_gh.json b/libraries/client/cached_info/osb_gh.json index 980bc3b2..87e91d41 100644 --- a/libraries/client/cached_info/osb_gh.json +++ b/libraries/client/cached_info/osb_gh.json @@ -208056,7 +208056,7 @@ "has_pages": false, "has_projects": true, "has_wiki": true, - "homepage": null, + "homepage": "", "hooks_url": "https://api.github.com/repos/OpenSourceBrain/NeuroMLSBMLShowcase/hooks", "html_url": "https://github.com/OpenSourceBrain/NeuroMLSBMLShowcase", "id": 870011764, @@ -208125,9 +208125,13 @@ "svn_url": "https://github.com/OpenSourceBrain/NeuroMLSBMLShowcase", "tags_url": "https://api.github.com/repos/OpenSourceBrain/NeuroMLSBMLShowcase/tags", "teams_url": "https://api.github.com/repos/OpenSourceBrain/NeuroMLSBMLShowcase/teams", - "topics": [], + "topics": [ + "neuroml", + "opensourcebrain", + "sbml" + ], "trees_url": "https://api.github.com/repos/OpenSourceBrain/NeuroMLSBMLShowcase/git/trees{/sha}", - "updated_at": "2024-12-04T13:08:26Z", + "updated_at": "2024-12-05T13:47:04Z", "url": "https://api.github.com/repos/OpenSourceBrain/NeuroMLSBMLShowcase", "visibility": "public", "watchers": 0, @@ -209544,7 +209548,7 @@ }, "private": false, "pulls_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/pulls{/number}", - "pushed_at": "2024-11-26T15:51:13Z", + "pushed_at": "2024-12-05T13:31:01Z", "releases_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/releases{/id}", "size": 43042, "ssh_url": "git@github.com:OpenSourceBrain/OSBv2.git", From b3f656f29a5a902c1e8432ad313d0e5b84d54e40 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 11 Dec 2024 10:03:00 +0000 Subject: [PATCH 4/4] Regenerate GH osb cache; enable actions --- .github/workflows/docker-jupyterlab.yml | 4 +-- .github/workflows/docker-netpyne.yml | 4 +-- .github/workflows/docker-nwbe.yml | 4 +-- libraries/client/cached_info/osb_gh.json | 32 ++++++++++++------------ 4 files changed, 22 insertions(+), 22 deletions(-) diff --git a/.github/workflows/docker-jupyterlab.yml b/.github/workflows/docker-jupyterlab.yml index 73165226..49484835 100644 --- a/.github/workflows/docker-jupyterlab.yml +++ b/.github/workflows/docker-jupyterlab.yml @@ -2,9 +2,9 @@ name: Docker Image Build Jupyterlab on: push: - branches: [ master, dev*, feature/docker* ] + branches: [ master, dev*, feature/docker*, feature/repo* ] pull_request: - branches: [ master, dev*, feature/docker* ] + branches: [ master, dev*, feature/docker*, feature/repo* ] jobs: diff --git a/.github/workflows/docker-netpyne.yml b/.github/workflows/docker-netpyne.yml index d1601ede..d6abed1d 100644 --- a/.github/workflows/docker-netpyne.yml +++ b/.github/workflows/docker-netpyne.yml @@ -2,9 +2,9 @@ name: Docker Image Build NetPyNE-UI on: push: - branches: [ master, dev*, feature/docker* ] + branches: [ master, dev*, feature/docker*, feature/repo* ] pull_request: - branches: [ master, dev*, feature/docker* ] + branches: [ master, dev*, feature/docker*, feature/repo* ] jobs: diff --git a/.github/workflows/docker-nwbe.yml b/.github/workflows/docker-nwbe.yml index e779fa3a..b9c15434 100644 --- a/.github/workflows/docker-nwbe.yml +++ b/.github/workflows/docker-nwbe.yml @@ -2,9 +2,9 @@ name: Docker Image Build NWB Explorer on: push: - branches: [ master, dev*, feature/docker* ] + branches: [ master, dev*, feature/docker*, feature/repo* ] pull_request: - branches: [ master, dev*, feature/docker* ] + branches: [ master, dev*, feature/docker*, feature/repo* ] jobs: diff --git a/libraries/client/cached_info/osb_gh.json b/libraries/client/cached_info/osb_gh.json index 87e91d41..eba6d0cc 100644 --- a/libraries/client/cached_info/osb_gh.json +++ b/libraries/client/cached_info/osb_gh.json @@ -201628,8 +201628,8 @@ "name": "CelegansNeuromechanicalGaitModulation", "node_id": "MDEwOlJlcG9zaXRvcnk2MjQ1MTIw", "notifications_url": "https://api.github.com/repos/OpenSourceBrain/CelegansNeuromechanicalGaitModulation/notifications{?since,all,participating}", - "open_issues": 2, - "open_issues_count": 2, + "open_issues": 1, + "open_issues_count": 1, "owner": { "avatar_url": "https://avatars.githubusercontent.com/u/1565478?v=4", "events_url": "https://api.github.com/users/OpenSourceBrain/events{/privacy}", @@ -201660,7 +201660,7 @@ }, "private": false, "pulls_url": "https://api.github.com/repos/OpenSourceBrain/CelegansNeuromechanicalGaitModulation/pulls{/number}", - "pushed_at": "2024-08-21T18:04:12Z", + "pushed_at": "2024-12-10T10:20:24Z", "releases_url": "https://api.github.com/repos/OpenSourceBrain/CelegansNeuromechanicalGaitModulation/releases{/id}", "size": 7375, "ssh_url": "git@github.com:OpenSourceBrain/CelegansNeuromechanicalGaitModulation.git", @@ -201674,7 +201674,7 @@ "teams_url": "https://api.github.com/repos/OpenSourceBrain/CelegansNeuromechanicalGaitModulation/teams", "topics": [], "trees_url": "https://api.github.com/repos/OpenSourceBrain/CelegansNeuromechanicalGaitModulation/git/trees{/sha}", - "updated_at": "2024-08-19T18:04:17Z", + "updated_at": "2024-12-10T10:20:31Z", "url": "https://api.github.com/repos/OpenSourceBrain/CelegansNeuromechanicalGaitModulation", "visibility": "public", "watchers": 5, @@ -209550,7 +209550,7 @@ "pulls_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/pulls{/number}", "pushed_at": "2024-12-05T13:31:01Z", "releases_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/releases{/id}", - "size": 43042, + "size": 45209, "ssh_url": "git@github.com:OpenSourceBrain/OSBv2.git", "stargazers_count": 12, "stargazers_url": "https://api.github.com/repos/OpenSourceBrain/OSBv2/stargazers", @@ -210774,7 +210774,7 @@ "releases_url": "https://api.github.com/repos/OpenSourceBrain/PyNNShowcase/releases{/id}", "size": 472, "ssh_url": "git@github.com:OpenSourceBrain/PyNNShowcase.git", - "stargazers_count": 3, + "stargazers_count": 4, "stargazers_url": "https://api.github.com/repos/OpenSourceBrain/PyNNShowcase/stargazers", "statuses_url": "https://api.github.com/repos/OpenSourceBrain/PyNNShowcase/statuses/{sha}", "subscribers_url": "https://api.github.com/repos/OpenSourceBrain/PyNNShowcase/subscribers", @@ -210784,11 +210784,11 @@ "teams_url": "https://api.github.com/repos/OpenSourceBrain/PyNNShowcase/teams", "topics": [], "trees_url": "https://api.github.com/repos/OpenSourceBrain/PyNNShowcase/git/trees{/sha}", - "updated_at": "2024-08-19T16:06:19Z", + "updated_at": "2024-12-09T06:15:49Z", "url": "https://api.github.com/repos/OpenSourceBrain/PyNNShowcase", "visibility": "public", - "watchers": 3, - "watchers_count": 3, + "watchers": 4, + "watchers_count": 4, "web_commit_signoff_required": false }, "https://api.github.com/repos/OpenSourceBrain/PyloricNetwork": { @@ -211068,8 +211068,8 @@ "name": "SBMLShowcase", "node_id": "MDEwOlJlcG9zaXRvcnk5ODMzNTU3", "notifications_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/notifications{?since,all,participating}", - "open_issues": 9, - "open_issues_count": 9, + "open_issues": 11, + "open_issues_count": 11, "owner": { "avatar_url": "https://avatars.githubusercontent.com/u/1565478?v=4", "events_url": "https://api.github.com/users/OpenSourceBrain/events{/privacy}", @@ -211100,9 +211100,9 @@ }, "private": false, "pulls_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/pulls{/number}", - "pushed_at": "2024-12-02T16:50:50Z", + "pushed_at": "2024-12-10T18:12:04Z", "releases_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/releases{/id}", - "size": 2281, + "size": 2529, "ssh_url": "git@github.com:OpenSourceBrain/SBMLShowcase.git", "stargazers_count": 1, "stargazers_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/stargazers", @@ -211114,7 +211114,7 @@ "teams_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/teams", "topics": [], "trees_url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase/git/trees{/sha}", - "updated_at": "2024-11-14T09:58:45Z", + "updated_at": "2024-12-06T17:45:30Z", "url": "https://api.github.com/repos/OpenSourceBrain/SBMLShowcase", "visibility": "public", "watchers": 1, @@ -215104,8 +215104,8 @@ "downloads_url": "https://api.github.com/repos/OpenSourceBrain/osb-model-validation/downloads", "events_url": "https://api.github.com/repos/OpenSourceBrain/osb-model-validation/events", "fork": false, - 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