{"id":18634610,"url":"https://github.com/abrg-models/barrelemerge","last_synced_at":"2026-01-23T09:34:04.621Z","repository":{"id":77802470,"uuid":"192934024","full_name":"ABRG-Models/BarrelEmerge","owner":"ABRG-Models","description":"Emergence of whisker barrels with modified Karbowski-Ermentrout-like axon branching population model","archived":false,"fork":false,"pushed_at":"2023-09-14T10:27:13.000Z","size":535458,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-17T12:37:21.454Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ABRG-Models.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-06-20T14:23:49.000Z","updated_at":"2022-06-21T06:17:23.000Z","dependencies_parsed_at":"2023-10-20T16:17:00.452Z","dependency_job_id":null,"html_url":"https://github.com/ABRG-Models/BarrelEmerge","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ABRG-Models/BarrelEmerge","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ABRG-Models%2FBarrelEmerge","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ABRG-Models%2FBarrelEmerge/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ABRG-Models%2FBarrelEmerge/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ABRG-Models%2FBarrelEmerge/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ABRG-Models","download_url":"https://codeload.github.com/ABRG-Models/BarrelEmerge/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ABRG-Models%2FBarrelEmerge/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28686532,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-23T05:48:07.525Z","status":"ssl_error","status_checked_at":"2026-01-23T05:48:07.129Z","response_time":59,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-07T05:19:50.865Z","updated_at":"2026-01-23T09:34:04.602Z","avatar_url":"https://github.com/ABRG-Models.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BarrelEmerge\n\nThis is a simulation of the growth of axons which demonstrates how the\nwhisker barrel field pattern can self-organize in the presence of only\ntwo orthogonal molecular guidance cues. It is the code behind the\nfollowing paper (archive branch: [eLife](https://github.com/ABRG-Models/BarrelEmerge/tree/eLife)):\n\nJames, Krubitzer \u0026 Wilson. 2020. *Modelling the emergence of whisker\nbarrels*. eLife. DOI: https://doi.org/10.7554/eLife.55588\n\nThe emergence of whisker barrels is demonstrated in a modified\nKarbowski-Ermentrout-like axon branching population model.\n\n![Shows Fig 1 from the paper](https://github.com/ABRG-Models/BarrelEmerge/blob/master/paper/briefpaper/Fig1.png?raw=true)\n*A: CO stain of the rat barrel field B: Centres of thalamic barreloids provide interaction parameters for axon bundles growing into the cortical subplate C: Cortical fields emerge D \u0026 E: Pattern quality measures*\n\n\nFor instructions on reproducing the results of the paper, see the\nREADME.md file in the scripts subdirectory.\n\nBefore you do that, you'll need to build this simulation code, which\nis compiled using our library of research software, morphologica.\n\nmorphologica is pulled in as a git submodule, but you'll still need to\ninstall the dependencies for the morphologica code, which are: OpenCV,\nArmadillo, OpenGL, HDF5, LAPACK and glfw.  Refer to the instructions\nin the morphologica README.install files, covering installation of\ndependences on Mac or Linux. On a Debian based Linux, this should\nwork:\n\n```bash\nsudo apt install build-essential cmake git \\\n                 freeglut3-dev libglu1-mesa-dev libxmu-dev libxi-dev \\\n                 libglfw3-dev libfreetype-dev\n\nsudo apt install libarmadillo-dev libhdf5-dev libopencv-dev\n```\n\nWith dependences installed you can build BarrelEmerge:\n\n```bash\n# Clone, making sure to get the submodules (morphologica)\ngit clone --recurse-submodules https://github.com/ABRG-Models/BarrelEmerge.git\n\n# If you ALREADY did a git clone *without* --recurse-submodules, then don't panic! just do:\n# cd BarrelEmerge\n# git submodule init\n# git submodule update\n\ncd BarrelEmerge\nmkdir build\npushd build\ncmake ..\nmake -j4 # or however many cores you have\n# (no need to install, you'll run the simulations in place)\npopd\n```\n\n**Note:** You'll ideally have an OpenMP-capable compiler. You'll\nprobably need libomp as well, because even though my code doesn't use\nthe runtime part of OpenMP, Armadillo does. You get OpenMP/libomp for free with gcc on a modern Linux\ncomputer; on a Mac, you will have to install libomp from source\n(follow instructions at https://openmp.llvm.org/ finishing up with a\nfinal `make install`).\n\nNow you can read how to reproduce the experiments. To reproduce all of\nthe results, see ./scripts/README.md. To graph the resulting data, see\n./analysis/README.md.\n\nTo reproduce, and simultaneously view, the main result, as presented\nin Fig. 1C, you can run one simulation:\n\n```bash\n./build/sim/james_comp2 ./configs/rat/41N2M_thalguide_Fig1.json\n```\n\n**Note:** The simulation is computationally demanding. It takes about\n11 minutes to run the 50000 steps of Fig. 1C simulation on a 6-core\ngaming laptop (with an 8th gen Intel Core i9 processor and with the code\ncompiled with OpenMP to use all the cores). An older, 6th gen Core i5\nlaptop (2 cores) needs 23 minutes to run the same simulation.\n\nIf you have any trouble, please post an issue on github at\nhttps://github.com/ABRG-Models/BarrelEmerge/issues and I will do my\nbest to help.\n\nSeb James, September 2020.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabrg-models%2Fbarrelemerge","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fabrg-models%2Fbarrelemerge","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fabrg-models%2Fbarrelemerge/lists"}