{"title":"INCF\/OCNS Software WG","link":[{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/","rel":"alternate"}},{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/feeds\/all.atom.xml","rel":"self"}}],"id":"https:\/\/ocns.github.io\/SoftwareWG\/","updated":"2024-06-26T11:24:52+01:00","subtitle":"The INCF\/OCNS Software Working Group","entry":[{"title":"WG meeting 9 July 2024: Software Tools for Systems Neuroscience (Adam\u00a0Tyson)","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2024\/06\/26\/wg-meeting-9-july-2024-software-tools-for-systems-neuroscience-adam-tyson-.html","rel":"alternate"}},"published":"2024-06-26T11:24:52+01:00","updated":"2024-06-26T11:24:52+01:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2024-06-26:\/SoftwareWG\/2024\/06\/26\/wg-meeting-9-july-2024-software-tools-for-systems-neuroscience-adam-tyson-.html","summary":"<p class=\"first last\">The next <span class=\"caps\">WG<\/span> meeting will be on July 9, 2024 at 1500 <span class=\"caps\">UTC<\/span>. Adam Tyson will present the tools that they develop for systems neuroscience at their research&nbsp;group.<\/p>\n","content":"<p>The next <span class=\"caps\">WG<\/span> meeting will be on July 9, 2024 at 1500 <span class=\"caps\">UTC<\/span>.\nAdam Tyson will present the tools that they develop for Systems Neuroscience at their research group.\nThe presentation will be followed by a Q&amp;A, followed by working group&nbsp;business.<\/p>\n<ul class=\"simple\">\n<li>When: <a class=\"reference external\" href=\"https:\/\/www.timeanddate.com\/worldclock\/fixedtime.html?msg=INCF%2FOCNS+Software+WG+meeting%3A+Software+Tools+Systems+Neuroscience+%28Adam+Tyson%29&amp;iso=20240709T16&amp;p1=136\">July 9, 1500 <span class=\"caps\">UTC<\/span><\/a> (<a class=\"reference external\" href=\"https:\/\/calendar.google.com\/calendar\/embed?src=0ae207588d5e8c6423bd3d71a1627b0d03c4bb047baa1bc92a9d62f56fc9c75a%40group.calendar.google.com&amp;ctz=Europe%2FLondon\">Event calendar<\/a>) (<a class=\"reference external\" href=\"https:\/\/calendar.google.com\/calendar\/ical\/0ae207588d5e8c6423bd3d71a1627b0d03c4bb047baa1bc92a9d62f56fc9c75a%40group.calendar.google.com\/public\/basic.ics\">iCal<\/a>)<\/li>\n<li><a class=\"reference external\" href=\"https:\/\/ucl.zoom.us\/j\/91017703246?pwd=RmdwMW9xL0FFaFVVL0Z6dUtnbkplZz09\">Zoom<\/a> (you will be required to be logged into Zoom to attend the&nbsp;session)<\/li>\n<\/ul>\n<center><div class=\"figure\">\n<a class=\"reference external image-reference\" href=\"#\">\n<img alt=\"The Neuroinformatics Unit at the Sainsbury Wellcome Centre develops software tools for systems neuroscience.\" class=\"img-responsive\" src=\"https:\/\/ocns.github.io\/SoftwareWG\/images\/20240626-neuroinformatics-dev.png\" style=\"width: 60%;\" \/>\n<\/a>\n<p class=\"caption\">The <a class=\"reference external\" href=\"https:\/\/neuroinformatics.dev\/\">Neuroinformatics Unit<\/a> at the Sainsbury Wellcome Centre develops software tools for systems&nbsp;neuroscience.<\/p>\n<\/div>\n<\/center>\n<br \/><p>Understanding the brain requires processing and analysing large, multidimensional datasets.\nSystems neuroscience, in particular, has undergone a drastic transformation, with individual labs now commonly generating terabytes or even petabytes of data annually.\nWhile there has been an increase in software tools to process this data, many of these tools are single-purpose, inadequately maintained, or poorly integrated with the broader software ecosystem.\nThis talk will outline some of the tools we are developing for <a class=\"reference external\" href=\"https:\/\/brainglobe.info\/\">computational neuroanatomy<\/a>, <a class=\"reference external\" href=\"https:\/\/movement.neuroinformatics.dev\/\">video behavioural analysis<\/a>, and <a class=\"reference external\" href=\"https:\/\/neuroblueprint.neuroinformatics.dev\/\">data management<\/a>.<\/p>\n<p>About the&nbsp;speaker:<\/p>\n<p>Adam Tyson is the Head Research Engineer at the <a class=\"reference external\" href=\"https:\/\/www.sainsburywellcome.org\/web\/\">Sainsbury Wellcome Centre<\/a> and <a class=\"reference external\" href=\"https:\/\/www.ucl.ac.uk\/gatsby\/gatsby-computational-neuroscience-unit\">Gatsby Computational Neuroscience<\/a> Unit at University College London.\nHe established the <a class=\"reference external\" href=\"https:\/\/neuroinformatics.dev\/\">Neuroinformatics Unit<\/a>, a research software engineering team dedicated to developing robust, maintainable, and user-friendly software tools for neuroscience and machine learning.\nAdam completed a PhD in neuroscience at King\u2019s College London before working as a software developer at the Institute of Cancer Research and the Sainsbury Wellcome&nbsp;Centre.<\/p>\n<p>Resources:<\/p>\n<ul class=\"simple\">\n<li>BrainGlobe: <a class=\"reference external\" href=\"https:\/\/brainglobe.info\/\">https:\/\/brainglobe.info\/<\/a><\/li>\n<li>Movement: <a class=\"reference external\" href=\"https:\/\/movement.neuroinformatics.dev\/\">https:\/\/movement.neuroinformatics.dev\/<\/a><\/li>\n<li>NeuroBluePrint: <a class=\"reference external\" href=\"https:\/\/neuroblueprint.neuroinformatics.dev\/\">https:\/\/neuroblueprint.neuroinformatics.dev\/<\/a><\/li>\n<li>Neuroinformatics Unit: <a class=\"reference external\" href=\"https:\/\/neuroinformatics.dev\/\">https:\/\/neuroinformatics.dev\/<\/a><\/li>\n<\/ul>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Analysis"}},{"@attributes":{"term":"Automation"}},{"@attributes":{"term":"Community"}},{"@attributes":{"term":"Computational Neuroanatomy"}},{"@attributes":{"term":"Free\/Open Source Software"}},{"@attributes":{"term":"Meeting"}},{"@attributes":{"term":"Software development"}},{"@attributes":{"term":"Software highlight"}},{"@attributes":{"term":"Neuroscience"}},{"@attributes":{"term":"Systems Neuroscience"}},{"@attributes":{"term":"Big data"}}]},{"title":"WG meeting 14 May 2024: SpikeInterface (Pierre\u00a0Yger)","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2024\/05\/07\/wg-meeting-14-may-2024-spikeinterface-pierre-yger-.html","rel":"alternate"}},"published":"2024-05-07T11:30:13+01:00","updated":"2024-05-07T11:30:13+01:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2024-05-07:\/SoftwareWG\/2024\/05\/07\/wg-meeting-14-may-2024-spikeinterface-pierre-yger-.html","summary":"<p class=\"first last\">The next <span class=\"caps\">WG<\/span> meeting will be on May 14, 2024 at 1500 <span class=\"caps\">UTC<\/span>. Pierre Yger will present <a class=\"reference external\" href=\"https:\/\/spikeinterface.readthedocs.io\/en\/latest\/\">SpikeInterface<\/a>.<\/p>\n","content":"<p>The next <span class=\"caps\">WG<\/span> meeting will be on May 14, 2024 at 1500 <span class=\"caps\">UTC<\/span> where Pierre Yger will present <a class=\"reference external\" href=\"https:\/\/spikeinterface.readthedocs.io\/en\/latest\/\">SpikeInterface<\/a>.\nThe presentation will be followed by a Q&amp;A, followed by working group&nbsp;business.<\/p>\n<ul class=\"simple\">\n<li>When: <a class=\"reference external\" href=\"https:\/\/www.timeanddate.com\/worldclock\/fixedtime.html?msg=INCF%2FOCNS+Software+WG+meeting%3A+SpikeInterface+%28Pierre+Yger%29&amp;iso=20240514T16&amp;p1=136\">May 14, 1500 <span class=\"caps\">UTC<\/span><\/a> (<a class=\"reference external\" href=\"https:\/\/calendar.google.com\/calendar\/u\/0?cid=MGFlMjA3NTg4ZDVlOGM2NDIzYmQzZDcxYTE2MjdiMGQwM2M0YmIwNDdiYWExYmM5MmE5ZDYyZjU2ZmM5Yzc1YUBncm91cC5jYWxlbmRhci5nb29nbGUuY29t\">Event calendar<\/a>)<\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.google.com\/url?q=https:\/\/ucl.zoom.us\/j\/91017703246?pwd%3DRmdwMW9xL0FFaFVVL0Z6dUtnbkplZz09&amp;sa=D&amp;source=calendar&amp;usd=2&amp;usg=AOvVaw0UfBxH8z9mz_0FYct0F-8f\">Zoom<\/a> (you will be required to be logged into Zoom to attend the&nbsp;session)<\/li>\n<\/ul>\n<center><div class=\"figure\">\n<a class=\"reference external image-reference\" href=\"#\">\n<img alt=\"Spike Interface\" class=\"img-responsive\" src=\"https:\/\/ocns.github.io\/SoftwareWG\/images\/20240407-spikeinterface.png\" style=\"width: 100%;\" \/>\n<\/a>\n<p class=\"caption\">Spike&nbsp;Interface<\/p>\n<\/div>\n<\/center>\n<br \/><p>Much development has been directed toward improving the performance and automation of spike sorting. This continuous development, while essential, has contributed to an over-saturation of new, incompatible tools that hinders rigorous benchmarking and complicates reproducible analysis. To address these limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sorting technologies into a single codebase and to facilitate straightforward comparison and adoption of different approaches. With a few lines of code, researchers can reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs; and more. In this paper, we provide an overview of SpikeInterface and, with applications to real and simulated datasets, demonstrate how it can be utilized to reduce the burden of manual curation and to more comprehensively benchmark automated spike&nbsp;sorters.<\/p>\n<p>Papers and&nbsp;resources:<\/p>\n<ul class=\"simple\">\n<li><a class=\"reference external\" href=\"https:\/\/spikeinterface.readthedocs.io\/en\/latest\/\">https:\/\/spikeinterface.readthedocs.io\/en\/latest\/<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/elifesciences.org\/articles\/61834\">https:\/\/elifesciences.org\/articles\/61834<\/a><\/li>\n<\/ul>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Meeting"}},{"@attributes":{"term":"Community"}},{"@attributes":{"term":"SpikeInterface"}}]},{"title":"WG meeting 09 October\u00a02023","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2023\/10\/10\/wg-meeting-09-october-2023.html","rel":"alternate"}},"published":"2023-10-10T10:29:42+01:00","updated":"2023-10-10T10:29:42+01:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2023-10-10:\/SoftwareWG\/2023\/10\/10\/wg-meeting-09-october-2023.html","summary":"<p class=\"first last\">These are the minutes from the working group meeting on 09 October,&nbsp;2023.<\/p>\n","content":"<center><div class=\"figure\">\n<a class=\"reference external image-reference\" href=\"#\">\n<img alt=\"Photo by Daria Nepriakhina on Unsplash\" class=\"img-responsive\" src=\"https:\/\/ocns.github.io\/SoftwareWG\/images\/20210107-meeting-logs.jpg\" style=\"width: 40%;\" \/>\n<\/a>\n<p class=\"caption\">Photo by <a class=\"reference external\" href=\"https:\/\/unsplash.com\/&#64;epicantus?utm_source=unsplash&amp;amp;utm_medium=referral&amp;amp;utm_content=creditCopyText\">Daria Nepriakhina<\/a> on&nbsp;Unsplash.<\/p>\n<\/div>\n<\/center>\n<br \/><p>These are the meeting logs (and additional progress notes) from the Software <span class=\"caps\">WG<\/span> meeting that was held on 09th October 2023.\nThe next progress meeting will be held <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/pages\/contact.html\">in November<\/a>.\nFor any clarifications and suggestions, please open a new&nbsp;ticket.<\/p>\n<div class=\"section\" id=\"attendees\">\n<h2>Attendees<a class=\"headerlink\" href=\"#attendees\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<ul class=\"simple\">\n<li>Marcel&nbsp;Stimberg<\/li>\n<li>Ankur&nbsp;Sinha<\/li>\n<\/ul>\n<p>Regrets:<\/p>\n<ul class=\"simple\">\n<li>Shailesh&nbsp;Appukuttan<\/li>\n<\/ul>\n<div class=\"section\" id=\"agenda\">\n<h3>Agenda<a class=\"headerlink\" href=\"#agenda\" title=\"Permalink to this headline\">\u22c6<\/a><\/h3>\n<ul class=\"simple\">\n<li>Introductions, get to know each&nbsp;other<\/li>\n<li>Announcements<ul>\n<li><span class=\"caps\">CNS<\/span> 2024 will be in Natal, Brazil. July 20-24, 2024: <a class=\"reference external\" href=\"https:\/\/www.cnsorg.org\/cns-2024\">https:\/\/www.cnsorg.org\/cns-2024<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Task force updates<ul>\n<li>Simselect<\/li>\n<li>Cookbook<\/li>\n<\/ul>\n<\/li>\n<li>Ideas for more sessions (tutorials\/spotlights\/dev&nbsp;sessions)<\/li>\n<li><span class=\"caps\">OCNS<\/span> Director elections: self nominations are open till 11th&nbsp;October<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"minutes\">\n<h3>Minutes<a class=\"headerlink\" href=\"#minutes\" title=\"Permalink to this headline\">\u22c6<\/a><\/h3>\n<div class=\"section\" id=\"tasks-from-last-meeting\">\n<h4>Tasks from last meeting<a class=\"headerlink\" href=\"#tasks-from-last-meeting\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>No tasks from last&nbsp;meeting<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"task-force-updates\">\n<h4>Task force updates<a class=\"headerlink\" href=\"#task-force-updates\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<div class=\"section\" id=\"simselect\">\n<h5>Simselect<a class=\"headerlink\" href=\"#simselect\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>v0.1 prototype live at: <a class=\"reference external\" href=\"https:\/\/simselect.fly.dev\/project_browser\">https:\/\/simselect.fly.dev\/project_browser<\/a><\/li>\n<li>meets every two weeks on Wednesday at 1300 <span class=\"caps\">UTC<\/span> (see <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/117\">this ticket<\/a> for&nbsp;announcements)<\/li>\n<li>consolidated notes are here: <a class=\"reference external\" href=\"https:\/\/hackmd.io\/LWjtz9ykQbm7yg5X_RKpCQ\">https:\/\/hackmd.io\/LWjtz9ykQbm7yg5X_RKpCQ<\/a><\/li>\n<li>working on next&nbsp;version<\/li>\n<li>looking for more people to get involved to<ul>\n<li>help with the design of the next&nbsp;iteration<\/li>\n<li>help us understand how to best display&nbsp;data<\/li>\n<li>help with&nbsp;implementation<\/li>\n<li>help with&nbsp;testing<\/li>\n<li>provide feedback on all updates to the&nbsp;application<\/li>\n<\/ul>\n<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur e-mail list calling for more&nbsp;participation<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"cookbook\">\n<h5>Cookbook<a class=\"headerlink\" href=\"#cookbook\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>lives at <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/CompNeuroCookBook\/index.html\">https:\/\/ocns.github.io\/CompNeuroCookBook\/index.html<\/a><\/li>\n<li>open for more&nbsp;contributions<\/li>\n<li>if you have a code snippet you use regularly, please share it with the community<ul>\n<li>how to contribute: <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/CompNeuroCookBook\/Contributing.html\">https:\/\/ocns.github.io\/CompNeuroCookBook\/Contributing.html<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<div class=\"section\" id=\"ocns-elections\">\n<h4><span class=\"caps\">OCNS<\/span> elections<a class=\"headerlink\" href=\"#ocns-elections\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>Candidate nominations are still open, there&#8217;s still time to nominate yourself: <a class=\"reference external\" href=\"https:\/\/www.cnsorg.org\/election-procedures\">https:\/\/www.cnsorg.org\/election-procedures<\/a><\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"other-discussion\">\n<h4>Other discussion<a class=\"headerlink\" href=\"#other-discussion\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<div class=\"section\" id=\"satellite-tutorials-in-2023-2024\">\n<h5>Satellite tutorials in 2023\/2024<a class=\"headerlink\" href=\"#satellite-tutorials-in-2023-2024\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>not sure if a week of online tutorials is the best format, given our experience in&nbsp;2021<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"replication-challenge\">\n<h5>Replication challenge<a class=\"headerlink\" href=\"#replication-challenge\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>Similar to the <a class=\"reference external\" href=\"https:\/\/paperswithcode.com\/rc2022\"><span class=\"caps\">ML<\/span> replication&nbsp;challenge<\/a><\/li>\n<li>Replicate published&nbsp;models<\/li>\n<li>Submit to <a class=\"reference external\" href=\"http:\/\/rescience.github.io\/read\/\">rescience-c<\/a> for review +&nbsp;publication<\/li>\n<li>Will involve lots of community members, who already replicate existing models in their&nbsp;projects<\/li>\n<li>Will involve simulator developers who can help people with their specific&nbsp;questions<\/li>\n<li>Fits in with both <span class=\"caps\">INCF<\/span>\/<span class=\"caps\">OCNS<\/span>&nbsp;goals<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur mail <span class=\"caps\">OCNS<\/span>\/<span class=\"caps\">INCF<\/span>, software wg, and simulator developers to get feedback on&nbsp;idea<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur open ticket to collect&nbsp;feedback<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Meeting logs"}},{"@attributes":{"term":"Community"}}]},{"title":"WG meeting 21 April\u00a02023","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2023\/09\/25\/wg-meeting-21-april-2023.html","rel":"alternate"}},"published":"2023-09-25T11:19:25+01:00","updated":"2023-09-25T11:19:25+01:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2023-09-25:\/SoftwareWG\/2023\/09\/25\/wg-meeting-21-april-2023.html","summary":"<p class=\"first last\">These are the minutes from the working group meeting on 21 April,&nbsp;2023.<\/p>\n","content":"<center><div class=\"figure\">\n<a class=\"reference external image-reference\" href=\"#\">\n<img alt=\"Photo by Daria Nepriakhina on Unsplash\" class=\"img-responsive\" src=\"https:\/\/ocns.github.io\/SoftwareWG\/images\/20210107-meeting-logs.jpg\" style=\"width: 40%;\" \/>\n<\/a>\n<p class=\"caption\">Photo by <a class=\"reference external\" href=\"https:\/\/unsplash.com\/&#64;epicantus?utm_source=unsplash&amp;amp;utm_medium=referral&amp;amp;utm_content=creditCopyText\">Daria Nepriakhina<\/a> on&nbsp;Unsplash.<\/p>\n<\/div>\n<\/center>\n<br \/><p>These are the meeting logs (and additional progress notes) from the Software <span class=\"caps\">WG<\/span> meeting that was held on 21st April 2023.\nThe next progress meeting will be held <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/pages\/contact.html\">in October<\/a>.\nFor any clarifications and suggestions, please open a new&nbsp;ticket.<\/p>\n<div class=\"section\" id=\"attendees\">\n<h2>Attendees<a class=\"headerlink\" href=\"#attendees\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<p>0800<\/p>\n<ul class=\"simple\">\n<li>Brent&nbsp;Huisman<\/li>\n<li>Ankur&nbsp;Sinha<\/li>\n<li>Marcel&nbsp;Stimberg<\/li>\n<li>Chitaranjan&nbsp;Mohaptra<\/li>\n<\/ul>\n<div class=\"section\" id=\"agenda\">\n<h3>Agenda<a class=\"headerlink\" href=\"#agenda\" title=\"Permalink to this headline\">\u22c6<\/a><\/h3>\n<ul class=\"simple\">\n<li>Tasks from last meeting: <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/2023\/03\/20\/wg-meeting-15-march-2023.html\">https:\/\/ocns.github.io\/SoftwareWG\/2023\/03\/20\/wg-meeting-15-march-2023.html<\/a><\/li>\n<li>Tasks force&nbsp;updates<\/li>\n<li><span class=\"caps\">RFC<\/span>: <span class=\"caps\">WG<\/span> presence at <span class=\"caps\">CNS<\/span> 2023&nbsp;#125<\/li>\n<li>Call for self-nominations for co-chairing the <span class=\"caps\">WG<\/span>&nbsp;#129<\/li>\n<li>Use of <a class=\"reference external\" href=\"https:\/\/gitter.im\/OCNS\/SoftwareWG\">https:\/\/gitter.im\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG<\/a><\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"minutes\">\n<h3>Minutes<a class=\"headerlink\" href=\"#minutes\" title=\"Permalink to this headline\">\u22c6<\/a><\/h3>\n<div class=\"section\" id=\"tasks-from-last-meeting\">\n<h4>Tasks from last meeting<a class=\"headerlink\" href=\"#tasks-from-last-meeting\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>All actions&nbsp;complete<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"presence-at-cns-2023\">\n<h4>Presence at <span class=\"caps\">CNS<\/span> 2023<a class=\"headerlink\" href=\"#presence-at-cns-2023\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>Informal get together in breaks\/after the&nbsp;conference.<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"task-force-updates\">\n<h4>Task force updates<a class=\"headerlink\" href=\"#task-force-updates\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<div class=\"section\" id=\"simselect\">\n<h5>Simselect<a class=\"headerlink\" href=\"#simselect\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>working towards a 0.1 <span class=\"caps\">MVP<\/span> release: <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/simselect\/milestone\/1\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/simselect\/milestone\/1<\/a><\/li>\n<li>prototype live here: <a class=\"reference external\" href=\"https:\/\/simselect.fly.dev\">https:\/\/simselect.fly.dev<\/a><\/li>\n<li>we continue to meet every two weeks, recurrent meeting at 1300 <span class=\"caps\">UTC<\/span> on Wednesday, next meeting on 3&nbsp;May<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"cookbook\">\n<h5>Cookbook<a class=\"headerlink\" href=\"#cookbook\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>It was decided another guideline isn&#8217;t needed. Many&nbsp;exist.<\/li>\n<li>Task force concluded. New task force:&nbsp;CompNeuroCookBook<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"new-task-force-compneurocookbook\">\n<h5>New task force: CompNeuroCookBook<a class=\"headerlink\" href=\"#new-task-force-compneurocookbook\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>example: <a class=\"reference external\" href=\"https:\/\/faircookbook.elixir-europe.org\/content\/home.html\">https:\/\/faircookbook.elixir-europe.org\/content\/home.html<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/CompNeuroCookBook\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/CompNeuroCookBook<\/a><\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/CompNeuroCookBook\/issues\/7\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/CompNeuroCookBook\/issues\/7<\/a>: <span class=\"caps\">DONE<\/span><\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur close old ticket on guidelines taskforce with explanation: <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/116\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/116<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<div class=\"section\" id=\"call-for-self-nominations-for-co-chairing-the-wg-129\">\n<h4>Call for self-nominations for co-chairing the <span class=\"caps\">WG<\/span> #129<a class=\"headerlink\" href=\"#call-for-self-nominations-for-co-chairing-the-wg-129\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>Marcel Stimberg is the\/a new&nbsp;co-chair<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"use-of-https-gitter-im-ocns-softwarewg\">\n<h4>Use of <a class=\"reference external\" href=\"https:\/\/gitter.im\/OCNS\/SoftwareWG\">https:\/\/gitter.im\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG<\/a><a class=\"headerlink\" href=\"#use-of-https-gitter-im-ocns-softwarewg\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>Create new issue to highlight gitter channel: <span class=\"caps\">DONE<\/span><\/li>\n<li>Ankur stress on Gitter channel in logs&nbsp;e-mail<\/li>\n<li>Use video call feature in Gitter\/Element for future meetings: <span class=\"caps\">DONE<\/span><\/li>\n<li>Pin message to <span class=\"caps\">GH<\/span> Discussions pointing users to Gitter: <span class=\"caps\">DONE<\/span><\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Meeting logs"}},{"@attributes":{"term":"Community"}}]},{"title":"WG meeting 15 March\u00a02023","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2023\/03\/20\/wg-meeting-15-march-2023.html","rel":"alternate"}},"published":"2023-03-20T18:09:22+00:00","updated":"2023-03-20T18:09:22+00:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2023-03-20:\/SoftwareWG\/2023\/03\/20\/wg-meeting-15-march-2023.html","summary":"<p class=\"first last\">These are the minutes from the working group meeting on 15 March,&nbsp;2023.<\/p>\n","content":"<center><div class=\"figure\">\n<a class=\"reference external image-reference\" href=\"#\">\n<img alt=\"Photo by Daria Nepriakhina on Unsplash\" class=\"img-responsive\" src=\"https:\/\/ocns.github.io\/SoftwareWG\/images\/20210107-meeting-logs.jpg\" style=\"width: 40%;\" \/>\n<\/a>\n<p class=\"caption\">Photo by <a class=\"reference external\" href=\"https:\/\/unsplash.com\/&#64;epicantus?utm_source=unsplash&amp;amp;utm_medium=referral&amp;amp;utm_content=creditCopyText\">Daria Nepriakhina<\/a> on&nbsp;Unsplash.<\/p>\n<\/div>\n<\/center>\n<br \/><p>These are the meeting logs (and additional progress notes) from the Software <span class=\"caps\">WG<\/span> meeting that was held on 15th March 2023.\nThe next progress meeting will be held <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/pages\/contact.html\">in March<\/a>.\nFor any clarifications and suggestions, please open a new&nbsp;ticket.<\/p>\n<div class=\"section\" id=\"attendees\">\n<h2>Attendees<a class=\"headerlink\" href=\"#attendees\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<p>0800<\/p>\n<ul class=\"simple\">\n<li>Ankur&nbsp;Sinha<\/li>\n<li>Marcel&nbsp;Stimberg<\/li>\n<li>Shailesh&nbsp;Appukuttan<\/li>\n<li>Chitaranjan&nbsp;Mohaptra<\/li>\n<\/ul>\n<p>1700<\/p>\n<ul class=\"simple\">\n<li>Ankur&nbsp;Sinha<\/li>\n<li><span class=\"caps\">AHSAN<\/span> <span class=\"caps\">UL<\/span> <span class=\"caps\">HAQ<\/span> (Masters student in&nbsp;Physics)<\/li>\n<li>KOffivi (Masters student in <span class=\"caps\">HPC<\/span>)<\/li>\n<\/ul>\n<div class=\"section\" id=\"agenda\">\n<h3>Agenda<a class=\"headerlink\" href=\"#agenda\" title=\"Permalink to this headline\">\u22c6<\/a><\/h3>\n<ul class=\"simple\">\n<li>Tasks from last meeting: <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/2023\/03\/08\/wg-meeting-14-february-2023.html\">https:\/\/ocns.github.io\/SoftwareWG\/2023\/03\/08\/wg-meeting-14-february-2023.html<\/a><\/li>\n<li><span class=\"caps\">RFC<\/span> <span class=\"caps\">CNS2023<\/span>: <span class=\"caps\">RFC<\/span>: <span class=\"caps\">WG<\/span> presence at <span class=\"caps\">CNS<\/span> 2023: <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/125\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/125<\/a><\/li>\n<li>Tasks force&nbsp;updates<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"minutes\">\n<h3>Minutes<a class=\"headerlink\" href=\"#minutes\" title=\"Permalink to this headline\">\u22c6<\/a><\/h3>\n<div class=\"section\" id=\"tasks-from-last-meeting\">\n<h4>Tasks from last meeting<a class=\"headerlink\" href=\"#tasks-from-last-meeting\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>All actions&nbsp;complete<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Shailesh open new ticket for new co-chair: <span class=\"caps\">DONE<\/span><ul>\n<li><a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/129\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/129<\/a><\/li>\n<li>Please self-nominate, or speak to colleagues and nominate&nbsp;them.<\/li>\n<li>To nominate, e-mail the current chairs (ankur <span class=\"caps\">DOT<\/span> sinha <span class=\"caps\">AT<\/span> ucl <span class=\"caps\">DOT<\/span> ac <span class=\"caps\">DOT<\/span> uk; appukuttan <span class=\"caps\">DOT<\/span> shailesh <span class=\"caps\">AT<\/span> gmail <span class=\"caps\">DOT<\/span>&nbsp;com)<\/li>\n<li>End of nomination period: March 31,&nbsp;2023.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"cns-2023\">\n<h4><span class=\"caps\">CNS<\/span> 2023<a class=\"headerlink\" href=\"#cns-2023\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>Definitely do a social&nbsp;gathering<\/li>\n<li>Defer decision on tutorial\/workshops until next meeting so we have information on&nbsp;submissions\/scheduling<\/li>\n<li>Raise question of extra day\/dedicated day for community development sessions (student\/postdoc related, career, funding, <span class=\"caps\">DEI<\/span>, general training that&#8217;s not specific to&nbsp;tools)<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur e-mail board to ask if there&#8217;s someplace we can feature the&nbsp;SoftwareWG<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur e-mail president to suggest Software <span class=\"caps\">WG<\/span> be added to members meeting&nbsp;agenda<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"task-force-updates\">\n<h4>Task force updates<a class=\"headerlink\" href=\"#task-force-updates\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<div class=\"section\" id=\"simselect\">\n<h5>Simselect<a class=\"headerlink\" href=\"#simselect\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li>working on <span class=\"caps\">UI<\/span>, dockerised&nbsp;prototype<\/li>\n<li><a class=\"reference external\" href=\"https:\/\/fly.io\/\">https:\/\/fly.io\/<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.netlify.com\/pricing\/#features\">https:\/\/www.netlify.com\/pricing\/#features<\/a><\/li>\n<li><a class=\"reference external\" href=\"https:\/\/www.heroku.com\/pricing\">https:\/\/www.heroku.com\/pricing<\/a><\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"cookbook\">\n<h5>Cookbook<a class=\"headerlink\" href=\"#cookbook\" title=\"Permalink to this headline\">\u22c6<\/a><\/h5>\n<ul class=\"simple\">\n<li><span class=\"caps\">ACTION<\/span>: Ankur rename software development guidelines repo for cookbook: <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareDevelopmentGuidelines\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareDevelopmentGuidelines<\/a><\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur set up template and submission&nbsp;process<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<div class=\"section\" id=\"misc\">\n<h4>Misc<a class=\"headerlink\" href=\"#misc\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li><span class=\"caps\">INCF<\/span> neuroinformatics assembly: September 18-20 2023, online: <a class=\"reference external\" href=\"https:\/\/neuroinformatics.incf.org\/\">https:\/\/neuroinformatics.incf.org\/<\/a><ul>\n<li>Call for workshops: <a class=\"reference external\" href=\"https:\/\/www.incf.org\/update\/call-workshops-incf-neuroinformatics-assembly-2023\">https:\/\/www.incf.org\/update\/call-workshops-incf-neuroinformatics-assembly-2023<\/a><\/li>\n<\/ul>\n<\/li>\n<li>GSoC: <a class=\"reference external\" href=\"https:\/\/neurostars.org\/c\/gsoc\/5\">https:\/\/neurostars.org\/c\/gsoc\/5<\/a><\/li>\n<li>Outreachy: <a class=\"reference external\" href=\"https:\/\/www.outreachy.org\/\">https:\/\/www.outreachy.org\/<\/a><ul>\n<li>Open Science pot for academic\/research&nbsp;projects<\/li>\n<\/ul>\n<\/li>\n<li>Next meeting in 3rd week of April, on account of the Easter&nbsp;break<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Meeting logs"}},{"@attributes":{"term":"Community"}}]},{"title":"WG meeting 14 February\u00a02023","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2023\/03\/08\/wg-meeting-14-february-2023.html","rel":"alternate"}},"published":"2023-03-08T17:35:35+00:00","updated":"2023-03-08T17:35:35+00:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2023-03-08:\/SoftwareWG\/2023\/03\/08\/wg-meeting-14-february-2023.html","summary":"<p class=\"first last\">These are the minutes from the working group meeting on 14 February,&nbsp;2023.<\/p>\n","content":"<center><div class=\"figure\">\n<a class=\"reference external image-reference\" href=\"#\">\n<img alt=\"Photo by Daria Nepriakhina on Unsplash\" class=\"img-responsive\" src=\"https:\/\/ocns.github.io\/SoftwareWG\/images\/20210107-meeting-logs.jpg\" style=\"width: 40%;\" \/>\n<\/a>\n<p class=\"caption\">Photo by <a class=\"reference external\" href=\"https:\/\/unsplash.com\/&#64;epicantus?utm_source=unsplash&amp;amp;utm_medium=referral&amp;amp;utm_content=creditCopyText\">Daria Nepriakhina<\/a> on&nbsp;Unsplash.<\/p>\n<\/div>\n<\/center>\n<br \/><p>These are the meeting logs (and additional progress notes) from the Software <span class=\"caps\">WG<\/span> meeting that was held on 14th February 2023.\nThe next progress meeting will be held <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/pages\/contact.html\">in March<\/a>.\nFor any clarifications and suggestions, please open a new&nbsp;ticket.<\/p>\n<div class=\"section\" id=\"attendees\">\n<h2>Attendees<a class=\"headerlink\" href=\"#attendees\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<p>0800<\/p>\n<ul class=\"simple\">\n<li>Shailesh&nbsp;Appukuttan<\/li>\n<li>Ankur&nbsp;Sinha<\/li>\n<\/ul>\n<p>1700<\/p>\n<ul class=\"simple\">\n<li>Ankur&nbsp;Sinha<\/li>\n<li>Marcel&nbsp;Stimberg<\/li>\n<li>Chitaranjan&nbsp;Mohaptra<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"agenda\">\n<h2>Agenda<a class=\"headerlink\" href=\"#agenda\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<p><a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/126\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/126<\/a><\/p>\n<ul class=\"simple\">\n<li>plans for <span class=\"caps\">CNS2023<\/span> (if any)<ul>\n<li><a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/125\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/125<\/a><\/li>\n<\/ul>\n<\/li>\n<li>(Shailesh): about having a new co-chair to replace myself. I have been finding it difficult in recent months to devote much time to the admin activities of the group, and it would therefore be useful to have someone else step-up and help manage the <span class=\"caps\">WG<\/span>. I will naturally continue to contribute as a member of the <span class=\"caps\">WG<\/span>. Forming the task forces (for the two ongoing tasks) was a nice example of how some of the workload could be distributed and&nbsp;managed.<\/li>\n<li>Code of Conduct<ul>\n<li><a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/123\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/123<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Task force&nbsp;updates<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"notes\">\n<h2>Notes<a class=\"headerlink\" href=\"#notes\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<ul class=\"simple\">\n<li><span class=\"caps\">CNS2023<\/span>: do not do satellite tutorials this year<ul>\n<li>continue with dev sessions and software&nbsp;highlights<\/li>\n<li>if\/when possible, do more things of general interest<ul>\n<li>reproducibility<\/li>\n<li>model&nbsp;visualisation<\/li>\n<li>etc.<\/li>\n<\/ul>\n<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur comment on ticket with updates (<span class=\"caps\">DONE<\/span>)<ul>\n<li>See: <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/125#issuecomment-1460539119\">ticket<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur mention in notifications that we&#8217;re looking for a new co-chair<ul>\n<li>if we do have lots of candidates, we can consider an&nbsp;election<\/li>\n<\/ul>\n<\/li>\n<li>Code of Conduct:<ul>\n<li>point to <span class=\"caps\">OCNS<\/span> Code of&nbsp;Conduct<\/li>\n<li>let co-chairs be in-charge of enforcement, with possibility of reaching out to externals when&nbsp;necessary<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur update website (<span class=\"caps\">DONE<\/span>)<\/li>\n<\/ul>\n<\/li>\n<li>Task force updates<ul>\n<li>Simselect: lots of steady progress<ul>\n<li>core team meets every two&nbsp;weeks<\/li>\n<li>agreement on database\/data&nbsp;description<\/li>\n<li>consensus on general idea of what the resource needs to look&nbsp;like<\/li>\n<li>at stage where prototyping is required to flesh out more&nbsp;details<\/li>\n<li>more information on ticket: <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/117\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/117<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Guidelines task force<ul>\n<li>no sense in writing another programming guide etc., which already exist in&nbsp;plenty<\/li>\n<li>needs to be something that addresses a niche that the Software <span class=\"caps\">WG<\/span> has expertise&nbsp;in<\/li>\n<li>replace with something like an informal cookbook that includes useful tips\/tricks\/snippets that can be used in computational neuroscience<ul>\n<li>See, for example: <a class=\"reference external\" href=\"https:\/\/web.archive.org\/web\/20170227062636\/http:\/\/neuralensemble.org\/cookbook\/\">https:\/\/web.archive.org\/web\/20170227062636\/http:\/\/neuralensemble.org\/cookbook\/<\/a><\/li>\n<\/ul>\n<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur comment on <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/116\">ticket<\/a> suggesting we (<span class=\"caps\">DONE<\/span>):<ul>\n<li>add section on &#8220;guidelines&#8221; to the <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/pages\/resources.html\">resources page on our&nbsp;website<\/a><\/li>\n<li>close <a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/116\">ticket<\/a><\/li>\n<li>suggest &#8220;cook book&#8221; instead of&nbsp;guidelines<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Meeting logs"}},{"@attributes":{"term":"Community"}}]},{"title":"Software highlight: Kay Robbins: HED (Hierarchical Event\u00a0Descriptors)","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2023\/02\/17\/software-highlight-kay-robbins-hed.html","rel":"alternate"}},"published":"2023-02-17T11:45:56+00:00","updated":"2023-02-17T11:45:56+00:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2023-02-17:\/SoftwareWG\/2023\/02\/17\/software-highlight-kay-robbins-hed.html","summary":"<p class=\"first last\"><a class=\"reference external\" href=\"https:\/\/www.utsa.edu\/sciences\/computer-science\/faculty\/KayRobbins.html\">Kay Robbins<\/a> will introduce and discuss <span class=\"caps\">HED<\/span>, a practical system for describing an experiment using an analysis-ready&nbsp;framework.<\/p>\n","content":"<p><a class=\"reference external\" href=\"https:\/\/www.utsa.edu\/sciences\/computer-science\/faculty\/KayRobbins.html\">Kay Robbins<\/a> will introduce and discuss <span class=\"caps\">HED<\/span>, a practical system for describing an experiment using an analysis-ready&nbsp;framework.<\/p>\n<ul class=\"simple\">\n<li>Zoom (<a class=\"reference external\" href=\"https:\/\/ucl.zoom.us\/rec\/share\/h-tszrMXevUhADQHl9CGwgP08ofJ77vmvFchUjrGZunm6MZB4F1txnUvuIXPAU2l.EiVd5lEKg7r-bh2M\">recordings<\/a>)<\/li>\n<li><a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/extras\/other\/INCF2023_SoftwareHighlightsFinal.pptx\">Slides<\/a><\/li>\n<\/ul>\n<\/center>\n<br \/>\n\n<center>\n <iframe width=\"560\" height=\"315\" style=\"height: 315px\" src=\"https:\/\/www.youtube.com\/embed\/0-VLzvwAaUQ?si=z1OL0hxUYkpSsf2-\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe>\n <\/center>\n<br \/><p>In human neuroimaging experiments, a record of what a participant experiences together with a clear understanding of the participant (task) intent are key to interpreting recorded brain dynamics.\n<span class=\"caps\">HED<\/span> (Hierarchical Event Descriptors, <a class=\"reference external\" href=\"https:\/\/www.hedtags.org\">https:\/\/www.hedtags.org<\/a>) annotations and supporting infrastructure can provide human-understandable machine-actionable descriptions of events experienced during laboratory and\/or real-world time series recordings.\n<span class=\"caps\">HED<\/span>, which is well-integrated into <span class=\"caps\">BIDS<\/span> (<a class=\"reference external\" href=\"https:\/\/bids.neuroimaging.io\/\">Brain Imaging Data Structure<\/a>) has an ecosystem of tools supporting researchers at various stages including data acquisition, annotation, sharing, and analysis.\nThis talk will describe <span class=\"caps\">HED<\/span> principles, focusing on basic representations of an experiment and its design.\nVarious tools in the <span class=\"caps\">HED<\/span> ecosystem to support search, summary and analysis will be introduced and demonstrated.\nFinally, we&#8217;ll discuss how tool developers can leverage the <span class=\"caps\">HED<\/span> infrastructure to build advanced analysis tools capable of automated analysis in support of machine learning.\n<span class=\"caps\">HED<\/span> is an entirely open-source project, and the <span class=\"caps\">HED<\/span> Working Group welcomes contributors and&nbsp;contributions.<\/p>\n<p>Papers and&nbsp;resources:<\/p>\n<ul class=\"simple\">\n<li>Capturing the nature of events and event context using Hierarchical Event Descriptors (<span class=\"caps\">HED<\/span>).&nbsp;NeuroImage. <a class=\"reference external\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1053811921010387\">Link<\/a>,<\/li>\n<li>Building <span class=\"caps\">FAIR<\/span> functionality: Annotating events in time series data using Hierarchical Event Descriptors (<span class=\"caps\">HED<\/span>). Neuroinformatics. <a class=\"reference external\" href=\"https:\/\/link.springer.com\/article\/10.1007\/s12021-021-09537-4\">Link<\/a>.<\/li>\n<li>Resources: <a class=\"reference external\" href=\"https:\/\/www.hed-resources.org\">https:\/\/www.hed-resources.org<\/a><\/li>\n<li>GitHub organization: <a class=\"reference external\" href=\"https:\/\/github.com\/hed-standard\">https:\/\/github.com\/hed-standard<\/a><\/li>\n<\/ul>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"HED"}},{"@attributes":{"term":"Software highlight"}},{"@attributes":{"term":"Neuroscience"}},{"@attributes":{"term":"Neuroimaging"}},{"@attributes":{"term":"BIDS"}}]},{"title":"WG meeting 16 January\u00a02023","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2023\/02\/01\/wg-meeting-16-january-2023.html","rel":"alternate"}},"published":"2023-02-01T10:30:55+00:00","updated":"2023-02-01T10:30:55+00:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2023-02-01:\/SoftwareWG\/2023\/02\/01\/wg-meeting-16-january-2023.html","summary":"<p class=\"first last\">These are the minutes from the working group meeting on 16 January,&nbsp;2023.<\/p>\n","content":"<center><div class=\"figure\">\n<a class=\"reference external image-reference\" href=\"#\">\n<img alt=\"Photo by Daria Nepriakhina on Unsplash\" class=\"img-responsive\" src=\"https:\/\/ocns.github.io\/SoftwareWG\/images\/20210107-meeting-logs.jpg\" style=\"width: 40%;\" \/>\n<\/a>\n<p class=\"caption\">Photo by <a class=\"reference external\" href=\"https:\/\/unsplash.com\/&#64;epicantus?utm_source=unsplash&amp;amp;utm_medium=referral&amp;amp;utm_content=creditCopyText\">Daria Nepriakhina<\/a> on&nbsp;Unsplash.<\/p>\n<\/div>\n<\/center>\n<br \/><p>These are the meeting logs (and additional progress notes) from the Software <span class=\"caps\">WG<\/span> meeting that was held on 16th January 2023.\nThe next progress meeting will be held <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/pages\/contact.html\">in February<\/a>.\nFor any clarifications and suggestions, please open a new&nbsp;ticket.<\/p>\n<div class=\"section\" id=\"attendees\">\n<h2>Attendees<a class=\"headerlink\" href=\"#attendees\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<p>1700<\/p>\n<ul class=\"simple\">\n<li>Marcel&nbsp;Stimberg<\/li>\n<li>Ankur&nbsp;Sinha<\/li>\n<li>Chitaranjan&nbsp;Mahapatra<\/li>\n<\/ul>\n<p>Apologies:<\/p>\n<ul class=\"simple\">\n<li>Shailesh&nbsp;Appukuttan<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"agenda\">\n<h2>Agenda<a class=\"headerlink\" href=\"#agenda\" title=\"Permalink to this headline\">\u22c6<\/a><\/h2>\n<p><a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/120\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/120<\/a><\/p>\n<ul class=\"simple\">\n<li>task force&nbsp;updates<\/li>\n<li>ideas for sessions (dev sessions, hightlights&nbsp;etc.)<\/li>\n<li>initial discussion on whether or not we want to host satellite tutorials along with (before?) <span class=\"caps\">CNS<\/span>*2023 (the conference is in Leipzig from July&nbsp;15-19)<\/li>\n<li>tasks from last meeting (no pending tasks from last&nbsp;meeting)<\/li>\n<\/ul>\n<div class=\"section\" id=\"task-force-updates\">\n<h3>Task force updates<a class=\"headerlink\" href=\"#task-force-updates\" title=\"Permalink to this headline\">\u22c6<\/a><\/h3>\n<div class=\"section\" id=\"guidelines-task-force\">\n<h4>Guidelines task force<a class=\"headerlink\" href=\"#guidelines-task-force\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>unsure of scope at the&nbsp;moment<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Chitaranjan set up new doodle to plan next meeting: meeting in week starting 30 January to allow time for doodle&nbsp;filling<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"simulator-selection-resource\">\n<h4>Simulator selection resource<a class=\"headerlink\" href=\"#simulator-selection-resource\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li>consolidated updates document: <a class=\"reference external\" href=\"https:\/\/hackmd.io\/LWjtz9ykQbm7yg5X_RKpCQ?view\">https:\/\/hackmd.io\/LWjtz9ykQbm7yg5X_RKpCQ?view<\/a><\/li>\n<li>progress on&nbsp;scope<\/li>\n<li>progress on inclusion&nbsp;criteria<\/li>\n<li>progress on &#8220;front end&#8221;&nbsp;design<\/li>\n<li>focus more on information useful to user\/newcomer rather than technical&nbsp;information\/criteria<\/li>\n<li>regular meeting schedule: alternate Wednesdays on 14 <span class=\"caps\">UTC<\/span>. Next meeting is 25th January at 1400 <span class=\"caps\">UTC<\/span><\/li>\n<li>4-5 regular task force members (more are always&nbsp;welcome!)<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"ideas-for-sessions\">\n<h4>Ideas for sessions<a class=\"headerlink\" href=\"#ideas-for-sessions\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<ul class=\"simple\">\n<li><span class=\"caps\">ACTION<\/span>: Ankur e-mail list asking for&nbsp;ideas<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Marcel e-mail Dendrify devs about software hightlight\/dev session and <span class=\"caps\">CC<\/span> Ankur\/Shailesh (<a class=\"reference external\" href=\"https:\/\/github.com\/OCNS\/SoftwareWG\/issues\/93\">https:\/\/github.com\/<span class=\"caps\">OCNS<\/span>\/SoftwareWG\/issues\/93<\/a>) (<span class=\"caps\">DONE<\/span>)<\/li>\n<\/ul>\n<\/div>\n<div class=\"section\" id=\"initial-discussion-on-satellite-tutorials-at-cns-2023\">\n<h4>Initial discussion on Satellite tutorials at <span class=\"caps\">CNS<\/span> 2023<a class=\"headerlink\" href=\"#initial-discussion-on-satellite-tutorials-at-cns-2023\" title=\"Permalink to this headline\">\u22c6<\/a><\/h4>\n<p><a class=\"reference external\" href=\"https:\/\/www.cnsorg.org\/\">https:\/\/www.cnsorg.org\/<\/a><\/p>\n<ul class=\"simple\">\n<li>2022: <a class=\"reference external\" href=\"https:\/\/ocns.github.io\/SoftwareWG\/pages\/software-wg-satellite-tutorials-at-cns-2022.html\">https:\/\/ocns.github.io\/SoftwareWG\/pages\/software-wg-satellite-tutorials-at-cns-2022.html<\/a><\/li>\n<li>unsure if people are interested in live teaching sessions when they can go through documentation\/videos\/notebooks at their own pace when&nbsp;required<\/li>\n<li>if we do a repeat of last year, we will charge a small registration fee to filter out people that are registering for meetings but not necessarily attending: it will be a small fee, that can be waived without requiring documentation (similar to Neuromatch&nbsp;conferences)<\/li>\n<li>we will use something like <a class=\"reference external\" href=\"https:\/\/sched.com\">Sched<\/a> to ensure regular reminders are sent to&nbsp;registrants<\/li>\n<li>we will ask either <span class=\"caps\">INCF<\/span>\/<span class=\"caps\">OCNS<\/span> to fund us, and they get whatever registration fees are collected in&nbsp;return<\/li>\n<li>alternatives<ul>\n<li>software wg open day with a mix of user and dev focussed sessions, open to everyone to&nbsp;attend<\/li>\n<li>short software highlights some time before the conference to give people an idea of the tools (and what to expect from tutorials at <span class=\"caps\">CNS<\/span>): open to&nbsp;everyone<\/li>\n<li>reproduction projects:<ul>\n<li>tutors (tool devs) list some models that they would like reproduced in their&nbsp;simulators<\/li>\n<li><span class=\"dquo\">&#8220;<\/span>students&#8221; work with them to reproduce&nbsp;them<\/li>\n<li>submit to&nbsp;rescience<\/li>\n<li>Issue: probably not doable in a day, so if done, will be a longer term project requiring multiple&nbsp;meetings<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<li>internships\n- usually require some buy in from institutions, so not easy to&nbsp;do<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur put all this in a GitHub issue for&nbsp;discussion<\/li>\n<li><span class=\"caps\">ACTION<\/span>: Ankur e-mail tutors from last year to see what they think and what they are ready to&nbsp;do<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Meeting logs"}},{"@attributes":{"term":"Community"}}]},{"title":"Software highlight: Michalis Pagkalos:\u00a0Dendrify","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2023\/01\/27\/dev-session-michalis-pagkalos-dendrify.html","rel":"alternate"}},"published":"2023-01-27T11:01:32+00:00","updated":"2023-01-27T11:01:32+00:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2023-01-27:\/SoftwareWG\/2023\/01\/27\/dev-session-michalis-pagkalos-dendrify.html","summary":"<p class=\"first last\"><a class=\"reference external\" href=\"https:\/\/dendrites.gr\/?page_id=265\">Michalis Pagkalos<\/a> will introduce and discuss <a class=\"reference external\" href=\"https:\/\/github.com\/Poirazi-Lab\/dendrify\">Dendrify<\/a>, a framework for incorporating dendrites to spiking neural networks, in this&nbsp;session.<\/p>\n","content":"<p><a class=\"reference external\" href=\"https:\/\/dendrites.gr\/?page_id=265\">Michalis Pagkalos<\/a> will introduce and discuss <a class=\"reference external\" href=\"https:\/\/github.com\/Poirazi-Lab\/dendrify\">Dendrify<\/a>, a framework for incorporating dendrites to spiking neural networks, in this&nbsp;session.<\/p>\n<ul class=\"simple\">\n<li>Zoom (<a class=\"reference external\" href=\"https:\/\/ucl.zoom.us\/rec\/share\/tEgyFcXjPflMGLmSclnH5p-qKGyjJ_4IdRdxF70wJPiN_T6dZQtmLXxnvYbKn6L3.tzGYABjJOHer90o4\">recordings<\/a>)<\/li>\n<\/ul>\n<!--\n\n<\/center>\n<br \/>\n\n<center>\n <iframe width=\"560\" height=\"315\" style=\"height: 315px\" src=\"https:\/\/www.youtube.com\/embed\/V3e_2OSfPsI\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe>\n <\/center>\n<br \/>\n\n--><p>The abstract for the talk is&nbsp;below:<\/p>\n<p>Current SNNs studies frequently ignore dendrites, the thin membranous extensions of biological neurons that receive and preprocess nearly all synaptic inputs in the brain.\nHowever, decades of experimental and theoretical research suggest that dendrites possess compelling computational capabilities that greatly influence neuronal and circuit functions.\nNotably, standard point-neuron networks cannot adequately capture most hallmark dendritic properties.\nMeanwhile, biophysically detailed neuron models can be suboptimal for practical applications due to their complexity, and high computational cost.\nFor this reason, we introduce Dendrify, a new theoretical framework combined with an open-source Python package (compatible with Brian2) that facilitates the development of bioinspired SNNs. Dendrify allows the creation of reduced compartmental neuron models with simplified yet biologically relevant dendritic and synaptic integrative properties.\nSuch models strike a good balance between flexibility, performance, and biological accuracy, allowing us to explore dendritic contributions to network-level functions while paving the way for developing more realistic neuromorphic&nbsp;systems.<\/p>\n<ul class=\"simple\">\n<li>Manuscript: <a class=\"reference external\" href=\"https:\/\/www.nature.com\/articles\/s41467-022-35747-8\">Introducing the Dendrify framework for incorporating dendrites to spiking neural networks | Nature&nbsp;Communications<\/a><\/li>\n<li>Source code: <a class=\"reference external\" href=\"https:\/\/github.com\/Poirazi-Lab\/dendrify\">Poirazi-Lab\/dendrify: Introducing dendrites to spiking neural networks. Designed for the Brian 2&nbsp;simulator.<\/a><\/li>\n<li>Documentation: <a class=\"reference external\" href=\"https:\/\/dendrify.readthedocs.io\/en\/latest\/\">https:\/\/dendrify.readthedocs.io\/en\/latest\/<\/a><\/li>\n<\/ul>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Dendrify"}},{"@attributes":{"term":"Software highlight"}},{"@attributes":{"term":"Neuroscience"}},{"@attributes":{"term":"Simulations"}},{"@attributes":{"term":"Analysis"}},{"@attributes":{"term":"Brian"}}]},{"title":"Dev session: Denis Alevi:\u00a0Brian2CUDA","link":{"@attributes":{"href":"https:\/\/ocns.github.io\/SoftwareWG\/2022\/10\/18\/dev-session-denis-alevi-brian2cuda.html","rel":"alternate"}},"published":"2022-10-18T10:38:20+01:00","updated":"2022-10-18T10:38:20+01:00","author":{"name":"Ankur Sinha"},"id":"tag:ocns.github.io,2022-10-18:\/SoftwareWG\/2022\/10\/18\/dev-session-denis-alevi-brian2cuda.html","summary":"<p class=\"first last\"><a class=\"reference external\" href=\"https:\/\/www.sprekelerlab.org\/denis\/\">Denis Alevi<\/a> will introduce the <a class=\"reference external\" href=\"https:\/\/brian2cuda.readthedocs.io\/en\/latest\/\">Brian2CUDA<\/a> tool in this session, and discuss its development. We will also have a discussion on <span class=\"caps\">GPU<\/span> based simulation in neuroscience after the&nbsp;presentation.<\/p>\n","content":"<p><a class=\"reference external\" href=\"https:\/\/www.sprekelerlab.org\/denis\/\">Denis Alevi<\/a> will introduce the <a class=\"reference external\" href=\"https:\/\/brian2cuda.readthedocs.io\/en\/latest\/\">Brian2CUDA<\/a> tool in this session, and discuss its development. We will also have a discussion on <span class=\"caps\">GPU<\/span> based simulation in neuroscience after the&nbsp;presentation.<\/p>\n<ul class=\"simple\">\n<li>Date: Thursday, November 3, 2022, 1600 <span class=\"caps\">UTC<\/span> (Click <a class=\"reference external\" href=\"https:\/\/www.timeanddate.com\/worldclock\/fixedtime.html?msg=Dev+session%3A+Denis+Alevi+Brian2CUDA&amp;iso=20221103T16&amp;p1=136&amp;ah=1\">here<\/a> to see your local&nbsp;time).<\/li>\n<li>Location (Zoom): <a class=\"reference external\" href=\"https:\/\/ucl.zoom.us\/j\/95692778384?pwd=VldIQ3hPTU1zczNpYjQxSSt4Z25xdz09\">Link<\/a> (Zoom login&nbsp;required)<\/li>\n<li><a class=\"reference external\" href=\"\/extras\/ics\/20221103-dev-session-denis-alevi-brian2cuda.ics\">Click here to download the calendar invite to add this meeting your&nbsp;calendar<\/a><\/li>\n<\/ul>\n<p>The abstract for the talk is&nbsp;below:<\/p>\n<p>Graphics processing units (GPUs) are widely available and have been used with\ngreat success to accelerate scientific computing in the last decade. These\nadvances, however, are often not available to researchers interested in\nsimulating spiking neural networks, but lacking the technical knowledge to\nwrite the necessary low-level code. Writing low-level code is not necessary\nwhen using the popular Brian simulator, which provides a framework to generate\nefficient <span class=\"caps\">CPU<\/span> code from high-level model definitions in Python. Here, we\npresent Brian2CUDA, an open-source software that extends the Brian simulator\nwith a <span class=\"caps\">GPU<\/span> backend. Our implementation generates efficient code for the\nnumerical integration of neuronal states and for the propagation of synaptic\nevents on GPUs, making use of their massively parallel arithmetic capabilities.\nWe benchmark the performance improvements of our software for several model\ntypes and find that it can accelerate simulations by up to three orders of\nmagnitude compared to Brian&#8217;s <span class=\"caps\">CPU<\/span> backend. Currently, Brian2CUDA is the only\npackage that supports Brian&#8217;s full feature set on GPUs, including arbitrary\nneuron and synapse models, plasticity rules, and heterogeneous delays. When\ncomparing its performance with Brian2GeNN, another <span class=\"caps\">GPU<\/span>-based backend for the\nBrian simulator with fewer features, we find that Brian2CUDA gives comparable\nspeedups, while being typically slower for small and faster for large networks.\nBy combining the flexibility of the Brian simulator with the simulation speed\nof GPUs, Brian2CUDA enables researchers to efficiently simulate spiking neural\nnetworks with minimal effort and thereby makes the advancements of <span class=\"caps\">GPU<\/span>\ncomputing available to a larger audience of&nbsp;neuroscientists.<\/p>\n<p>References:<\/p>\n<ul class=\"simple\">\n<li>Publication: <a class=\"reference external\" href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2022.883700\/abstract\">Brian2CUDA: flexible and efficient simulation of spiking neural network models on GPUs (Frontiers in&nbsp;Neuroinformatics)<\/a><\/li>\n<li>Documentation: <a class=\"reference external\" href=\"https:\/\/brian2cuda.readthedocs.io\/en\/latest\/\">https:\/\/brian2cuda.readthedocs.io\/en\/latest\/<\/a><\/li>\n<li>Source code: <a class=\"reference external\" href=\"https:\/\/github.com\/brian-team\/brian2cuda\">https:\/\/github.com\/brian-team\/brian2cuda<\/a><\/li>\n<\/ul>\n","category":[{"@attributes":{"term":"Events"}},{"@attributes":{"term":"Brian2CUDA"}},{"@attributes":{"term":"Dev session"}},{"@attributes":{"term":"GPU"}},{"@attributes":{"term":"Python"}},{"@attributes":{"term":"C++"}},{"@attributes":{"term":"CUDA"}},{"@attributes":{"term":"Nvidia"}},{"@attributes":{"term":"Simulation"}},{"@attributes":{"term":"Code generation"}}]}]}