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Add newsletter for Sept to website
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‎header-content.html

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<li>
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<a data-pjax href="./get_involved.html">Get Involved</a>
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</li>
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<li>
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<a data-pjax href="./news.html">News</a>
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</li>
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<li>
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<a data-pjax href="./downloads.html">Downloads</a>
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</li>

‎index.html

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</p>
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<ul class="masthead-links">
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<li>
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<a href="http://blog.openworm.org" target="_blank">Blog</a>
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<a href="news.html">News</a>
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</li>
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<li>
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<a href="http://docs.openworm.org/projects" target="_blank">Projects</a>
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<div class="row-fluid">
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<div class="span6" style="color: #292929;">
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<h2>Latest news</h2>
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<p class="marketing-byline clear">
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See the most recent OpenWorm newslatter <a href="./news.html">here</a>.
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</p>
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<ul id="news-feed">
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‎news.html

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<title>OpenWorm News</title>
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<meta name="description" content="OpenWorm Studentships">
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<link href="css/bootstrap.css" rel="stylesheet">
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<link rel="stylesheet" href="css/font-awesome.css">
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<link href="css/bootstrap-responsive.css" rel="stylesheet">
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<link href="css/main.css" rel="stylesheet">
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<link href="css/docs.css" rel="stylesheet">
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<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
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<![endif]-->
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<link rel="shortcut icon" href="favicon.ico">
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<div class="navbar navbar-inverse navbar-fixed-top">
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<div class="navbar-inner" id="head-nav">
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</div>
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</div>
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<script src="js/jquery-3.6.0.js"></script>
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<script>
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// get head-nav and foot-nav with jquery (get is async)
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$.get('header-content.html', function(data) {
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$('#head-nav').html(data);
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})
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$.get('footer-content.html', function(data) {
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$('#foot-nav').html(data);
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})
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</script>
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</head>
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<body>
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<div id="pjax-content">
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<header class="jumbotron subhead" id="overview">
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<div class="container">
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<!--<div class="openworm_logo_header"></div>-->
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<h1>OpenWorm News</h1>
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<p class="lead">
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Recent updates from the OpenWorm project
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</p>
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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="span3 bs-docs-sidebar">
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<ul class="nav nav-list bs-docs-sidenav">
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<li>
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<a href="#September2022"><i class="fa fa-chevron-right"></i> September 2022</a>
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</li>
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</ul>
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</div>
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<div class="span9">
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<section id="September2022">
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<div class="page-header">
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<h1>September 2022</h1>
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<h3>1) OpenCollective as a new funding stream</h3>
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<p align="center"><img src="https://raw.githubusercontent.com/openworm/Newsletter/main/img/opencollective.png" alt="OpenWorm" width="400"/></p>
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<p class="lead">We have added <a href="https://opencollective.com/openworm">OpenCollective</a> as a new and easy way to donate to OpenWorm.
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Regular contributions to the project (monthly/yearly) are possible through this funding stream.
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See <a href="https://openworm.org/donate">here</a> for more details.</p>
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<p class="lead">One of the first uses of these funds will be to support <b>OpenWorm Studentships</b> (see below).</p>
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<h3>2) OpenWorm Studentships - first successful project completed</h3>
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<p class="lead">OpenWorm Studentships are a new way to incentivize contribution to the OpenWorm project,
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offering small stipends and recognition to junior researchers who want to spend time bringing their research
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into OpenWorm and making it more accessible for the wider community. See
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<a href="https://openworm.org/studentships.html">here</a> for more information.</p>
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<p class="lead">The first person to complete an OpenWorm Studentship project has been <b>Tyson Wheelwright</b>. He has made significant updates to
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the <a href="https://github.com/openworm/Blender2NeuroML/">Blender 2 NeuroML</a> subproject.</p>
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<p align="center"><img src="https://github.com/openworm/Blender2NeuroML/raw/master/images/Blender_ADAL.png" width="400"/>&nbsp;&nbsp;
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<img src="https://github.com/openworm/Blender2NeuroML/raw/master/images/ADAL.png" width="400"/></p>
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<p align="center"><i>Figure showing a single cell (<a href="https://www.wormatlas.org/neurons/Individual%20Neurons/ADAframeset.html">ADAL</a>) highlighted in orange in the original
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<a href="https://github.com/openworm/Blender2NeuroML/blob/master/src/Data/Virtual_Worm_March_2011.blend">3D Blender file</a> (from the
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<a href="http://caltech.wormbase.org/virtualworm">Virtual Worm Project</a>) on the left, and corresponding images of the cell on its own in Blender (middle 2 panels) and in
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<a href="https://docs.neuroml.org/Userdocs/NeuroMLv2.html">NeuroML 2</a> format (right 2 panels). The NeuroML version is being used in our
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<a href="https://github.com/openworm/c302">biophysical model of the worm nervous system</a>. See
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<a href="https://github.com/openworm/Blender2NeuroML/blob/master/src/NeuroMLImages/README.md">here</a> for more examples.</i></p>
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<p class="lead">More Studentships will be offered to the community in late 2022.</p>
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<h3>3) NeuroPAL</h3>
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<p class="lead">The recent paper <a href="https://www.sciencedirect.com/science/article/pii/S0092867420316822">NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in <i>C. elegans</i></a> described a groundbreaking new technique to create a genetic strain of the worm where each neuron
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is labelled with a fluorescent marker of a specific color, allowing easy identification of neurons across experiments and animals.</p>
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<p class="lead">We have converted one of these datasets containing positions of cell bodies and the expressed NeuroPAL colors to NeuroML,
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to allow it to be used in OpenWorm models and associated applications. Full details can be found
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<a href="https://github.com/openworm/NeuroPAL">here</a>.</p>
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<p align="center"><kbd><img src="https://raw.githubusercontent.com/openworm/NeuroPAL/main/NeuroML2/Screenshot_Canonical.png" alt="NeuroPAL" width="550"></kbd></p>
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<p align="center"><i>The above image shows the canonical positions and colors of a NeuroPAL dataset which has been <a href="https://github.com/openworm/NeuroPAL/tree/main/NeuroML2">converted into NeuroML</a>, allowing it to be <a href="https://www.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_Canonical.net.nml">visualised on Open Source Brain</a>.</i></p>
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<h3>4) Electrophysiological data from worm neurons</h3>
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<p class="lead">Electrical recordings from individual neurons in <i>C. elegans</i> are crucial experimental data required for
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creating biologically realistic computational models of the worm.</p>
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<p class="lead">Electrophysiological recordings of the activity of the
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<a href="https://www.wormatlas.org/neurons/Individual%20Neurons/ASHframeset.html">ASH neuron</a> made by the
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<a href="https://med.stanford.edu/goodmanlab.html">Wormsense Lab</a> of Miriam Goodman were converted to open, standardized
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<a href="http://nwb.org">Neurodata Without Borders</a> format as part of a
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<a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a> project in 2021 by Steph Prince. Further details,
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as well as all of the converted datasets, can be found
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<a href="https://github.com/openworm/WormsenseLab_ASH">here</a>.</p>
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<p align="center"><img src="https://raw.githubusercontent.com/openworm/WormsenseLab_ASH/main/images/example_goodman_lab_file.png" width=600/></p>
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<p align="center"><i>A view of the
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<a href="http://nwbexplorer.opensourcebrain.org/">NWB Explorer</a> interface showing one of the converted electrophysiological datasets. Click
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<a href="https://github.com/openworm/WormsenseLab_ASH/blob/main/test_data/README.md">here</a> to explore other datasets and get direct
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links to NWB Explorer to browse them.</i></p>
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<h3>5) DevoWorm updates</h3>
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<p align="center"><img src="https://raw.githubusercontent.com/OREL-group/GSoC/main/Media/DW.png" height="150"/></p>
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<p class="lead">Over the past year, <a href="https://devoworm.weebly.com/">DevoWorm</a> has been involved in a number of initiatives.
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DevoWorm hosted four <a href="https://summerofcode.withgoogle.com/">Google Summer of Code</a> students in 2022: Karan Lohaan and Harikrishna
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Pillai worked on the Digital Microspheres project (a spherical platform for embryo data), while Jiahang Li and Wataru Kawakami worked
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on developing a Graph Neural Network pipeline for the DevoLearn platform.</p>
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<p class="lead">DevoWorm also had a presence at <a href="https://netsci2022.net/">NetSci 2022</a> (virtual conference hosted in Shanghai).
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Bradly Alicea presented on the group's Embodied Hypernetworks work in the main conference, as well as serving to represent the group
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at the Network Neuroscience satellite session as a presenter and participant.</p>
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<p class="lead">Our <a href="https://www.youtube.com/playlist?list=PLJ8ZcBZeKeci2ACwfllCDFn_eZAXlbGQN">weekly meetings</a> are a continuing success.
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We cover a number of technical topics and a wide variety of topical reviews spanning biophysics, developmental biology, computational
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analysis, and more. Join us on Mondays at 2pm UTC (1pm UTC in winter) to get involved.</p>
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<h3>6) OpenWorm simulation stack updates</h3>
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<p align="center"><img src="https://raw.githubusercontent.com/openworm/OpenWorm/master/img/worm-crawling.gif" alt="Worm Crawling" width="550"></p>
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<p align="center"><i>Example movie generated when the Docker container containing the OpenWorm simulation stack runs for 5
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seconds of simulated time.</i></p>
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<p class="lead">We have made a new release of the
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<a href="https://hub.docker.com/r/openworm/openworm">Docker container</a> that pulls together
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the major components of our simulation stack and allows it to be run on your machine. It includes
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<a href="https://github.com/openworm/sibernetic">Sibernetic</a>,
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<a href="https://github.com/openworm/c302">c302</a> and
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<a href="https://github.com/openworm/owmeta">owmeta</a>.
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See details <a href="https://github.com/openworm/OpenWorm/blob/master/README.md#quickstart">here</a>.</p>
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<h3>7) Other announcements</h3>
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<p align="center"><kbd><a href="docs/OpenWormPoster_C_elegans_meeting_June_2021.pdf">
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<img src="https://raw.githubusercontent.com/openworm/Newsletter/main/img/OpenWormPoster2022.png" alt="OpenWormPoster2022" width="450"></a></kbd></p>
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<p class="lead">A poster presenting the latest status of the OpenWorm project was presented at the
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<a href="https://genetics-gsa.org/celegans-2021/">main global
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conference in the <i>C. elegans</i> field</a> in June 2021. Click on the image above to download the poster.</p>
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