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#Cytoscape

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Josep Pueyo-Ros :rstats:<p>I&#39;m a bit desperate trying to create an app to visualizes a cytoscape graph on a leaflet map. I even tried to ask chatGPT... </p><p>Any help would be appreciated: <a href="https://stackoverflow.com/questions/79654144/cytoscape-leaflet-not-visualizes-map" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">stackoverflow.com/questions/79</span><span class="invisible">654144/cytoscape-leaflet-not-visualizes-map</span></a></p><p><a href="https://fosstodon.org/tags/javascript" class="mention hashtag" rel="tag">#<span>javascript</span></a> <a href="https://fosstodon.org/tags/cytoscape" class="mention hashtag" rel="tag">#<span>cytoscape</span></a> <a href="https://fosstodon.org/tags/leaflet" class="mention hashtag" rel="tag">#<span>leaflet</span></a></p>
WikiPathways<p>October 2024 WikiPathways update: 167 edits by 4 contributors and 2 new pathways in the last month. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a>, <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="tag">#<span>rstats</span></a>, <a href="https://fosstodon.org/tags/pathvisio" class="mention hashtag" rel="tag">#<span>pathvisio</span></a> and <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a> Supported by <a href="https://fosstodon.org/tags/AWSOpen" class="mention hashtag" rel="tag">#<span>AWSOpen</span></a> </p><p><a href="https://wikipathways.org/index.php/Download_Pathways" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">wikipathways.org/index.php/Dow</span><span class="invisible">nload_Pathways</span></a></p><p><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a></p>
Anna Dorofeeva<p>I'm playing around with <a href="https://mastodon.online/tags/network" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>network</span></a> <a href="https://mastodon.online/tags/visualization" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>visualization</span></a> of <a href="https://mastodon.online/tags/medieval" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>medieval</span></a> <a href="https://mastodon.online/tags/manuscripts" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>manuscripts</span></a> using <a href="https://mastodon.online/tags/Cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Cytoscape</span></a>, and enjoying how simple and easy it is compared to other tools. This view is rough and ready, and fairly simplistic, but it didn't take long to get and has already yielded valuable information about the (complex and messy) data.</p>
Christopher Nunn<p>Let's sum up my impressions on <a href="https://fedihum.org/tags/networkanalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>networkanalysis</span></a> tools: <a href="https://fedihum.org/tags/Gephi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Gephi</span></a> seems to be the tool for the network in-between and continues to be standard for starting. However, <a href="https://fedihum.org/tags/networkx" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>networkx</span></a> gives most freedom in modelling, but requires advanced Python skills. If you work in the 1500-1800 period, you should use <a href="https://fedihum.org/tags/Palladio" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Palladio</span></a> for linking your data with others. If your data is really big, you might go straight to <a href="https://fedihum.org/tags/Cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Cytoscape</span></a> and if you want to combine with webscraping having too much money you can use <a href="https://fedihum.org/tags/NodeXL" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>NodeXL</span></a>. Agree? ;-)</p>
WikiPathways<p>September 2024 WikiPathways update: 179 edits by 6 contributors and 4 new pathways in the last month. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a>, <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="tag">#<span>rstats</span></a>, <a href="https://fosstodon.org/tags/pathvisio" class="mention hashtag" rel="tag">#<span>pathvisio</span></a> and <a href="https://fosstodon.org/tags/cytoscape" class="mention hashtag" rel="tag">#<span>cytoscape</span></a>. Supported by <a href="https://fosstodon.org/tags/awsopen" class="mention hashtag" rel="tag">#<span>awsopen</span></a> . <a href="https://wikipathways.org/index.php/Download_Pathways" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">wikipathways.org/index.php/Dow</span><span class="invisible">nload_Pathways</span></a> </p><p><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a></p>
Egon Willighagen<p>new blog post about a not so new anymore paper: <a href="https://chem-bla-ics.linkedchemistry.info/2024/07/31/directed-metabolic-network.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">chem-bla-ics.linkedchemistry.i</span><span class="invisible">nfo/2024/07/31/directed-metabolic-network.html</span></a></p><p>"This paper explains how various <a href="https://social.edu.nl/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> resources (<span class="h-card" translate="no"><a href="https://wikis.world/@wikidata" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikidata</span></a></span>, <span class="h-card" translate="no"><a href="https://mastodon.social/@reactome" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>reactome</span></a></span>, <span class="h-card" translate="no"><a href="https://fosstodon.org/@wikipathways" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wikipathways</span></a></span>) are used to visualize the biological story of the data from two <a href="https://social.edu.nl/tags/metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>metabolomics</span></a> experiments archived in <a href="https://social.edu.nl/tags/MetaboLights" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MetaboLights</span></a>. Using <a href="https://social.edu.nl/tags/Neo4J" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Neo4J</span></a> and <a href="https://social.edu.nl/tags/Cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Cytoscape</span></a> she visualizes the data onto a network created with RDF, <a href="https://social.edu.nl/tags/SPARQL" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SPARQL</span></a> from the above resources"</p>
Bharath M. Palavalli<p><span class="h-card"><a href="https://vis.social/@alexrind" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>alexrind</span></a></span> Thank you! I had forgotten about Gephi, I've been using <a href="https://mastodon.sdf.org/tags/cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cytoscape</span></a>.</p>
WikiPathways<p>March 2024 WikiPathways release: 542 edits by 9 contributors and 10 new pathways. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a>. Supported by AWSOpen. <a href="https://wikipathways.org/#download" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">wikipathways.org/#download</span><span class="invisible"></span></a> <a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a></p>
RasterInterrupt<p><a href="https://oldbytes.space/tags/AdventOfCode" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AdventOfCode</span></a> 2023 Day 19: Aplenty</p><p><a href="https://adventofcode.com/2023/day/19" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">adventofcode.com/2023/day/19</span><span class="invisible"></span></a></p><p>That was fun. I had a small mistake in part 2. In order to debug it, I was looking for a tool to visualize the decision graph. I found that <a href="https://oldbytes.space/tags/networkx" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>networkx</span></a> in combination with <a href="https://oldbytes.space/tags/cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cytoscape</span></a> works fantastic. Attached are the graphs from the test input and my real input.</p><p>Code is here:<br><a href="https://github.com/nharrer/AdventOfCode/blob/main/2023/day19/solve-day19.py" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/nharrer/AdventOfCod</span><span class="invisible">e/blob/main/2023/day19/solve-day19.py</span></a></p><p>NetworkX: <a href="https://networkx.org/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">networkx.org/</span><span class="invisible"></span></a><br>Cytoscape: <a href="https://cytoscape.org/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">cytoscape.org/</span><span class="invisible"></span></a></p><p><a href="https://oldbytes.space/tags/AdventOfCode2023" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AdventOfCode2023</span></a> <a href="https://oldbytes.space/tags/AoC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AoC</span></a> <a href="https://oldbytes.space/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python</span></a></p>
Jan Hutter<p><span class="h-card"><a href="https://colearn.social/@simondueckert" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>simondueckert</span></a></span> Geht mir ähnlich. Ich habe bemerkt, dass damit sehr einfach mit Active Directory interagiert werden kann. ChatGPT ist genial beim Coden meiner Python-Script-Wünsche. Was zudem hilft ist mein Software-Entwicklungs-Background, z.B. beim Finden von Bugs und Anpassen des initialen Codes. Und auch bei Graph-Visualisierungs-Tools wie <a href="https://colearn.social/tags/Cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Cytoscape</span></a> scheint <a href="https://colearn.social/tags/python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>python</span></a> die erste Wahl...</p>
WikiPathways<p>July 2023 WikiPathways release: 232 edits by 32 contributors and 12 new pathways. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a> Supported by AWSOpen. <a href="https://wikipathways.org/#download" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">wikipathways.org/#download</span><span class="invisible"></span></a> <a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a></p>
WikiPathways<p>June 2023 WikiPathways release: 137 edits by 22 contributors and 2 new pathways. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a> Supported by AWSOpen. <a href="https://wikipathways.org/#download" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="">wikipathways.org/#download</span><span class="invisible"></span></a><br /><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a></p>
Christof Schöch<p>Very impressive that <a href="https://fedihum.org/tags/Cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Cytoscape</span></a> 3.10 – the <a href="https://fedihum.org/tags/network" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>network</span></a> <a href="https://fedihum.org/tags/visualization" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>visualization</span></a> tool – still supports <a href="https://fedihum.org/tags/Ubuntu" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Ubuntu</span></a> 14.04 (from, you guessed it, Apil 2014). However, it does not yet support Ubuntu 22.04 LTS... which is really a pity.</p>
WikiPathways<p>May 2023 WikiPathways release: 316 edits by 13 contributors and 15 new pathways. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a>. Supported by <a href="https://fosstodon.org/tags/AWSOpen" class="mention hashtag" rel="tag">#<span>AWSOpen</span></a>. <a href="https://www.wikipathways.org/download.html" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://www.</span><span class="">wikipathways.org/download.html</span><span class="invisible"></span></a><br /><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a> <a href="https://fosstodon.org/tags/nomoa" class="mention hashtag" rel="tag">#<span>nomoa</span></a></p>
WikiPathways<p>April 2023 WikiPathways release: 276 edits by 32 contributors and 6 new pathways. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a>. Supported by <a href="https://fosstodon.org/tags/AWSOpen" class="mention hashtag" rel="tag">#<span>AWSOpen</span></a>. <a href="https://www.wikipathways.org/download.html" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://www.</span><span class="">wikipathways.org/download.html</span><span class="invisible"></span></a><br /><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a> <a href="https://fosstodon.org/tags/nomoa" class="mention hashtag" rel="tag">#<span>nomoa</span></a></p>
postmodern<p>What are people's favorite JavaScript library for drawing dynamic network node graphs? Cytoscape? D3? paper.js? p5.js? Or something else (comment below)?<br><a href="https://ruby.social/tags/javascript" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>javascript</span></a> <a href="https://ruby.social/tags/visualization" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>visualization</span></a> <a href="https://ruby.social/tags/cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cytoscape</span></a> <a href="https://ruby.social/tags/d3" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>d3</span></a> <a href="https://ruby.social/tags/paperjs" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>paperjs</span></a> <a href="https://ruby.social/tags/p5js" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>p5js</span></a></p>
WikiPathways<p>March 2023 WikiPathways release: 293 edits by 30 contributors and 22 new pathways. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a>. Supported by <a href="https://fosstodon.org/tags/AWSOpen" class="mention hashtag" rel="tag">#<span>AWSOpen</span></a>. <a href="https://www.wikipathways.org/download.html" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://www.</span><span class="">wikipathways.org/download.html</span><span class="invisible"></span></a><br /><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a> <a href="https://fosstodon.org/tags/nomoa" class="mention hashtag" rel="tag">#<span>nomoa</span></a></p>
Miriam Posner<p>Any <a href="https://dair-community.social/tags/cytoscape" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cytoscape</span></a> enthusiasts on here? Now that CyNetShare seems to be down, what’s the absolute simplest way to publish a Cytoscape graph to the web?</p>
WikiPathways<p>February 2023 WikiPathways release: 283 edits by 32 contributors. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a>. Supported by <a href="https://fosstodon.org/tags/AWSOpen" class="mention hashtag" rel="tag">#<span>AWSOpen</span></a>. <a href="https://wikipathways.org/index.php/Download_Pathways" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">wikipathways.org/index.php/Dow</span><span class="invisible">nload_Pathways</span></a><br /><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a> <a href="https://fosstodon.org/tags/nomoa" class="mention hashtag" rel="tag">#<span>nomoa</span></a></p>
WikiPathways<p>January 2023 WikiPathways release: 151 edits by 13 contributors and 11 new pathways. Accessible via <a href="https://fosstodon.org/tags/webservices" class="mention hashtag" rel="tag">#<span>webservices</span></a> and in <a href="https://fosstodon.org/tags/PathVisio" class="mention hashtag" rel="tag">#<span>PathVisio</span></a>, <a href="https://fosstodon.org/tags/Cytoscape" class="mention hashtag" rel="tag">#<span>Cytoscape</span></a>. Supported by <a href="https://fosstodon.org/tags/AWSOpen" class="mention hashtag" rel="tag">#<span>AWSOpen</span></a>. <a href="https://wikipathways.org/index.php/Download_Pathways" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">wikipathways.org/index.php/Dow</span><span class="invisible">nload_Pathways</span></a><br /><a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="tag">#<span>bioinformatics</span></a> <a href="https://fosstodon.org/tags/openscience" class="mention hashtag" rel="tag">#<span>openscience</span></a> <a href="https://fosstodon.org/tags/opensource" class="mention hashtag" rel="tag">#<span>opensource</span></a> <a href="https://fosstodon.org/tags/nomoa" class="mention hashtag" rel="tag">#<span>nomoa</span></a></p>