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<!doctype html><html><head><title>scverse × BioContextAI: Community Infrastructure for Agentic Analysis</title><link rel=stylesheet type=text/css href=/bootstrap/css/bootstrap.min.css><link rel=stylesheet type=text/css href=/bootstrap/icons/bootstrap-icons.css><link rel=stylesheet type=text/css href=/main.min.css><link rel=apple-touch-icon sizes=180x180 href=/img/favicon/apple-touch-icon.png><link rel=icon type=image/png sizes=32x32 href=/img/favicon/favicon-32x32.png><link rel=icon type=image/png sizes=16x16 href=/img/favicon/favicon-16x16.png><link rel=manifest href=/img/favicon/site.webmanifest><link rel=mask-icon href=/img/favicon/safari-pinned-tab.svg color=#000000><link rel="shortcut icon" href=/img/favicon/favicon.ico><meta name=msapplication-TileColor content="#00aba9"><meta name=msapplication-config content="/img/favicon/browserconfig.xml"><meta name=theme-color content="#ffffff"><meta charset=utf-8><meta content="utf-8" http-equiv=encoding><meta name=twitter:card content="summary"><meta name=twitter:title content="scverse × BioContextAI: Community Infrastructure for Agentic Analysis"><meta name=twitter:description content="scverse partners with BioContextAI to build biomedical MCPs."><meta property="og:url" content="https://scverse.org/blog/2025-11-biocontextai/"><meta property="og:site_name" content="scverse"><meta property="og:title" content="scverse × BioContextAI: Community Infrastructure for Agentic Analysis"><meta property="og:description" content="scverse partners with BioContextAI to build biomedical MCPs."><meta property="og:locale" content="en_us"><meta property="og:type" content="article"><meta property="article:section" content="blog"><meta property="article:published_time" content="2025-11-08T00:00:05+01:00"><meta property="article:modified_time" content="2025-11-08T00:00:05+01:00"><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><script src=/main.js async></script><script src=/bootstrap/js/bootstrap.bundle.min.js async></script><script data-goatcounter=https://scverse.goatcounter.com/count async src=//gc.zgo.at/count.js></script></head><body><header><div class=container style=max-width:850px><nav class="navbar navbar-expand-lg navbar-light"><div class=container-fluid><a class="navbar-brand row align-items-center m-0" href=/><div id=scverse-logo class=col></div><span class=visually-hidden>scverse</span>
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</a><button class=navbar-toggler type=button data-bs-toggle=collapse data-bs-target=#navbarSupportedContent aria-controls=navbarSupportedContent aria-expanded=false aria-label="Toggle navigation">
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<span class=navbar-toggler-icon></span></button><div class="collapse navbar-collapse justify-content-end" id=navbarSupportedContent><ul class="navbar-nav mb-2 mb-lg-0 nav-buttons"><li class="nav-item dropdown"><a class="nav-link dropdown-toggle" href=/packages id=packages-dropdown role=button aria-expanded=false>Packages</a><ul class=dropdown-menu aria-labelledby=packages-dropdown><li><a class=dropdown-item href=/packages#core-packages>Core</a></li><li><a class=dropdown-item href=/packages/#ecosystem>Ecosystem</a></li></ul></li><li class=nav-item><a class=nav-link href=/learn>Learn</a></li><li class=nav-item><a class=nav-link href=/people>People</a></li><li class=nav-item><a class="nav-link
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active" href=/blog>Blog</a></li><li class=nav-item><a class=nav-link href=/events>Events</a></li><li class="nav-item dropdown"><a class="nav-link dropdown-toggle" href=/about id=about-dropdown role=button aria-expanded=false>About</a><ul class=dropdown-menu aria-labelledby=about-dropdown><li><a class=dropdown-item href=/about>About scverse</a></li><li><a class=dropdown-item href=/about/mission>Mission statement</a></li><li><a class=dropdown-item href=/about/roles>Roles</a></li><li><a class=dropdown-item href=/about/code_of_conduct>Code of Conduct</a></li><li><a class=dropdown-item href=/join>Contact</a></li></ul></li><li class=nav-item><a id=join-button class="nav-link nav-button-hl" href=/join>Join</a></li></ul></div></div></nav></div></header><div id=wrapper><div id=content><div id=page-content><article class=post><h1 class=post-title>scverse × BioContextAI: Community Infrastructure for Agentic Analysis</h1><div class=post-subtitle><span class=post-date>November 08, 2025</span><div class=rss-icon><a href=/blog/index.xml><svg viewBox="0 0 20 20"><path d="M5 3a1 1 0 000 2c5.523.0 10 4.477 10 10a1 1 0 102 0C17 8.373 11.627 3 5 3z"/><path d="M4 9a1 1 0 011-1 7 7 0 017 7 1 1 0 11-2 0 5 5 0 00-5-5A1 1 0 014 9zM3 15a2 2 0 114 0 2 2 0 01-4 0z"/></svg></a></div></div><span class=post-author>Malte Kuehl, Lukas Heumos</span><div class=post-content><h1 id=scverse--biocontextai-community-infrastructure-for-agentic-analysis>scverse × BioContextAI: Community Infrastructure for Agentic Analysis</h1><p>We&rsquo;re excited to announce that we are partnering with <a href=https://biocontext.ai/>BioContextAI</a>, a new open-source initiative for building agentic systems in biomedical research.
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BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
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These are standardized tools that allow AI systems to access specialized databases and software.
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This project was recently published as a <a href=https://www.nature.com/articles/s41587-025-02900-9>Nature Biotechnology correspondence</a> and we are actively starting to explore and contribute scverse MCP servers.</p><img src=/img/blog/biocontextai_overview.png style=max-width:100% alt="BioContextAI overview"><h2 id=what-were-building>What we&rsquo;re building</h2><p>BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
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There&rsquo;s a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
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By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
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This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.</p><h2 id=how-to-get-involved>How to get involved</h2><p>Check out the Registry at <a href=https://biocontext.ai/>biocontext.ai</a> to explore community-built MCP servers.
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If you&rsquo;re interested in building new servers, try the <a href=https://github.com/biocontext-ai/mcp-server-cookiecutter/>cookiecutter template</a> to get started.
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Join the conversation on the <a href=https://scverse.zulipchat.com/#narrow/channel/518508-biocontext-ai>BioContextAI channel</a> within the scverse Zulip to connect with other developers and researchers working in this space.
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We&rsquo;re excited to see what the community builds together.</p><h2 id=learn-more>Learn more</h2><p>Learn more about BioContextAI in the <a href=https://www.nature.com/articles/s41587-025-02900-9>Nature Biotechnology correspondence</a> and on the <a href=https://biocontext.ai/>BioContextAI website</a>.</p><p><em>— The scverse core & BioContextAI teams</em></p></div></article></div></div></div><footer><div id=footer-content class=container><div class=row><div class="col-12 col-md-6 col-lg-3"><h5>Pages</h5><ul class=list-unstyled><li><a href=/packages>Packages</a></li><li><a href=/learn>Learn</a></li><li><a href=/people>People</a></li><li><a href=/blog>Blog</a></li><li><a href=/events>Events</a></li><li><a href=/about>About</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><h5>Governance</h5><ul class=list-unstyled><li><a href=/about/mission/>Mission statement</a></li><li><a href=/about/code_of_conduct>Code of conduct</a></li><li><a href=/about/roles>Roles</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><h5>Join scverse</h5><ul class=list-unstyled><li><a href=https://github.com/scverse target=_blank>GitHub</a></li><li><a href=https://discourse.scverse.org/ target=_blank>Discourse</a></li><li><a href=https://scverse.zulipchat.com/ target=_blank>Zulip</a></li><li><a href=https://x.com/scverse_team target=_blank>X (Twitter)</a></li><li><a href=https://bsky.app/profile/scverse.bsky.social target=_blank>Bluesky</a></li><li><a href=https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA target=_blank>YouTube</a></li></ul></div></div><div class=signature><p>scverse® core team, 2025</p></div></div></footer></body></html>

blog/index.html

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<!doctype html><html><head><title>Blogs</title><link rel=stylesheet type=text/css href=/bootstrap/css/bootstrap.min.css><link rel=stylesheet type=text/css href=/bootstrap/icons/bootstrap-icons.css><link rel=stylesheet type=text/css href=/main.min.css><link rel=apple-touch-icon sizes=180x180 href=/img/favicon/apple-touch-icon.png><link rel=icon type=image/png sizes=32x32 href=/img/favicon/favicon-32x32.png><link rel=icon type=image/png sizes=16x16 href=/img/favicon/favicon-16x16.png><link rel=manifest href=/img/favicon/site.webmanifest><link rel=mask-icon href=/img/favicon/safari-pinned-tab.svg color=#000000><link rel="shortcut icon" href=/img/favicon/favicon.ico><meta name=msapplication-TileColor content="#00aba9"><meta name=msapplication-config content="/img/favicon/browserconfig.xml"><meta name=theme-color content="#ffffff"><meta charset=utf-8><meta content="utf-8" http-equiv=encoding><meta name=twitter:card content="summary"><meta name=twitter:title content="Blogs"><meta property="og:url" content="https://scverse.org/blog/"><meta property="og:site_name" content="scverse"><meta property="og:title" content="Blogs"><meta property="og:locale" content="en_us"><meta property="og:type" content="website"><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><script src=/main.js async></script><script src=/bootstrap/js/bootstrap.bundle.min.js async></script><script data-goatcounter=https://scverse.goatcounter.com/count async src=//gc.zgo.at/count.js></script><link rel=alternate type=application/rss+xml href=https://scverse.org/blog/index.xml title=scverse descr=rol></head><body><header><div class=container style=max-width:850px><nav class="navbar navbar-expand-lg navbar-light"><div class=container-fluid><a class="navbar-brand row align-items-center m-0" href=/><div id=scverse-logo class=col></div><span class=visually-hidden>scverse</span>
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<span class=navbar-toggler-icon></span></button><div class="collapse navbar-collapse justify-content-end" id=navbarSupportedContent><ul class="navbar-nav mb-2 mb-lg-0 nav-buttons"><li class="nav-item dropdown"><a class="nav-link dropdown-toggle" href=/packages id=packages-dropdown role=button aria-expanded=false>Packages</a><ul class=dropdown-menu aria-labelledby=packages-dropdown><li><a class=dropdown-item href=/packages#core-packages>Core</a></li><li><a class=dropdown-item href=/packages/#ecosystem>Ecosystem</a></li></ul></li><li class=nav-item><a class=nav-link href=/learn>Learn</a></li><li class=nav-item><a class=nav-link href=/people>People</a></li><li class=nav-item><a class="nav-link
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active" href=/blog>Blog</a></li><li class=nav-item><a class=nav-link href=/events>Events</a></li><li class="nav-item dropdown"><a class="nav-link dropdown-toggle" href=/about id=about-dropdown role=button aria-expanded=false>About</a><ul class=dropdown-menu aria-labelledby=about-dropdown><li><a class=dropdown-item href=/about>About scverse</a></li><li><a class=dropdown-item href=/about/mission>Mission statement</a></li><li><a class=dropdown-item href=/about/roles>Roles</a></li><li><a class=dropdown-item href=/about/code_of_conduct>Code of Conduct</a></li><li><a class=dropdown-item href=/join>Contact</a></li></ul></li><li class=nav-item><a id=join-button class="nav-link nav-button-hl" href=/join>Join</a></li></ul></div></div></nav></div></header><div id=wrapper><div id=content><div id=page-content class=items-list><h1>Blog</h1><a href=/blog/2025-anndata-012/><article class=page-item><div class=page-item-date><span>July 29, 2025</span></div><div class=page-item-content><h2>Improved i/o in anndata 0.12</h2><span>With zarr v3 support and xarray integration, anndata takes a big step forward when it comes to i/o tasks.</span></div></article></a><a href=/blog/2025-07-biomni/><article class=page-item><div class=page-item-date><span>July 28, 2025</span></div><div class=page-item-content><h2>scverse × Biomni: Agentic Single-Cell Analysis</h2><span>Biomni, the general-purpose biomedical AI agent now supports scverse tooling.</span></div></article></a><a href=/blog/2025-core-expansion/><article class=page-item><div class=page-item-date><span>July 01, 2025</span></div><div class=page-item-content><h2>Four new scverse core packages</h2><span>scverse expands with new core packages.</span></div></article></a><a href=/blog/2024-conference-summary/><article class=page-item><div class=page-item-date><span>November 14, 2024</span></div><div class=page-item-content><h2>Highlights from the inaugural scverse conference</h2><span>A recap from the very first scverse conference</span></div></article></a><a href=/blog/hello-world/><article class=page-item><div class=page-item-date><span>May 17, 2022</span></div><div class=page-item-content><h2>Hello world</h2><span>Introducing scverse</span></div></article></a></div></div></div><footer><div id=footer-content class=container><div class=row><div class="col-12 col-md-6 col-lg-3"><h5>Pages</h5><ul class=list-unstyled><li><a href=/packages>Packages</a></li><li><a href=/learn>Learn</a></li><li><a href=/people>People</a></li><li><a href=/blog>Blog</a></li><li><a href=/events>Events</a></li><li><a href=/about>About</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><h5>Governance</h5><ul class=list-unstyled><li><a href=/about/mission/>Mission statement</a></li><li><a href=/about/code_of_conduct>Code of conduct</a></li><li><a href=/about/roles>Roles</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><h5>Join scverse</h5><ul class=list-unstyled><li><a href=https://github.com/scverse target=_blank>GitHub</a></li><li><a href=https://discourse.scverse.org/ target=_blank>Discourse</a></li><li><a href=https://scverse.zulipchat.com/ target=_blank>Zulip</a></li><li><a href=https://x.com/scverse_team target=_blank>X (Twitter)</a></li><li><a href=https://bsky.app/profile/scverse.bsky.social target=_blank>Bluesky</a></li><li><a href=https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA target=_blank>YouTube</a></li></ul></div></div><div class=signature><p>scverse® core team, 2025</p></div></div></footer></body></html>
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active" href=/blog>Blog</a></li><li class=nav-item><a class=nav-link href=/events>Events</a></li><li class="nav-item dropdown"><a class="nav-link dropdown-toggle" href=/about id=about-dropdown role=button aria-expanded=false>About</a><ul class=dropdown-menu aria-labelledby=about-dropdown><li><a class=dropdown-item href=/about>About scverse</a></li><li><a class=dropdown-item href=/about/mission>Mission statement</a></li><li><a class=dropdown-item href=/about/roles>Roles</a></li><li><a class=dropdown-item href=/about/code_of_conduct>Code of Conduct</a></li><li><a class=dropdown-item href=/join>Contact</a></li></ul></li><li class=nav-item><a id=join-button class="nav-link nav-button-hl" href=/join>Join</a></li></ul></div></div></nav></div></header><div id=wrapper><div id=content><div id=page-content class=items-list><h1>Blog</h1><a href=/blog/2025-11-biocontextai/><article class=page-item><div class=page-item-date><span>November 08, 2025</span></div><div class=page-item-content><h2>scverse × BioContextAI: Community Infrastructure for Agentic Analysis</h2><span>scverse partners with BioContextAI to build biomedical MCPs.</span></div></article></a><a href=/blog/2025-anndata-012/><article class=page-item><div class=page-item-date><span>July 29, 2025</span></div><div class=page-item-content><h2>Improved i/o in anndata 0.12</h2><span>With zarr v3 support and xarray integration, anndata takes a big step forward when it comes to i/o tasks.</span></div></article></a><a href=/blog/2025-07-biomni/><article class=page-item><div class=page-item-date><span>July 28, 2025</span></div><div class=page-item-content><h2>scverse × Biomni: Agentic Single-Cell Analysis</h2><span>Biomni, the general-purpose biomedical AI agent now supports scverse tooling.</span></div></article></a><a href=/blog/2025-core-expansion/><article class=page-item><div class=page-item-date><span>July 01, 2025</span></div><div class=page-item-content><h2>Four new scverse core packages</h2><span>scverse expands with new core packages.</span></div></article></a><a href=/blog/2024-conference-summary/><article class=page-item><div class=page-item-date><span>November 14, 2024</span></div><div class=page-item-content><h2>Highlights from the inaugural scverse conference</h2><span>A recap from the very first scverse conference</span></div></article></a><a href=/blog/hello-world/><article class=page-item><div class=page-item-date><span>May 17, 2022</span></div><div class=page-item-content><h2>Hello world</h2><span>Introducing scverse</span></div></article></a></div></div></div><footer><div id=footer-content class=container><div class=row><div class="col-12 col-md-6 col-lg-3"><h5>Pages</h5><ul class=list-unstyled><li><a href=/packages>Packages</a></li><li><a href=/learn>Learn</a></li><li><a href=/people>People</a></li><li><a href=/blog>Blog</a></li><li><a href=/events>Events</a></li><li><a href=/about>About</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><h5>Governance</h5><ul class=list-unstyled><li><a href=/about/mission/>Mission statement</a></li><li><a href=/about/code_of_conduct>Code of conduct</a></li><li><a href=/about/roles>Roles</a></li></ul></div><div class="col-12 col-md-6 col-lg-3"><h5>Join scverse</h5><ul class=list-unstyled><li><a href=https://github.com/scverse target=_blank>GitHub</a></li><li><a href=https://discourse.scverse.org/ target=_blank>Discourse</a></li><li><a href=https://scverse.zulipchat.com/ target=_blank>Zulip</a></li><li><a href=https://x.com/scverse_team target=_blank>X (Twitter)</a></li><li><a href=https://bsky.app/profile/scverse.bsky.social target=_blank>Bluesky</a></li><li><a href=https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA target=_blank>YouTube</a></li></ul></div></div><div class=signature><p>scverse® core team, 2025</p></div></div></footer></body></html>

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