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Organisms <span class="text-primary"> <svg viewBox="0 0 40 40" width="1.2em" height="1.2em" class="inline-block -mt-1 ml-1 h-4 w-4"><path fill="currentColor" d="M4.659 11.833h30.682L20 32.167z"></path></svg></span> </label> <ul tabindex="0" class="dropdown-content z-20 menu p-1 shadow bg-base-100 rounded-btn absolute top-full -left-4"> <li> <a href="/cchf" class="text-primary-1500"> Crimean-Congo Hemorrhagic Fever Virus </a> </li><li> <a href="/ebola-sudan" class="text-primary-1500"> Ebola Sudan </a> </li><li> <a href="/ebola-zaire" class="text-primary-1500"> Ebola Zaire </a> </li><li> <a href="/mpox" class="text-primary-1500"> Mpox Virus </a> </li><li> <a href="/west-nile" class="text-primary-1500"> West Nile Virus </a> </li> </ul> </div> </div> </div> <div class="flex justify-end relative"> <div class="subtitle hidden md:flex md:z-6 gap-4"> <a href="/organism-selector/search">Browse</a><a href="/organism-selector/submission">Submit</a><a href="/seqsets">SeqSets</a><a 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burger3--closed"></div></div><style> .hamburger { width: 2rem; height: 2rem; display: flex; justify-content: space-around; flex-flow: column nowrap; z-index: 1001; } .burger { width: 2rem; height: 0.25rem; border-radius: 10px; transform-origin: 1px; transition: all 0.3s linear; } .burger1--open { transform: rotate(45deg); } .burger1--closed { transform: rotate(0); } .burger2--open { opacity: 0; } .burger2--closed { opacity: 1; } .burger3--open { transform: rotate(-45deg); } .burger3--closed { transform: rotate(0); } </style></div></button><div class="font-bold p-5 flex flex-col justify-between min-h-screen max-h-screen overflow-y-auto"><div><div class="h-10"><a href="/">Loculus</a></div><div class="flex-grow divide-y-2 divide-gray-300 divide-solid border-t-2 border-b-2 border-gray-300 border-solid "><div><div class="flex items-center"><div class="ml-4 py-3"><a href="/organism-selector/search"> Browse</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-3"><a href="/organism-selector/submission"> Submit</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-3"><a href="/seqsets"> SeqSets</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-3"><a href="/news"> News</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-3"><a href="/about"> About</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-3"><a href="/docs/"> Docs</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-3"><a href="https://authentication.pathoplexus.org/realms/loculus/protocol/openid-connect/auth?client_id=backend-client&scope=openid&response_type=code&redirect_uri=https%3A%2F%2Fpathoplexus.org%2F"> Login</a></div></div></div></div></div><div class="mt-auto mb-10"><div class="flex justify-end items-center py-5"><a href="https://github.com/pathoplexus/pathoplexus"><img src="/github-mark.svg" class="w-8" alt="GitHub logo"/></a></div><div class="font-light divide-y-2 divide-gray-300 divide-solid border-t-2 border-b-2 border-gray-300 border-solid "><div><div class="flex items-center"><div class="ml-4 py-1"><a href="/api-documentation"> API docs</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-1"><a href="/about/governance"> Governance</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-1"><a href="/contact"> Contact</a></div></div></div><div><div class="flex items-center"><div class="ml-4 py-1"><a href="https://status.pathoplexus.org/"> Status</a></div></div></div></div></div></div></div></div></astro-island> </div> </div> </nav> <hr class="border-t border-gray-1000"> </header> <div class="flex-grow mt-3 mb-5 px-4"> <div class="max-w-6xl mx-auto"> <h2 class="text-lg font-semibold text-main my-3 mt-6">Welcome to Pathoplexus!</h2> <p class="my-4"> Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response. </p> <div class="flex justify-center"> <div class="flex flex-wrap justify-center gap-x-4 gap-y-4 max-w-4xl"> <a href="/cchf" class="block rounded border box-border border-gray-300 m-2 w-56 hover:bg-gray-100 mx-auto sm:mx-0"> <img src="/images/organisms/cchf_small.jpg" class="h-40 w-full object-cover rounded-t-[3px]" alt="Crimean-Congo Hemorrhagic Fever Virus"> <div class="my-4 mx-4 h-28 flex flex-col justify-between"> <h3 class="font-semibold mb-2">Crimean-Congo Hemorrhagic Fever Virus</h3> <p class="text-sm leading-7"> <span class="font-bold"> 2,762 </span> sequences <br> <span class="text-slate-400 text-sm"> <span class="text-slate-500"> +25 </span> in last 30 days </span> <span class="hidden">Last updated 4 days ago</span> </p> </div> </a><a href="/ebola-sudan" class="block rounded border box-border border-gray-300 m-2 w-56 hover:bg-gray-100 mx-auto sm:mx-0"> <img src="/images/organisms/ebolasudan_small.jpg" class="h-40 w-full object-cover rounded-t-[3px]" alt="Ebola Sudan"> <div class="my-4 mx-4 h-28 flex flex-col justify-between"> <h3 class="font-semibold mb-2">Ebola Sudan</h3> <p class="text-sm leading-7"> <span class="font-bold"> 166 </span> sequences <br> <span class="text-slate-400 text-sm"> <span class="text-slate-500"> +0 </span> in last 30 days </span> <span class="hidden">Last updated 14 days ago</span> </p> </div> </a><a href="/ebola-zaire" class="block rounded border box-border border-gray-300 m-2 w-56 hover:bg-gray-100 mx-auto sm:mx-0"> <img src="/images/organisms/ebolazaire_small.jpg" class="h-40 w-full object-cover rounded-t-[3px]" alt="Ebola Zaire"> <div class="my-4 mx-4 h-28 flex flex-col justify-between"> <h3 class="font-semibold mb-2">Ebola Zaire</h3> <p class="text-sm leading-7"> <span class="font-bold"> 3,698 </span> sequences <br> <span class="text-slate-400 text-sm"> <span class="text-slate-500"> +9 </span> in last 30 days </span> <span class="hidden">Last updated 1 day ago</span> </p> </div> </a><a href="/mpox" class="block rounded border box-border border-gray-300 m-2 w-56 hover:bg-gray-100 mx-auto sm:mx-0"> <img src="/images/organisms/mpox_small.jpg" class="h-40 w-full object-cover rounded-t-[3px]" alt="Mpox Virus"> <div class="my-4 mx-4 h-28 flex flex-col justify-between"> <h3 class="font-semibold mb-2">Mpox Virus</h3> <p class="text-sm leading-7"> <span class="font-bold"> 10,240 </span> sequences <br> <span class="text-slate-400 text-sm"> <span class="text-slate-500"> +266 </span> in last 30 days </span> <span class="hidden">Last updated 5 days ago</span> </p> </div> </a><a href="/west-nile" class="block rounded border box-border border-gray-300 m-2 w-56 hover:bg-gray-100 mx-auto sm:mx-0"> <img src="/images/organisms/wnv_small.jpg" class="h-40 w-full object-cover rounded-t-[3px]" alt="West Nile Virus"> <div class="my-4 mx-4 h-28 flex flex-col justify-between"> <h3 class="font-semibold mb-2">West Nile Virus</h3> <p class="text-sm leading-7"> <span class="font-bold"> 7,831 </span> sequences <br> <span class="text-slate-400 text-sm"> <span class="text-slate-500"> +3 </span> in last 30 days </span> <span class="hidden">Last updated 1 day ago</span> </p> </div> </a> </div> </div> <div class="mdContainer"> <div class="faqWrapper"><h3 id="what-makes-pathoplexus-different">What makes Pathoplexus different?</h3><p>Pathoplexus offers flexible data-sharing options: users can choose to share their data openly, or with time-limited protections to help ensure proper attribution and credit. Pathoplexus integrates smoothly with existing INSDC-member databases (NCBI, ENA, and DDBJ), enabling data that’s ‘open’ on Pathoplexus to also appear on INSDC, and INSDC data to be accessed through Pathoplexus. Pathoplexus is built on the latest tools for filtering, searching, and accessing data, making data sharing and analysis more accessible (through both the website and API) and fostering a connected, collaborative global research community.</p><h3 id="can-i-use-the-data-on-pathoplexus">Can I use the data on Pathoplexus?</h3><p>Yes! Pathoplexus is designed to be used by everyone, and so all data is accessible. However, Pathoplexus does have restrictions on how some data (“Restricted-Use Data”) can be used, particularly in publications and preprints, and has requirements on how all Restricted-Use Data is acknowledged. You can find out more about these protections and how you can use data by reading our <a href="/about/terms-of-use/data-use-terms">Data Use Terms</a>. We also have summaries on you can use <a href="/about/terms-of-use/open-data">Open Data</a> and <a href="/about/terms-of-use/restricted-data">Restricted-Use Data</a>.</p><h3 id="how-can-i-contribute-data-to-pathoplexus">How can I contribute data to Pathoplexus?</h3><p>We’ve tried to make sharing your data as easy and flexible as possible!</p><p>You can upload data to any of our supported pathogens by first <a href="/docs/how-to/create-account">creating an account</a> and then <a href="/docs/how-to/upload-sequences">submitting your sequences</a> on the website or via the API (useful for computational pipelines). At submission, you can choose whether you’d like your data to be <a href="/about/terms-of-use/restricted-data">protected for up to one year</a>, or <a href="/about/terms-of-use/open-data">open immediately</a>. Once the data is open, it also appears on INSDC-member databases.</p><h3 id="how-can-i-try-pathoplexus-out">How can I try Pathoplexus out?</h3><p>If you don’t have sequences to upload for the pathogens we currently support - or just want to try out Pathoplexus before deciding if you want to use it - you can always use our <a href="https://demo.pathoplexus.org/">Demo Instance</a>! Our Demo Instance works just like the ‘real’ Pathoplexus, but is wiped regularly and <em>no data is sent onward to INSDC</em>.</p><p>It’s perfect for trying out Pathoplexus or testing your API requests. Do note that since it is wiped regularly, you will have to make a new account and group - but it’s ok if these aren’t as detailed as your ‘real’ accounts. Remember that the Demo Instance is public, so don’t upload data that you can’t or don’t want to share. If you’d like to try out Pathoplexus but don’t have any data to hand, you can use our <a href="https://pathoplexus.github.io/example_data/">example data</a> for the pathogens we support!</p><p><em>(See our <a href="/docs">Docs</a> for more information on how to do things like create an account, upload sequences, and more in Pathoplexus!)</em></p><h3 id="who-is-behind-pathoplexus">Who is behind Pathoplexus?</h3><p>Pathoplexus is a transparent, non-profit association with <a href="/about/members">members</a> from 10 countries in 5 continents, and an <a href="/about/eb">Executive Board</a> from around the globe. Pathoplexus’ members and Executive Board are committed to running Pathoplexus according to our <a href="/about/governance/values">Values</a>. Pathoplexus is proud to work closely with <a href="https://pha4ge.org/">PHA4GE</a>, an international group working to establish better standards for public health and bioinformatics. PHA4GE was also key in helping to develop Pathoplexus from the ground up.</p><p>At the moment, Pathoplexus is run almost entirely on donations and volunteer efforts, thus is independent of influence by larger players, and is truly a community-driven project. See our <a href="/about">About</a> page for more information about Pathoplexus, and our <a href="/about/eb">Executive Board</a>, <a href="/about/sab">Scientific Advisory Board</a>, <a href="about/members">Members page</a> and <a href="/about/development-team">Development Team</a> pages for more information about some of the people involved.</p><h3 id="where-can-i-read-more">Where can I read more?</h3><div class="indent"><ul> <li>You can read more about the purpose of Pathoplexus and our pledges to the community in our <a href="/about/governance/values">Pathoplexus Values</a>.</li> <li>You can read about the legal structure of Pathoplexus and how it runs in our <a href="/about/governance/pathoplexus-statutes">Statutes</a></li> <li>To find out more about how data in Pathoplexus can be used and must be credited, see our <a href="/about/terms-of-use/data-use-terms">Data Use Terms</a>.</li> <li>You can see our <a href="/about/eb">Executive Board</a>, <a href="about/members">Members</a>, and <a href="/about/sab">Scientific Advisory Board</a></li> <li>To find out more about our Governance, see our <a href="/about/governance">list of Governance documents</a>.</li> <li>To read more about how to use Pathoplexus, check out our <a href="/docs/how-to">‘How-To’ documents</a>.</li> <li>To become part of the scientific community that helps drive Pathoplexus, you can join <a href="https://pha4ge.org/">PHA4GE</a> and be part of the Data Repositories Working Group</li> </ul></div><p><a href="/about/faq"><em>See more of our Frequently Asked Questions here!</em></a></p></div> </div> </div> </div> <hr class="border-t border-gray-1000"> <footer class="hidden sm:flex sm:z-6 sm:z-6 flex justify-between items-center h-20"> <div class="flex gap-5"> <a href="/api-documentation" class="text-gray-600"> API docs </a><a href="/about/governance" class="text-gray-600"> Governance </a><a href="/contact" class="text-gray-600"> Contact </a><a href="https://status.pathoplexus.org/" class="text-gray-600"> Status </a> </div> <a href="https://github.com/pathoplexus/pathoplexus" class="h-full py-6"> <img src="/github-mark.svg" class="h-full object-scale-down" alt="github-icon"> </a> </footer> </div> </body></html>