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Introducing Pathoplexus - Software - Virological
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By combining modern open-source software with transparent governance structures, Pathoplexus fills a niche within the existing genomic sequencing database landscape, aiming to meet requests from both data submitters and users and striving to improve equity. Today we launch with four virus species, Ebolavirus sudan, Ebolavirus zaire, West Nile virus and Crimean-Congo haemorrhagic fever virus. P..." /> <meta name="twitter:description" content="We are announcing Pathoplexus, a specialised genomic database for viruses of public health importance. By combining modern open-source software with transparent governance structures, Pathoplexus fills a niche within the existing genomic sequencing database landscape, aiming to meet requests from both data submitters and users and striving to improve equity. Today we launch with four virus species, Ebolavirus sudan, Ebolavirus zaire, West Nile virus and Crimean-Congo haemorrhagic fever virus. P..." /> <meta property="og:article:section" content="Software" /> <meta property="og:article:section:color" content="BF1E2E" /> <meta name="twitter:label1" value="Reading time" /> <meta name="twitter:data1" value="1 mins 🕑" /> <meta name="twitter:label2" value="Likes" /> <meta name="twitter:data2" value="3 ❤" /> <meta property="article:published_time" content="2024-08-27T15:31:14+00:00" /> <meta property="og:ignore_canonical" content="true" /> </head> <body class="crawler browser-update"> <header> <a href="/"> Virological </a> </header> <div id="main-outlet" class="wrap" role="main"> <div id="topic-title"> <h1> <a href="/t/introducing-pathoplexus/977">Introducing Pathoplexus</a> </h1> <div class="topic-category" itemscope itemtype="http://schema.org/BreadcrumbList"> <span itemprop="itemListElement" itemscope itemtype="http://schema.org/ListItem"> <a href="/c/software/26" class="badge-wrapper bullet" itemprop="item"> <span class='badge-category-bg' style='background-color: #BF1E2E'></span> <span class='badge-category clear-badge'> <span class='category-name' itemprop='name'>Software</span> </span> </a> <meta itemprop="position" content="1" /> </span> </div> </div> <div itemscope itemtype='http://schema.org/DiscussionForumPosting'> <meta itemprop='headline' content='Introducing Pathoplexus'> <link itemprop='url' href='https://virological.org/t/introducing-pathoplexus/977'> <meta itemprop='datePublished' content='2024-08-27T15:31:14Z'> <meta itemprop='articleSection' content='Software'> <meta itemprop='keywords' content=''> <div itemprop='publisher' itemscope itemtype="http://schema.org/Organization"> <meta itemprop='name' content='Virological'> <div itemprop='logo' itemscope itemtype="http://schema.org/ImageObject"> <meta itemprop='url' content='https://virological.org/uploads/default/original/1X/7897c4e655617c4b6fe71a98eaa97a38778f0623.png'> </div> </div> <div id='post_1' class='topic-body crawler-post'> <div class='crawler-post-meta'> <span class="creator" itemprop="author" itemscope itemtype="http://schema.org/Person"> <a itemprop="url" href='https://virological.org/u/emmahodcroft'><span itemprop='name'>emmahodcroft</span></a> </span> <link itemprop="mainEntityOfPage" href="https://virological.org/t/introducing-pathoplexus/977"> <span class="crawler-post-infos"> <time datetime='2024-08-27T15:31:14Z' class='post-time'> August 27, 2024, 3:31pm </time> <meta itemprop='dateModified' content='2024-08-30T07:28:30Z'> <span itemprop='position'>1</span> </span> </div> <div class='post' itemprop='text'> <p>We are announcing Pathoplexus, a specialised genomic database for viruses of public health importance. By combining modern open-source software with transparent governance structures, Pathoplexus fills a niche within the existing genomic sequencing database landscape, aiming to meet requests from both data submitters and users and striving to improve equity. Today we launch with four virus species, Ebolavirus sudan, Ebolavirus zaire, West Nile virus and Crimean-Congo haemorrhagic fever virus.</p> <p>Pathoplexus aims to offer the best features of existing platforms, and to supplement these with new approaches that optimise data utility and preserve data autonomy. In particular, data submitters can easily <a href="https://pathoplexus.org/news/2024-08-27-hello-world#ease-of-submission" rel="noopener nofollow ugc">share</a> their data via Pathoplexus and receive credit through <a href="https://pathoplexus.org/news/2024-08-27-hello-world#new-tools-for-recognising-contributions" rel="noopener nofollow ugc">citable Pathoplexus datasets</a>. Submitters can choose to have their data immediately deposited in the International Nucleotide Sequence Database Collaboration (INSDC) databases, without additional effort. Alternatively, submitters can choose to submit <a href="https://pathoplexus.org/news/2024-08-27-hello-world#as-open-as-possible-as-closed-as-necessary" rel="noopener nofollow ugc">data with a time-limited restriction</a>, during which use in publications is not permitted without involvement of the submitters. Only after this restriction ends is the data released to the INSDC. However, all users can freely access, explore, and download all data hosted in Pathoplexus. <a href="https://pathoplexus.org/news/2024-08-27-hello-world#pathogen-tailored-tools-for-search-and-retrieval" rel="noopener nofollow ugc">Data querying</a> can be done both in an interactive and programmable fashion, the latter enabling the embedding of Pathoplexus into other tools.</p> <p>Pathoplexus is powered by a new <a href="https://pathoplexus.org/news/2024-08-27-hello-world#open-source-and-community-focused" rel="noopener nofollow ugc">open-source software</a> package, Loculus. Loculus is a general purpose tool for running virus sequence databases: anyone can use it to launch their own database for their pathogens of interest. These might include internal laboratory databases, or databases for collaborations or consortia.</p> <p>Pathoplexus is a <a href="https://pathoplexus.org/news/2024-08-27-hello-world#transparency-and-governance" rel="noopener nofollow ugc">transparent</a>, non-profit association with members from 10 countries in 5 continents. The <a href="https://pathoplexus.org/about/eb" rel="noopener nofollow ugc">Executive Board</a> of Pathoplexus consists of five members from North and South America, Africa, Asia, and Europe. We are really excited to engage with the community - please check out our <a href="https://pathoplexus.org" rel="noopener nofollow ugc">website</a>, connect with us on <a href="https://mstdn.science/@pathoplexus" rel="noopener nofollow ugc">Mastodon</a>, <a href="https://bsky.app/profile/pathoplexus.org" rel="noopener nofollow ugc">Bluesky</a>, or <a href="https://x.com/pathoplexus" rel="noopener nofollow ugc">Twitter</a> or join our open-source community on <a href="https://github.com/pathoplexus/pathoplexus" rel="noopener nofollow ugc">GitHub</a>.</p> <p>To read more please check out our announcement at:</p><aside class="onebox allowlistedgeneric" data-onebox-src="https://pathoplexus.org/news/2024-08-27-hello-world"> <header class="source"> <img src="https://pathoplexus.org/favicon.svg" class="site-icon" width="77" height="74"> <a href="https://pathoplexus.org/news/2024-08-27-hello-world" target="_blank" rel="noopener nofollow ugc">pathoplexus.org</a> </header> <article class="onebox-body"> <div class="aspect-image" style="--aspect-ratio:690/355;"><img src="https://pathoplexus.org/images/pathoplexus-preview.png" class="thumbnail" width="690" height="355"></div> <h3><a href="https://pathoplexus.org/news/2024-08-27-hello-world" target="_blank" rel="noopener nofollow ugc">Pathoplexus | Introducing Pathoplexus</a></h3> <p>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> </article> <div class="onebox-metadata"> </div> <div style="clear: both"></div> </aside> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/LikeAction"/> <meta itemprop="userInteractionCount" content="3" /> <span class='post-likes'>3 Likes</span> </div> <div itemprop="interactionStatistic" itemscope itemtype="http://schema.org/InteractionCounter"> <meta itemprop="interactionType" content="http://schema.org/CommentAction"/> <meta itemprop="userInteractionCount" content="0" /> </div> </div> </div> </div> <footer class="container wrap"> <nav class='crawler-nav'> <ul> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/' itemprop="url">Home </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/categories' itemprop="url">Categories </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/guidelines' itemprop="url">FAQ/Guidelines </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/tos' itemprop="url">Terms of Service </a> </span> </li> <li itemscope itemtype='http://schema.org/SiteNavigationElement'> <span itemprop='name'> <a href='/privacy' itemprop="url">Privacy Policy </a> </span> </li> </ul> </nav> <p class='powered-by-link'>Powered by <a href="https://www.discourse.org">Discourse</a>, best viewed with JavaScript enabled</p> </footer> <div class="buorg"><div>Unfortunately, <a href="https://www.discourse.org/faq/#browser">your browser is unsupported</a>. 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