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preview-biocafe-splash-page/assets/css/style-v12.css

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preview-biocafe-splash-page/assets/search/index.json

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preview-biocafe-splash-page/assets/search/metadata.json

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preview-biocafe-splash-page/fellowships/index.html

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<h2 id="featured-fellow">Featured Fellow</h2>
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<div id="wil-cram" class="bg-white team-card justify-content-center mb-3 flex-grow-1">
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<div id="thinh-nguyen" class="bg-white team-card justify-content-center mb-3 flex-grow-1">
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<div class="uw-card-content shadow">
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<img src="/web-preview/preview-biocafe-splash-page/staff-list/images/wil_cram.jpg" alt="Headshot for Wil Cram" />
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<img src="/web-preview/preview-biocafe-splash-page/staff-list/images/thinh_nguyen.jpg" alt="Headshot for Thinh Nguyen" />
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<div>
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<h2 class="uw-mini-bar mb-0 mt-3">
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Wil Cram
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Thinh Nguyen
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</h2>
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<div><h6 class="mt-2">Mentor(s):</h6> Greg Thain</div>
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<div><h6 class="mt-2">Mentor(s):</h6> Justin Hiemstra</div>
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</div>
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</div>
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<div class="col-12">
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<h4 class="mt-3">Schedd performance analysis for human</h4>
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<h4 class="mt-3">ML for failure classification in the OSPool</h4>
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<div class="pt-2">
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<p>The condor_schedd is a single threaded program, and when it is overloaded,
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it is difficult for administrators to understand why. There are some
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statistics about what it is doing, but there is no clear way to present
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this information in a useful way to an administrator. Students working
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on this project would build visualizations of complex data, and work
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with end users and facilitators to tune output for real world human
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consumption.</p>
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<p>The OSPool runs hundreds of thousands of jobs every day on dozens of
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different sites, each unique in their own way. Naturally, there are
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many hundreds of failures, most of which the system works around, but
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with added latency to workflow completion. This project would attempt
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to automatically classify failures from job logs to detect common
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patterns and highlight places for humans to look to fix common failures
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with the most payoff. Students working on this project will gain
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experience applying ML techniques to real world problems.</p>
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</div>
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<div>
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<a class="btn btn-primary" href="./reports/2024/wil-cram">Read Final Report</a>
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<a class="btn btn-primary" href="./reports/2024/thinh-nguyen">Read Final Report</a>
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</div>
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preview-biocafe-splash-page/uw-research-computing/bioinformatics-cafe.html

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<h2 id="connect-and-find-resources-with-the-bioinformatics-community">Connect and find resources with the Bioinformatics community</h2>
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<p>Welcome to the <strong>Bioinformatics Café</strong>—a monthly, hands‑on meetup for life‑science researchers using CHTC. Come for a short tutorial, stay to co‑work on your analyses with Facilitator support, and meet peers solving similar problems. Bring a laptop, a dataset, and your questions.</p>
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<p>Welcome to the <strong>Bioinformatics Café</strong>—a monthly, hands‑on meetup for life‑science researchers using CHTC resources. Come for a short tutorial, stay to co‑work on your analyses with Facilitator support, and meet peers solving similar problems. Bring a laptop, a dataset, and your questions.</p>
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<blockquote>
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<p>Whether you’re brand new to high‑throughput computing or a seasoned CHTC user, the Café is your place to share knowledge, troubleshoot together, and learn approaches that make your research run more efficiently.</p>
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<p>Whether you’re brand new to high‑throughput computing or a seasoned CHTC user, the Café is your place to share knowledge, troubleshoot together, and learn best practices for using computing resources for your research.</p>
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<p>The Café blends quick, practical lessons (read mapping, assembly at scale, microbiome workflows) with time to make real progress on your project. <strong>New to CHTC?</strong> You’ll gain step-by-step guidance, introductions to core tools, and a supportive environment to build your skills. <strong>Experienced?</strong> You’ll find opportunities to refine workflows, exchange advanced tips, and contribute your expertise to strengthen the community.</p>
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<ul>
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<li><strong>New to CHTC?</strong> Learn about research computing with step-by-step guidance, introductions to core tools, and a supportive environment to build your skills.</li>
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<li><strong>Are you an experienced user?</strong> Find opportunities to refine workflows, exchange advanced tips, and contribute your expertise to the community.</li>
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</ul>
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<img src="/web-preview/preview-biocafe-splash-page/uw-research-computing/guide-icons/noun_open%20book_1179297.png" alt="Book icon" style="max-height: 200px" />
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<img src="/web-preview/preview-biocafe-splash-page/uw-research-computing/guide-icons/noun_open%20book_1179297.png" alt="Book icon" style="max-height: 200px; width: auto;" />
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<h2 class="uw-mini-bar">Resources</h2>
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<p>Get oriented and level up fast:</p>
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<ul>
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<li><a href="/uw-research-computing/htc-roadmap">HTC Roadmap: how CHTC works</a></li>
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<li><a href="/uw-research-computing/htc-roadmap">Roadmap to getting started on CHTC</a></li>
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<li><a href="/uw-research-computing/transfer-files-computer">Moving data to/from CHTC</a></li>
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<li><a href="/uw-research-computing/software-overview-htc#quickstart">Containers &amp; reproducible software</a></li>
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<li><a href="/uw-research-computing/tutorials#Bioinformatics">CHTC Bioinformatics Tutorials</a></li>
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<li><a href="https://github.com/CHTC/recipes/tree/main/software">Cafe GitHub Repository</a></li>
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<!--<li><a href="/uw-research-computing/tutorials#Bioinformatics">CHTC Bioinformatics Tutorials</a></li>-->
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<!--<li><a href="https://github.com/CHTC/recipes/tree/main/software">Café GitHub Repository</a></li>-->
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<img src="/web-preview/preview-biocafe-splash-page/uw-research-computing/guide-icons/noun_people_1188645.png" alt="People icon" style="max-height: 200px" />
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<img src="/web-preview/preview-biocafe-splash-page/uw-research-computing/guide-icons/noun_people_1188645.png" alt="People icon" style="max-height: 200px; width: auto;" />
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<h2 class="uw-mini-bar">Community</h2>
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<li><a href="/uw-research-computing/get-help.html#office-hours">CHTC Office Hours</a></li>
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<li><a href="https://go.wisc.edu/schedule-chtc">Request a 1-on-1 consult</a></li>
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<li><a href="https://community.chtc.wisc.edu">Join the Community Discourse</a></li>
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<li><a href="/uw-research-computing/get-help.html#office-hours">CHTC Office Hours</a></li>
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<li><a href="https://go.wisc.edu/schedule-chtc">Schedule a 1-on-1 consultation</a></li>
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<li><a href="/events">Event calendar</a></li>
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<img src="/web-preview/preview-biocafe-splash-page/uw-research-computing/guide-icons/calendar-text.svg" alt="Calendar icon" style="max-height: 200px" />
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<img src="/web-preview/preview-biocafe-splash-page/uw-research-computing/guide-icons/calendar-text.svg" alt="Calendar icon" style="max-height: 200px; width: auto;" />
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<h2 id="get-involved">Get Involved</h2>
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<h2 class="uw-mini-bar">Get Involved</h2>
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<div class="row" style="padding: 0 0 2em;">
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<h3>When &amp; Where (Fall 2025)</h3>
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<p>Second Wednesday of each month</p>
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<li><strong>Time:</strong> 2:30–4:30 PM CT</li>
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<li><strong>Time:</strong> 2:30–4:30 PM CST</li>
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<li><strong>Location:</strong> Discovery Building, <strong>Orchard View Room (Rm. 3820)</strong> (posted on the <a href="/events">events page</a>)</li>
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<li><strong>Dates:</strong>
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<li>Wed, September 10, 2025</li>
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<li><a href="/events/2025/09/10/Bioinformatics-Cafe">Wed, September 10, 2025</a></li>
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<li>Wed, October 8, 2025</li>
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<li>Wed, November 12, 2025</li>
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<li>Wed, December 10, 2025</li>
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<h3>Format</h3>
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<li><strong>Mini‑tutorial:</strong> topics include intro to advanced computing, high‑throughput read mapping, genome assembly at scale, and microbiome analysis.</li>
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<p><strong>New here?</strong> Start with the <a href="/uw-research-computing/htc-roadmap">HTC Roadmap</a> and come anyway—we’ll help you get set up.</p>
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<h3 id="faq">FAQ</h3>
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<p><strong>Keep the conversation going online</strong> on our Community Discourse! Share your resources or ask questions on our forum.</p>
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<a class="btn btn-primary" href="https://community.chtc.wisc.edu">Join the Community Discourse</a>
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<h2 class="uw-mini-bar">FAQ</h2>
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<summary><strong>Do I need prior commandline or Linux experience?</strong></summary>
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<p>No. We’ll meet you where you are. Beginners get step‑by‑step guidance and pointers to the <a href="/uw-research-computing/htc-roadmap">HTC Roadmap</a> and starter tutorials.</p>
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<summary><strong>Do I need prior command line or Linux experience?</strong></summary>
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<p>No. We’ll meet you where you are! We offer step‑by‑step guidance. Some good places to start are the <a href="/uw-research-computing/htc-roadmap">HTC Roadmap</a> and starter tutorials.</p>
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<summary><strong>Will I get 1‑on‑1 help?</strong></summary>
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<p>Yes. Each session includes a dedicated project co-working time and check‑ins with the facilitators. For deeper dives, we may have you <a href="https://go.wisc.edu/schedule-chtc">book a 1‑on‑1 consult</a> or visit <a href="/uw-research-computing/get-help.html#office-hours">Office Hours</a>.</p>
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<summary><strong>Can I get 1‑on‑1 help?</strong></summary>
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<p>Yes. Each session includes a dedicated project co-working time and check‑ins with the facilitators. For more in-depth help, we may have you <a href="https://go.wisc.edu/schedule-chtc">book a 1‑on‑1 consultation</a> or visit <a href="/uw-research-computing/get-help.html#office-hours">Office Hours</a>.</p>
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<summary><strong>What should I bring?</strong></summary>
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<p>Your laptop, project notes, and (if available) small test inputs or scripts. We can help stage larger data and set up containers. <br /><b>Don't have a project or data yet?</b><br />You should still come and bring your computational ideas, our facilitators will be able to help you get started and familiarized with the system for when you are ready to submit your research analysis workflows.</p>
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<p>Bring your laptop, project notes, and (if available) small test inputs or scripts. We can help stage larger data and set up containers.</p><p><b>Don't have a project or data yet?</b><br />You should still come and bring your computational ideas, our facilitators will be able to help you get started and familiarized with the system for when you are ready to submit your research analysis workflows.</p>
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<p>If have any questions or have ideas for topics, <a href="/uw-research-computing/get-help.html#help-via-email">reach out</a> and mention “Bioinformatics Café.”</p>
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<p><br />
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If have any questions or have ideas for topics, <a href="get-help.html#help-via-email">reach out</a> and mention “Bioinformatics Café.”</p>
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