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<!DOCTYPE html>
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<title>MemPanG25</title>
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<body class="article toc2 toc-left">
<div id="header">
<h1><strong>MemPanG25</strong></h1>
<div id="toc" class="toc2">
<div id="toctitle">MemPanG25</div>
<ul class="sectlevel1">
<li><a href="#_important_dates"><strong>Important Dates</strong></a></li>
<li><a href="#_venues"><strong>Venues</strong></a>
<ul class="sectlevel2">
<li><a href="#_practical_course_workshop">Practical course / Workshop</a></li>
<li><a href="#_conference">Conference</a></li>
<li><a href="#_biohackathon">Biohackathon</a></li>
<li><a href="#_hotels_in_memphis">Hotels in Memphis</a></li>
<li><a href="#_transportation_in_memphis">Transportation in Memphis</a></li>
</ul>
</li>
<li><a href="#_about_the_practical_course_workshop"><strong>About the Practical Course / Workshop</strong></a></li>
<li><a href="#_about_the_conference"><strong>About the Conference</strong></a></li>
<li><a href="#_about_the_biohackathon"><strong>About the Biohackathon</strong></a></li>
<li><a href="#_people"><strong>People</strong></a>
<ul class="sectlevel2">
<li><a href="#_practical_course_workshop_instructors">Practical Course / Workshop Instructors</a></li>
<li><a href="#_practical_course_helpers">Practical Course Helpers</a></li>
<li><a href="#_conference_invited_speakers">Conference Invited speakers</a></li>
<li><a href="#_organizers">Organizers</a></li>
</ul>
</li>
<li><a href="#_program"><strong>Program</strong></a>
<ul class="sectlevel2">
<li><a href="#_practical_course_workshop_2">Practical course / Workshop</a></li>
<li><a href="#_conference_2">Conference</a></li>
<li><a href="#_biohackathon_2">Biohackathon</a></li>
</ul>
</li>
<li><a href="#_registration_and_practical_information"><strong>Registration and Practical Information</strong></a>
<ul class="sectlevel2">
<li><a href="#_cost">Cost</a></li>
<li><a href="#_selection_criteria">Selection criteria</a></li>
</ul>
</li>
<li><a href="#_contact"><strong>Contact</strong></a></li>
</ul>
</div>
</div>
<div id="content">
<div id="preamble">
<div class="sectionbody">
<div class="paragraph">
<p>Computational pangenomics course, conference, and biohackathon in Memphis, TN, exploring the cutting edge of pangenomes, biology, methods, software, and artificial intelligence (AI).</p>
</div>
<div class="imageblock">
<div class="content">
<img src="images/DRB1-3123.fa.gz.pggb-E-s5000-l15000-p80-n10-a0-K16-k8-w50000-j5000-e5000-I0-R0-N.smooth.chop.og.lay.draw_mqc.CROP.png" alt="400">
</div>
</div>
<div class="imageblock">
<div class="content">
<img src="images/bridge.png" alt="400">
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_important_dates"><strong>Important Dates</strong></h2>
<div class="sectionbody">
<div class="ulist">
<ul>
<li>
<p>Practical course/Conference/Biohackathon Registration Deadline: <strong>1st April 2025</strong></p>
</li>
<li>
<p>Selected Participant will be notified by: <strong>15th April 2025</strong></p>
</li>
<li>
<p>Payment Deadline: <strong>29th April 2025</strong></p>
</li>
<li>
<p>Practical course / Workshop: <strong>XX-YY May 2025</strong></p>
</li>
<li>
<p>Conference: <strong>XX May 2025</strong></p>
</li>
<li>
<p>Biohackathon: <strong>XX-YY May 2025</strong></p>
</li>
</ul>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_venues"><strong>Venues</strong></h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_practical_course_workshop">Practical course / Workshop</h3>
<div class="paragraph">
<p><strong>Freeman Auditorium at the Hamilton Eye Institute</strong><br>
930 Madison Ave,<br>
3rd floor,<br>
Memphis, TN 38103<br>
United States<br>
→ <a href="https://www.google.com/maps/place/930+Madison+Ave,+Memphis,+TN+38103/@35.1405526,-90.0321798,17z/data=!3m1!4b1!4m6!3m5!1s0x87d57e65083437ab:0x975bb3c7cbb47cf0!8m2!3d35.1405526!4d-90.0296049!16s%2Fg%2F11c26jf2ws?entry=ttu">See the venue on the map</a></p>
</div>
</div>
<div class="sect2">
<h3 id="_conference">Conference</h3>
<div class="paragraph">
<p><strong>Freeman Auditorium at the Hamilton Eye Institute</strong><br>
930 Madison Ave,<br>
3rd floor,<br>
Memphis, TN 38103<br>
United States<br>
→ <a href="https://www.google.com/maps/place/930+Madison+Ave,+Memphis,+TN+38103/@35.1405526,-90.0321798,17z/data=!3m1!4b1!4m6!3m5!1s0x87d57e65083437ab:0x975bb3c7cbb47cf0!8m2!3d35.1405526!4d-90.0296049!16s%2Fg%2F11c26jf2ws?entry=ttu">See the venue on the map</a></p>
</div>
</div>
<div class="sect2">
<h3 id="_biohackathon">Biohackathon</h3>
<div class="paragraph">
<p><strong>Room 101, UTHSC Translational Research Science Building</strong><br>
71 S Manassas St,<br>
Memphis, TN 38103<br>
United States<br>
→ <a href="https://maps.app.goo.gl/QpQgUyRyjzjxP1vM9">See the venue on the map</a></p>
</div>
</div>
<div class="sect2">
<h3 id="_hotels_in_memphis">Hotels in Memphis</h3>
<div class="ulist">
<ul>
<li>
<p><a href="https://goo.gl/maps/arRZWkjPCNBAFfCf9">La Quinta Hotel Memphis Downtown</a></p>
</li>
<li>
<p><a href="https://goo.gl/maps/Dwf9LgHeJLXsAJcf7">Double Tree Hotel</a></p>
</li>
<li>
<p><a href="https://goo.gl/maps/h5A6LpmToTD7DepH8">River Inn at Harbor Town Hotel</a></p>
</li>
<li>
<p><a href="https://goo.gl/maps/o7XrW3DZHTNqXXT26">Comfort Inn</a></p>
</li>
<li>
<p><a href="https://goo.gl/maps/e365A6rNjZUPvFqRA">Hampton Inn</a></p>
</li>
<li>
<p><a href="https://goo.gl/maps/rjdSg46kZFPsmKxS7">Hyatt Centric Beale Street</a></p>
</li>
<li>
<p><a href="https://goo.gl/maps/e4BcvEabefsqEhC4A">HU Hotel</a></p>
</li>
<li>
<p><a href="https://goo.gl/maps/Erq5cwVtM4hh8c8e7">Sheraton Memphis Downtown Hotel</a></p>
</li>
</ul>
</div>
</div>
<div class="sect2">
<h3 id="_transportation_in_memphis">Transportation in Memphis</h3>
<div class="paragraph">
<p>If you stay in Downtown, the Medical District, South City, or New Chicago, you can reach the event venue by getting on-demand, convenient, and affordable rides with <a href="https://city.ridewithvia.com/groove-on-demand">Groove On-Demand</a>.</p>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_about_the_practical_course_workshop"><strong>About the Practical Course / Workshop</strong></h2>
<div class="sectionbody">
<div class="paragraph">
<p><strong>Monday, May 12, 2025 - Tuesday, May 13, 2025</strong><br>
The use of a single reference genome in bioinformatics can lead to reference bias and miss important information about genome variability and relationships. New assembly methods have made it easier to generate high-quality complete genome assemblies, and using a pangenome graph that expresses many genomes and their mutual alignment can help address these issues.
This practical course / workshop will focus on building such graphs from whole genome assemblies and using them in various downstream applications in comparative genomics, evolution, variation analysis, sequence alignment, and phenotype association.</p>
</div>
<div class="paragraph">
<p>Participants will learn about pangenome concepts and gain practical experience building and analyzing pangenome graphs. They will apply these methods to complex research questions that require understanding the relationships between multiple genomes or accounting for variability when analyzing new genomes.
By the end of the practical course / workshop, participants will have a strong understanding of pangenome methods based on whole genome assemblies.</p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_about_the_conference"><strong>About the Conference</strong></h2>
<div class="sectionbody">
<div class="paragraph">
<p><strong>Wednesday, May 14, 2025</strong><br>
We will gather for an in-person conference on the day after the practical course / workshop.
This will bring together practical course / workshop participants and virtual and in-person speakers who are actively working on diverse aspects of pangenome research.
The virtual meeting will be open to the public.
Speakers will cover topics at the intersection of pangenome methods and biology, including a focus on basic methods, data structures, genome assembly, data visualization, and public collaborative pangenome projects.
We expect to draw speakers from a diverse set of species contexts.</p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_about_the_biohackathon"><strong>About the Biohackathon</strong></h2>
<div class="sectionbody">
<div class="paragraph">
<p><strong>Thursday, May 15, 2025 - Friday, May 16, 2025</strong><br></p>
</div>
<div class="paragraph">
<p>We have a focus on software.
We will work with/on pangenomic tools (such as <a href="https://github.com/pangenome/pggb/">PGGB</a>, <a href="https://github.com/waveygang/wfmash/">WFMASH</a>, <a href="https://github.com/ekg/seqwish/">SEQWISH</a>, <a href="https://github.com/pangenome/odgi/">ODGI</a>, <a href="https://github.com/pangenome/smoothxg/">SMOOTHXG</a>, <a href="https://github.com/vgteam/vg">VG</a>, <a href="https://github.com/vcflib/vcflib/">VCFLIB</a>, <a href="https://github.com/genetics-statistics/GEMMA/">GEMMA</a>) with software project leadership.
<strong>You are welcome to bring your own projects!</strong></p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_people"><strong>People</strong></h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_practical_course_workshop_instructors">Practical Course / Workshop Instructors</h3>
<div class="paragraph">
<p>TBD</p>
</div>
</div>
<div class="sect2">
<h3 id="_practical_course_helpers">Practical Course Helpers</h3>
<div class="paragraph">
<p>TBD</p>
</div>
</div>
<div class="sect2">
<h3 id="_conference_invited_speakers">Conference Invited speakers</h3>
<div class="paragraph">
<p>TBD</p>
</div>
<hr>
</div>
<div class="sect2">
<h3 id="_organizers">Organizers</h3>
<div class="ulist">
<ul>
<li>
<p><a href="https://andreaguarracino.github.io/">Andrea Guarracino</a>, University of Tennessee Health Science Center, Memphis, TN, US</p>
</li>
<li>
<p><a href="http://hypervolu.me/~erik/erik_garrison.html">Erik Garrison</a>, University of Tennessee Health Science Center, Memphis, TN, US</p>
</li>
<li>
<p><a href="https://github.com/Flavia95">Flavia Villani</a>, University of Tennessee Health Science Center, Memphis, TN, US</p>
</li>
<li>
<p><a href="https://thebird.nl/">Pjotr Prins</a>, University of Tennessee Health Science Center, Memphis, TN, US</p>
</li>
<li>
<p><a href="https://www.uthsc.edu/faculty/profile/?netid=vcolonna">Vincenza Colonna</a>, University of Tennessee Health Science Center, Memphis, TN, US</p>
</li>
<li>
<p><a href="https://uthsc.edu/search/detail.php?id=T100344325">Tamara Brock</a>, University of Tennessee Health Science Center, Memphis, TN, US</p>
</li>
</ul>
</div>
<div class="paragraph">
<p><span class="image"><img src="images/UTHSC.png" alt="uthsc" width="300"></span></p>
</div>
<div class="paragraph">
<p>University of Tennessee Health Science Center, Department of Genetics, Genomics and Informatics</p>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_program"><strong>Program</strong></h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_practical_course_workshop_2">Practical course / Workshop</h3>
<div class="paragraph">
<p><strong>Time:</strong> Monday-Tuesday, 12nd-13rd May 2025<br></p>
</div>
<div class="paragraph">
<p><strong>Place</strong>: <a href="https://www.google.com/maps/place/930+Madison+Ave,+Memphis,+TN+38103/@35.1405526,-90.0321798,17z/data=!3m1!4b1!4m6!3m5!1s0x87d57e65083437ab:0x975bb3c7cbb47cf0!8m2!3d35.1405526!4d-90.0296049!16s%2Fg%2F11c26jf2ws?entry=ttu">930 Madison Ave, Freeman Auditorium at the Hamilton Eye Institute, 3rd floor</a></p>
</div>
<div class="paragraph">
<p>TBD</p>
</div>
</div>
<div class="sect2">
<h3 id="_conference_2">Conference</h3>
<div class="paragraph">
<p><strong>Time:</strong> Wednesday, 14 May 2025<br></p>
</div>
<div class="paragraph">
<p>TBD</p>
</div>
</div>
<div class="sect2">
<h3 id="_biohackathon_2">Biohackathon</h3>
<div class="paragraph">
<p><strong>Time:</strong> Thursday-Friday, 15th-16th May 2025<br></p>
</div>
<div class="paragraph">
<p><strong>Place:</strong> <a href="https://maps.app.goo.gl/QpQgUyRyjzjxP1vM9">Room 101, UTHSC Translational Research Science Building</a></p>
</div>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 22.2222%;">
<col style="width: 11.1111%;">
<col style="width: 22.2222%;">
<col style="width: 44.4445%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">Day</th>
<th class="tableblock halign-left valign-top">Time</th>
<th class="tableblock halign-left valign-top">Speaker(s)</th>
<th class="tableblock halign-left valign-top">Topic</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Thursday, May 15, 2025</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">09:30-10:30</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">10:30-11:00</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Coffee break</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">11:00-12:30</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock"><strong>12:30-14:30</strong></p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock"><strong>Everyone</strong></p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock"><strong>Lunch</strong></p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">14:30-15:30</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">15:30-16:00</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Coffee break</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">16:00-17:00</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
</tbody>
</table>
<table class="tableblock frame-all grid-all stretch">
<colgroup>
<col style="width: 22.2222%;">
<col style="width: 11.1111%;">
<col style="width: 22.2222%;">
<col style="width: 44.4445%;">
</colgroup>
<thead>
<tr>
<th class="tableblock halign-left valign-top">Day</th>
<th class="tableblock halign-left valign-top">Time</th>
<th class="tableblock halign-left valign-top">Speaker(s)</th>
<th class="tableblock halign-left valign-top">Topic</th>
</tr>
</thead>
<tbody>
<tr>
<td class="tableblock halign-left valign-top"><p class="tableblock">Friday, May 16, 2025</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">09:30-10:30</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">10:30-11:00</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Coffee break</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">11:00-12:30</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock"><strong>12:30-14:30</strong></p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock"><strong>Everyone</strong></p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock"><strong>Lunch</strong></p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">14:30-15:30</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">15:30-16:00</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Coffee break</p></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">16:00-17:00</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Everyone</p></td>
<td class="tableblock halign-left valign-top"><p class="tableblock">Hacking</p></td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_registration_and_practical_information"><strong>Registration and Practical Information</strong></h2>
<div class="sectionbody">
<div class="paragraph">
<p>Registration includes access to: all lectures and practical sessions, all course materials.</p>
</div>
<div class="sect2">
<h3 id="_cost">Cost</h3>
<div class="paragraph">
<p>The cost includes all expenses associated with the event, with lunches, coffee, and snacks. In certain circumstances, we can waive the fees.</p>
</div>
<div class="ulist">
<ul>
<li>
<p>Academic - $200, with financial support if needed</p>
</li>
<li>
<p>Industry - $400</p>
</li>
</ul>
</div>
</div>
<div class="sect2">
<h3 id="_selection_criteria">Selection criteria</h3>
<div class="paragraph">
<p>This practical course / workshop is intended for biologists and bioinformaticians interested in studying organisms with high genetic diversity or without a reference genome, as well as those involved in comparative genomics and the assembly of pangenomes for any species.</p>
</div>
<div class="paragraph">
<p>Selection of participants will be based on:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>good knowledge of Linux operating system and basic shell commands. This will be a mandatory prerequisite.</p>
</li>
<li>
<p>familiarity with genomics data formats (e.g., FASTA, VCF, BED, …​) is a plus.</p>
</li>
<li>
<p>impact of the practical course / workshop for the participant and his/her research group.</p>
</li>
<li>
<p>stage of the research project: priority will be given to participants with data already available and ready to be analyzed (participants data will not be analyzed during the practical course / workshop).</p>
</li>
</ul>
</div>
<div class="paragraph">
<p>Fulfillment of these conditions by participants will be assessed through the registration form.</p>
</div>
<table class="tableblock frame-none grid-none stretch">
<colgroup>
<col style="width: 33.3333%;">
<col style="width: 33.3333%;">
<col style="width: 33.3334%;">
</colgroup>
<tbody>
<tr>
<td class="tableblock halign-right valign-top"><div class="content"><div class="imageblock">
<div class="content">
<img src="images/memphis.jpg" alt="memphis" width="300" height="300">
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<div class="content">
<img src="images/bridge.jpg" alt="bridge" width="300" height="300">
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</tr>
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<div class="paragraph">
<p><a href="https://www.memphistravel.com/sports-outdoors?gclid=Cj0KCQiAgOefBhDgARIsAMhqXA4Gt_kloBAAqe5LDWNW3199TI8DzRrUo4fCqSQ_cKLkRPd4xv46TUgaAt4WEALw_wcB">memphistravel</a></p>
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<div class="paragraph">
<p><br>
<br></p>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_contact"><strong>Contact</strong></h2>
<div class="sectionbody">
<div class="ulist">
<ul>
<li>
<p><a href="mailto:[email protected]">[email protected]</a></p>
</li>
</ul>
</div>
</div>
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Last updated 2024-11-27 11:08:18 -0600
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