-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathdummy_temp.html
More file actions
229 lines (201 loc) · 22.8 KB
/
dummy_temp.html
File metadata and controls
229 lines (201 loc) · 22.8 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
<!DOCTYPE HTML>
<!--
Apex by Pixelarity
pixelarity.com | hello@pixelarity.com
License: pixelarity.com/license
-->
<html>
<head>
<title>UW Genome Sciences: Hackathon</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<!--[if lte IE 8]><script src="assets/js/ie/html5shiv.js"></script><![endif]-->
<link rel="stylesheet" href="../assets/css/main.css" />
<style type="text/css">
.style30 {font-family: Arial, Helvetica, sans-serif}
.style34 {font-weight: bold}
.style36 {font-size: 10pt; font-weight: bold; }
.style37 {font-family: Arial, Helvetica, sans-serif; font-size: 10pt; font-weight: bold; }
.style44 {font-size: 10pt}
</style>
<!--[if lte IE 8]><link rel="stylesheet" href="assets/css/ie8.css" /><![endif]-->
</head>
<body>
<div id="page-wrapper">
<!-- Header Wrapper -->
<div id="header-wrapper">
<!-- Header -->
<div class="container">
<header id="page-header">
<h1><a href="../index.htm" id="logo"><span>UW Genome Sciences</span></a></h1>
<nav id="nav">
<ul>
<li><a href="../index.htm">Home</a></li>
<li>
<a href="../about/index.htm" class="arrow">About</a>
<ul>
<li><a href="../about/welcome.htm">Welcome</a></li>
<li><a href="../about/contact.htm">Contact</a></li>
<li><a href="../about/directory/index.htm">Directory</a></li>
<li><a href="../about/history.htm">History</a></li>
<li><a href="../about/support.htm">Support Genome Sciences</a></li>
</ul>
</li>
<li><a href="../faculty/index.htm">Faculty</a></li>
<li>
<a href="../academics/index.htm" class="arrow">Academics</a>
<ul>
<li><a href="../academics/gradprogram/index.htm">Ph.D. Program</a></li>
<li><a href="../office/postdocs/index.htm">Postdoctoral Program</a></li>
<li><a href="../academics/courses/index.htm">Courses</a></li>
<li><a href="../academics/tg.htm">Training Grants</a></li>
<li><a href="../academics/summer/index.htm">Summer Research</a></li>
<li><a href="../academics/diversity.htm">Diversity</a></li>
</ul>
</li>
<li>
<a href="index.htm" class="arrow">News & Events</a>
<ul>
<li><a href="calendar.htm">Events Calendar</a></li>
<li><a href="seminar.htm">GS Seminar</a></li>
<li><a href="combi.htm">Combi Seminar</a></li>
<li><a href="journal.htm">Journal Club</a></li>
<li><a href="reports.htm">Research Reports</a></li>
<li><a href="outreach.htm">Outreach</a></li>
<li><a href="wigs.htm">Women In Genome Sciences (WiGS)</a></li>
<li><a href="salon.htm">Genomics Salon</a></li>
<li><a href="news.htm">Department News</a></li>
<li><a href="itcalendar.htm">IT Outages</a></li>
</ul>
</li>
<li>
<a href="#" class="arrow">Administration</a>
<ul>
<li><a href="../computing/index.htm">Computing</a></li>
<li><a href="../office/rooms.htm">Conference Rooms</a></li>
<li><a href="../about/directory.htm">Directory</a></li>
<li><a href="../office/employment/index.htm">Employment</a></li>
<li><a href="../office/facilities/index.htm">Facilities</a></li>
<li><a href="../office/facultyresources/index.htm">Faculty Resources</a></li>
<li><a href="../office/operations/hr/index.htm">Human Resources</a></li>
<li><a href="../office/operations/index.htm">Operations</a></li>
<li><a href="../office/researchsupport/index.htm">Research Support</a></li>
</ul>
</li>
</ul>
</nav>
</header>
</div>
</div>
<!-- Search Wrapper -->
<div id="search-wrapper">
<!-- Search -->
<div class="container" id="search">
<span>Model Organism Genetics -- Human and Medical Genetics -- Genomics and Proteomics -- Computational Biology </span>
<div class="row">
<div class="-8u 12u(mobile) 4u 12u(mobile)">
<div class="side-padded">
<form method="GET" action="http://www.google.com/search">
<div>
<input type=hidden name=ie value=UTF-8>
<input type=hidden name=oe value=UTF-8>
<INPUT TYPE=text name=q size=40 maxlength=255 value="">
<input type=hidden name=sitesearch value="http://www.gs.washington.edu">
</div>
</form>
</div>
</div>
</div>
</div>
</div>
<!-- Main -->
<div id="main-wrapper">
<div class="container">
<div class="row">
<div class="12u important(mobile)">
<!-- Content -->
<div id="content">
<!-- Article -->
<article class="featured">
<header>
<h2>Genome Sciences Hackathon</h2>
<p> </p>
</header>
<div>
<p align="center"><img src="images/hackathon.png" width="355" height="178" alt=""/ ></p>
<p>Do you love innovation and challenge? Do you like problem solving in collaborative environments? Do you want to learn new technical skills outside of your current projects? Most importantly, do you want to make tools that will improve the field of genomics and make it more accessible to the public?</p>
<p>If so, the department of Genome Sciences proudly invites you to participate in our second annual Hackathon! The Hackathon will span 5 days, from Monday September 18th through Friday September 22nd. All GS trainees and faculty (graduate, post-doctoral, and staff) are invited to participate. There will be four teams led by your amazing colleagues, where each team will build a deliverable by the end of the five days. This is an opportunity to build something cool, learn from colleagues outside of your lab, and have fun!</p>
<p>If you’re interested, please read the project details below and fill out the interest form: <br>
<a href="https://forms.gle/eDxhcwNoa34wwkSm8" target="_blank" class="aaastandout">https://forms.gle/eDxhcwNoa34wwkSm8</a></p>
<p>If you have any questions about the event, please contact Sayeh Gorjifard <sgorji [ a t ] uw.edu></p>
<p class="aaastandout"><strong>EVENT DETAILS:</strong><br>
<strong>Location: Each team will have a conference room in Foege <br>
Dates: September 18-22, 2023<br>
Times: 9 am - 5 pm (with afternoon review sessions in Foege auditorium 3 pm on Monday and Wednesday and a final presentation on Friday). </strong><br>
<strong>Food: Coffee/snacks are provided daily<br>
Final celebration (beer hour + food) will be Friday at 5 pm on the 3rd floor common area.</strong></p>
<p><span class="aaastandout"><strong>Project #1: </strong><br>
<strong>Leading lab</strong>:</span> Dunham Lab<br>
<span class="aaastandout"><strong>Stakeholders</strong>:</span> Maitreya Dunham and Leah Anderson <br>
<strong class="aaastandout">Hackathon project title: </strong>Developing bioinformatics and data visualization resources for yEvo (<a href="https://yevo.org/" target="_blank" class="aaastandout">https://yevo.org/</a>), which teaches high schoolers about evolution and genetics using yeast.<br>
<span class="aaastandout"><strong>Desired deliverable</strong>:</span> Website tools for high school students to see and interact with whole genome sequencing data, along with curricular materials to guide students through a lab about whole genome sequencing and bioinformatics. Long term deliverable is to offer a bioinformatics module as a standalone product that teachers could use in their classes without direct intervention from us. If this is successful, other yeast labs that have less access to computational resources would probably use it, and we hope that SGD will host the tool. <br>
<span class="aaastandout">Expected coding experience level: </span>Beginner-Intermediate-Advanced</p>
<p><span class="aaastandout">Abstract: </span><br>
Whole-genome sequencing is not accessible for users who lack access to expert training or coding expertise, like biologists at non-elite schools or high schoolers. To address this problem, the desired deliverable will be a web-based tool that associated protocol users can use to analyze and visualize their whole genome sequencing data. We aim to have a simple user interface that would allow the students to understand each step in the analysis pipeline. We were thrilled that yEvo was one of the Hackathon teams last year, as we were able to move our sequencing data analysis pipeline into Snakemake and build a Shiny app, Mutation Browser: <a href="https://yevo.org/mutation-browser/" target="_blank" class="aaastandout">https://yevo.org/mutation-browser/</a>. To expand the tool further, we aim to create a website where students can see pile-ups and mutation calls and interact with their “raw” data. Further improvements to the Mutation Browser Shiny app will allow students to compare mutations across and between classes, and to link out to SGD and other resources to learn about their mutations. The stretch goal would be to build this as a website to help all yeast geneticists. </p>
<p><strong> </strong></p>
<p><span class="aaastandout"><strong>Project #2: </strong><br>
<strong>Leading lab</strong>:</span> Beliveau Lab<br>
<span class="aaastandout"><strong>Stakeholder</strong>:</span> Conor Camplisson <concamp [ a t ] uw.edu><br>
<span class="aaastandout"><strong>Hackathon project title</strong>:</span> Genome-wide simulation of <em>in situ </em>hybridization<br>
<strong class="aaastandout">Desired deliverable: </strong>A web app that allows users to input oligonucleotide probe sequence(s) and visualize their predicted binding genome-wide.<br>
<strong class="aaastandout">Expected coding experience level: </strong>Intermediate-Advanced. </p>
<p><strong class="aaastandout">Abstract: </strong><br>
Several tools exist for designing oligonucleotide probes for use in fluorescence <em>in situ </em>hybridization (FISH) experiments. However, there is an unmet need for a tool that can simulate the genome-wide binding profile of candidate probes under experimental hybridization conditions. Existing tools vary in the level of sophistication of their approaches to analyzing probe specificity as well as in the level of coding expertise needed to use the tools. This project will produce a tool that maximizes both of these dimensions, leveraging a state of the art specificity analysis pipeline based on short-read alignment and nearest-neighbor thermodynamics to simulate the genome-wide binding of candidate probes and visualize the predicted binding profile under experimental conditions. The app will include a web interface that can be used without any coding experience, allowing the users to easily and accurately predict the <em>in situ </em>performance of their candidate probes. The Beliveau lab has several related web tools (PaintSHOP, TigerFISH) as well as existing algorithms that will form the back-end bioinformatics component of the web app. For this project we will need to create a containerized app that can be deployed to a cloud server, design and implement the web interface, functionalize the app so that the bioinformatics algorithms can be integrated into the back-end, and create infrastructure that allows for the running of analysis jobs in the background (i.e. using a task queue framework) and exposing front-end parameters so that users can configure the simulations that run on the back-end.</p>
<p><strong> </strong></p>
<p><span class="aaastandout"><strong>Project #3: </strong><br>
<strong>Leading lab</strong>:</span> Noble Lab<br>
<span class="aaastandout"><strong>Stakeholder</strong>:</span> Gang Li (gangliuw [ a t ] uw.edu), Hyeon-Jin Kim (khj3017 [ a t ] uw.edu), Borislav Hristov (borislav [ a t ] uw.edu)<br>
<span class="aaastandout"><strong>Hackathon project title</strong>:</span> Integrating single-cell Hi-C and single-cell RNA sequencing data<br>
<strong class="aaastandout">Desired deliverable: </strong>Benchmarking results comparing multiple existing software tools for integrating scHiC and scRNA data.<br>
<strong class="aaastandout">Expected coding experience level: </strong>Intermediate-Advanced. </p>
<p><span class="aaastandout">Abstract:</span><br>
Recently, Liu et al. developed HiRES, a multi-omics sequencing approach to simultaneously profile 3D chromatin contacts and gene expression in single cells. The HiRES assay thus directly links chromatin conformation and gene expression profiles within single cells. Previous studies that aimed to investigate the interplay between chromatin interactions and transcriptomic profiles necessarily generated unpaired single-cell RNA-sequencing and chromatin conformation data. For the hackathon, we will use the newly available HiRES data to benchmark existing software tools developed for matching cells across modalities. In particular, we evaluate GLUE, LS-MMDMA (<a href="https://academic.oup.com/bioinformatics/article/39/7/btad420/7221538" target="_blank" class="aaastandout">Meng 2023</a>), Pomona (<a href="https://pubmed.ncbi.nlm.nih.gov/34398192/" target="_blank" class="aaastandout">Cao 2021</a>), SCOT (<a href="https://pubmed.ncbi.nlm.nih.gov/35050714/" target="_blank" class="aaastandout">Demetci 2022</a>), Synmatch (<a href="https://academic.oup.com/bioinformatics/article/38/Supplement_2/ii148/6702005?login=false" target="_blank" class="aaastandout">Hristov 2022</a>), and CMOT (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02989-8" target="_blank" class="aaastandout">Alatkar 2023</a>). In addition, we will consider four different techniques for representing the scHi-C contact matrices, including the contact decay profile, the HiCRep (<a href="https://academic.oup.com/bioinformatics/article/37/18/2996/6133255?login=false" target="_blank" class="aaastandout">Lin 2021</a>) similarity score, a latent Dirichlet allocation model (<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008173" target="_blank" class="aaastandout">Kim 2020</a>), and the scGAD method (<a href="https://academic.oup.com/bioinformatics/article/38/14/3642/6598798" target="_blank" class="aaastandout">Shen 2022</a>). Our results will compare and contrast the performance of these tools and Hi-C representation techniques in the context of integration with scRNA-seq data. <br>
For the hackathon, we will use co-assay data to validate integration of scRNA-seq and scHi-C. </p>
<p><span class="aaastandout"><strong>Project #4</strong><br>
<strong>Leading lab</strong>:</span> Nunn lab<br>
<span class="aaastandout"><strong>Stakeholder</strong>:</span> Brook L. Nunn brookh [ a t ] uw.edu<br>
<span class="aaastandout"><strong>Hackathon project title</strong>:</span> Metagenomic time series portal to interrogate bacterial taxonomic groups and their functions as they relate to temporal chemical and physical data<br>
<span class="aaastandout">Expected coding experience level: </span>Beginner(HTML/CSS) - Advanced(experience with back-end web development) </p>
<p><span class="aaastandout">Abstract: </span><br>
The Nunn Lab envisions a transformative metagenomic time series portal to dissect bacterial taxonomic groups and functions in relation to temporal chemical and physical data. The portal's deliverable is a user-friendly website granting access to 133 metagenomes from ocean water samples, each collected at distinct time points. Currently, the Joint Genome Institute (JGI) does not link time points together, so you cannot visualize how a gene is changing through time. <br>
However, JGI has rich gene annotations. Our goal is to consolidate all of this data in usable formats. If this data can be interrogated through a website portal by inquiring how a specific gene or taxonomic group or keyword located within a gene set is changing through time, then the data set will be utilized more frequently. The website should allow users to query using keywords like protein names, KEGG annotations, and PFam annotations, with results displayed in a comprehensive web page showcasing gene abundance, taxonomic profiles, and more across the 133 time points. We anticipate the portal will be utilized in middle school and high school classrooms. In agreement with JGI when the funding was received we will be publishing a scientific data report within the year providing all metadata to the public. We aim to include this portal as part of the publication. </p>
<p> </p>
<p><span class="aaastandout"><strong>Project #5</strong><br>
<strong>Leading lab</strong>:</span> Stergachis lab<br>
<span class="aaastandout"><strong>Stakeholder</strong>: </span>Morgan Hamm mhamm [ a t ] uw.edu<br>
<span class="aaastandout"><strong>Hackathon project title</strong> : </span> Improving m6A methylation calling from Oxford Nanopore data<br>
<strong class="aaastandout">Expected coding experience level: </strong>Intermediate-Advanced </p>
<p><span class="aaastandout">Abstract:</span> <br>
Fiber-seq is a method to assess chromatin accessibility using a nonspecific adenine methyltransferase that selectively labels accessible, but not occluded, adenine bases. Major benefits of this method over other accessibility techniques is that DNA sequence is preserved and it is amenable to long-read sequencing. PacBio sequencing is typically used as the sequencing technology in Fiber-seq assays. Oxford Nanopore sequencing technology is also capable of calling Adenine methylation, however, methylation calling is less accurate than with PacBio data, and false positive calls disrupt downstream analysis steps such as labeling nucleosomes. For this hackathon project, we will train a model to improve m6A methylation calling for Oxford Nanopore sequencing data. The model will use the existing methylation calls, along with quality metrics, and the sequence context of the methylation base calls to reduce false positive calls. The Stergachis lab has sequenced methyltransferase treated samples for use in this project. The Stergachis lab Hackathon project last year performed a similar task, improving methylation calling for PacBio data, that project led to a currently in review manuscript for Nature Methods. </p>
<h1> </h1>
<p class="style37"> </p>
<p class="style37"> </p>
<p class="aaastandout"> </p>
</div>
</article>
</div>
</div>
</div>
</div>
</div>
<!-- Scripts -->
<script src="../assets/js/jquery.min.js"></script>
<script src="../assets/js/jquery.dropotron.min.js"></script>
<script src="../assets/js/jquery.slidertron.min.js"></script>
<script src="../assets/js/skel.min.js"></script>
<script src="../assets/js/skel-viewport.min.js"></script>
<script src="../assets/js/util.js"></script>
<!--[if lte IE 8]><script src="assets/js/ie/respond.min.js"></script><![endif]-->
<script src="../assets/js/main.js"></script>
</body>
</html>