Initial commit

.gitignore

+
+!.gitkeep
+/public
+/static/images/*
+
+# Created by https://www.gitignore.io/api/git,linux,macos,windows
+# Edit at https://www.gitignore.io/?templates=git,linux,macos,windows
+
+### Git ###
+# Created by git for backups. To disable backups in Git:
+# $ git config --global mergetool.keepBackup false
+*.orig
+
+# Created by git when using merge tools for conflicts
+*.BACKUP.*
+*.BASE.*
+*.LOCAL.*
+*.REMOTE.*
+*_BACKUP_*.txt
+*_BASE_*.txt
+*_LOCAL_*.txt
+*_REMOTE_*.txt
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.gitignore.io/api/git,linux,macos,windows
\ No newline at end of file

.gitlab-ci.yml

+
+image: monachus/hugo
+
+variables:
+  GIT_SUBMODULE_STRATEGY: recursive
+
+pages:
+  script:
+  - hugo
+  artifacts:
+    paths:
+    - public
+  only:
+  - master
\ No newline at end of file

.gitmodules

+[submodule "themes/blackburn"]
+	path = themes/blackburn
+	url = https://github.com/yoshiharuyamashita/blackburn.git

archetypes/default.md

+---
+title: "{{ replace .Name "-" " " | title }}"
+date: {{ .Date }}
+draft: true
+---
+

archetypes/people.md

+---
+title: "{{ replace .Name "-" " " | title }}"
+date: {{ .Date }}
+draft: true
+name: ""
+degree: ""
+pic: "NoPic.jpg"
+tit: ""
+orcid: ""
+weight: ""
+---
+

archetypes/publications.md

+---
+title: "{{ replace .Name "-" " " | title }}"
+date: {{ .Date }}
+draft: true
+pname: ""
+pauthor: ""
+pjournal: ""
+pdate: ""
+odate: ""
+ppubmed: ""
+plink: ""
+ppic: "NoImage.jpg"
+prepo:
+    - title: ""
+      loc: ""
+---
+

config.toml

+baseurl = "https://www.StrandLab.net/"
+title = "Strand Lab"
+author = "Gervaise H. Henry"
+# Shown in the side menu
+copyright = "© 2019. All rights reserved."
+canonifyurls = true
+paginate = 10
+
+[indexes]
+  tag = "tags"
+  topic = "topics"
+
+[params]
+  # Shown in the home page
+  institution = "UT Southwestern Medical Center"
+  isite = "https://www.utsouthwestern.edu/"
+  brand = "Strand Lab"
+  department = "Department of Urology"
+  dsite = "https://www.utsouthwestern.edu/education/medical-school/departments/urology/"
+  description = "Investigating lower urinary tract biology"
+  googleAnalytics = "UA-120971283-2"
+  # CSS name for highlight.js
+  highlightjs = "androidstudio"
+  highlightjs_extra_languages = ["yaml"]
+  dateFormat = "02 Jan 2006, 15:04"
+  # Include any custom CSS and/or JS files
+  # (relative to /static folder)
+  custom_css = [""]
+  custom_js = [""]
+
+  [params.piwikAnalytics]
+    siteid = 2
+    piwikroot = ""
+
+[menu]
+  # Shown in the side menu.
+  [[menu.main]]
+    name = "Research"
+    pre = "<i class='fa fa-home fa-fw'></i>"
+    weight = 1
+    identifier = "research"
+    url = "/research"
+  [[menu.main]]
+    name = "People"
+    pre = "<i class='fa fa-user fa-fw'></i>"
+    weight = 2
+    identifier = "people"
+    url = "/people/"
+  [[menu.main]]
+    name = "Publications"
+    pre = "<i class='fa fa-book fa-fw'></i>"
+    weight = 3
+    identifier = "publications"
+    url = "/publications/"
+  [[menu.main]]
+    name = "Biorepository"
+    pre = "<i class='fa fa-stethoscope fa-fw'></i>"
+    weight = 4
+    identifier = "repository"
+    url = "/repository/"
+  [[menu.main]]
+    name = "Single-Cell Data"
+    pre = "<i class='fa fa-bar-chart fa-fw'></i>"
+    weight = 5
+    identifier = "data"
+    url = "/data"
+  [[menu.main]]
+    name = "Contact"
+    pre = "<i class='fa fa-phone fa-fw'></i>"
+    weight = 6
+    url = "/contact"
+
+[social]
+  # Link your social networking accounts to the side menu
+  # by entering your username or ID.
+
+  # SNS microblogging
+  twitter = "strand_lab"
+
+  # Techie
+  biohpcgitlab = "StrandLab/"
\ No newline at end of file

content/contact.md

+---
+title: "KEEP IN TOUCH WITH US"
+date: 2019-05-19T13:49:34-05:00
+draft: true
+---
+<style>
+    .map {
+        position: relative;
+        padding-bottom: 50%;
+        height: 0;
+        overflow: hidden;
+    }
+    .map iframe {
+        position: absolute;
+        top: 0;
+        left: 0;
+        width: 100% !important;
+        height: 100% !important;
+    }
+    @media (min-width: 1000px) {
+        .column {
+            float: left;
+        }
+        .left {
+            width: 10%;
+        }
+        .right {
+            width: 90%;
+        }
+        .row:after {
+            content: "";
+            display: table;
+            clear: both;
+        }
+    }
+</style>
+
+<p style='text-align: center;'>
+Questions about our research or need a tip on one of our protocols? Interested in collaborations? Email us, mention any person, project, or activity of interest,and we will get back to you soon!
+</p>
+
+<div class="map">
+<iframe src="https://www.google.com/maps/embed?pb=!1m14!1m12!1m3!1d5666.067598000117!2d-96.84034317995817!3d32.81593873821668!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!5e0!3m2!1sen!2sus!4v1558292028882!5m2!1sen!2sus" frameborder="0" style="border:0" allowfullscreen></iframe>
+</div>
+
+<div class="row">
+<div class="column left">
+<i class="fa fa-map-marker fa-2x"></i><br>
+</div>
+<div class="column right">
+UT Southwestern Medical Center,<br>
+Department of Urology,<br>
+5323 Harry Hines Blvd,<br>
+Mail Code: 9110,<br>
+Dallas, TX 75390-9110<br>
+</div>
+</div>
+___
+<div class="row">
+<div class="column left">
+<i class="fa fa-envelope-open fa-2x"></i><br>
+</div>
+<div class="column right">
+[douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
+</div>
+</div>
+___
+<div class="row">
+<div class="column left">
+<i class="fa fa-phone fa-2x"></i><br>
+</div>
+<div class="column right">
+214-648-6096
+</div>
+</div>
+___
\ No newline at end of file

content/data.md

+---
+title: "Single-Cell RNA-seq Data"
+date: 2019-06-10T21:49:01-05:00
+draft: true
+type: "custom"
+layout: "data"
+---
+
+<style>
+  .content{
+    margin: 0;
+    max-width: none;
+  }
+  .select {
+    float: top;
+    z-index: 1;
+    top: 0px;
+    background: #191818;
+    overflow-x: hidden;
+    padding: 8px 10px;
+  }
+  .columnS {
+    float: left;
+    text-align: center;
+    width: 33.33%;
+  }
+  .columnF {
+    float: left;
+    text-align: center;
+    width: 33.33%;
+  }
+  .row:after {
+    content: "";
+    display: table;
+    clear: both;
+  }
+  img{
+    max-width: 100%;
+    height: auto;
+  }
+  @media (max-width: 1000px) {
+    .columnS {
+      text-align: right;
+      width: 100%;
+    }
+    .columnF {
+      width: 100%;
+    }
+    br {
+      display: none;
+    }
+  }
+</style>
+<body>
+  <div class = "select">
+      <div class = "columnS ui-widget">
+        <label for = "gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
+        <br>
+        <input id = "gene">
+      </div>
+    <div class = "columnS">
+      <label for="lineage" style="font-size:18px;"><b>Select a cell lineage to display:</b></label>
+      <br>
+      <select name="lineage" id="lineage">
+        <option selected="selected" value="all">All Cells</option>
+        <option value="epi">Epithelial Cells Only</option>
+        <option value="st">Stromal Cells Only</option>
+      </select>
+    </div>
+    <div class = "columnS">
+      <label for="populations" style="font-size:18px;"><b>Select a group of cell populations:</b></label>
+      <br>
+      <select name="populations" id="populations">
+        <option>Lineage</option>
+        <option>Patient</option>
+        <option selected="selected" value="Populations"> Cell Populations</option>
+        <option value="Zone">Prostatic Zone</option>
+      </select>
+    </div>
+    <br>
+    <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
+    <hr>
+    <div>
+      <span style="font-size:16px; font-weight:bold; " >Experimental details:</span>
+      <br>
+      <span style="font-size:16px;">Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can be compared by population identity, cell lineage, patient, or dissected prostatic zone.</span>
+    </div>
+  </div>
+  <div align = "center">
+    <h1 id="label.gene">NO GENE SELECTED</h1>
+    <h2 id="label.lineage"></h2>
+    <div class = "columnF">
+    <h3 id="label.ClusterVis"></h3>
+    <div class = "img">
+    <img id="img.ClusterVis" src=""/>
+    </div>
+    <br>
+    </div>
+    <div class = "columnF">
+    <h3 id="label.Feature"></h3>
+    <div class = "img">
+    <img id="img.Feature" src=""/>
+    </div>
+    <br>
+    </div>
+    <div class = "columnF">
+    <h3 id="label.ViolinBox"></h3>
+    <div class = "img">
+    <img id="img.ViolinBox" src=""/>
+    </div>
+    <br>
+    </div>
+  </div>
+  <hr>
+  <div align = "left">
+    <div><span style="font-size:18px; font-weight:bold; " >Publication found at:</span></div>
+    <div><span style="font-size:16px;" > <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875">Cell Reports</a></span></div>
+    <div><span style="font-size:18px; font-weight:bold;" >Raw data found at:</span></div>
+    <div><span style="font-size:16px;" > <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403">GEO: GSE117403</a></span></div>
+    <div><span style="font-size:16px;" ><a href="https://doi.org/10.25548/W-R8CM">GUDMAP: W-R8CM</a></span></div>
+  </div>
+</body>

content/people/_index.md

+---
+title: "Team Members"
+date: 2019-05-18T20:10:31-05:00
+draft: true
+type: "custom"
+layout: "people"
+---
+

content/people/henry_g.md

+---
+title: "Henry_g"
+date: 2019-05-18T21:34:35-05:00
+draft: true
+name: "Gervaise H. Henry"
+degree: "M.S."
+pic: "henry_g.jpg"
+tit: "Research Technician"
+orcid: "0000-0001-7772-9578"
+weight: "10"
+---
+
+Gervaise obtained his master's degree at American University in 2015. He joined Dr. Strand’s lab in 2015.
\ No newline at end of file

content/people/joseph_d.md

+---
+title: "Joseph_d"
+date: 2019-05-18T21:33:56-05:00
+draft: true
+name: "Diya B. Joseph"
+degree: "Ph.D."
+pic: "joseph_d.jpeg"
+tit: "Postdoctoral Researcher"
+orcid: "0000-0002-0587-9558"
+weight: "4"
+---
+
+Diya obtained her PhD at the University of Wisconsin: Madison in the Vezina Lab. She joined the Dr. Strand's Lab in 2019.
\ No newline at end of file

content/people/malewska_a.md

+---
+title: "Malewska_a"
+date: 2019-05-18T21:34:09-05:00
+draft: true
+name: "Alicia Malewska"
+degree: "M.S."
+pic: "malewska_a.jpg"
+tit: "Research Technician"
+orcid: ""
+weight: "5"
+---
+
+Alicia obtained her master's degree at UT Dallas in 2005 and has worked at UT Southwestern ever since. She joined Dr. Strand’s lab in 2014.
\ No newline at end of file

content/people/mcalanis_c.md

+---
+title: "Mcalanis_c"
+date: 2019-06-06T14:38:43-05:00
+draft: true
+name: "Caitlin L. Mcalanis"
+degree: ""
+pic: "mcalanis_c.jpg"
+tit: "STARS Student (2019)"
+orcid: ""
+weight: "15"
+---
+
+Senior at North Forney High School. Caitlin is joining us in the Strand lab for the summer of 2019.
\ No newline at end of file