Merge branch 'develop' into 'master'

Develop

See merge request !9

.gitignore

 
 !.gitkeep
 /public
-/static/images/*
+/static/images/scRNAseq_huPr_D/*
 
 # Created by https://www.gitignore.io/api/git,linux,macos,windows
 # Edit at https://www.gitignore.io/?templates=git,linux,macos,windows

.gitlab-ci.yml

@@ -7,6 +7,7 @@ variables:
 pages:
   script:
   - hugo
+  - hugo deploy aws --maxDeletes -1
   artifacts:
     paths:
     - public

archetypes/people.md

@@ -8,5 +8,7 @@ pic: "NoPic.jpg"
 tit: ""
 orcid: ""
 weight: ""
+current: true
 ---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
 

archetypes/sc_data.md

+---
+title: "{{ replace .Name "-" " " | title }}"
+description: "Single-Cell RNA-sequencing Data"
+name: "(PENDING)"
+date: {{ .Date }}
+draft: true
+weight: ""
+type: "custom"
+layout: ""
+---
+
+**PENDING**
\ No newline at end of file

config.toml

-baseurl = "https://www.StrandLab.net/"
+baseurl = "http://www.strandlab.net.s3-website.us-east-2.amazonaws.com/"
 title = "Strand Lab"
 author = "Gervaise H. Henry"
+theme = "blackburn"
 # Shown in the side menu
 copyright = "© 2019. All rights reserved."
 canonifyurls = true
@@ -28,45 +29,41 @@ paginate = 10
   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>"
+    pre = "<i class='fas fa-home fa-fw'></i>"
     weight = 1
     identifier = "research"
     url = "/research"
   [[menu.main]]
     name = "People"
-    pre = "<i class='fa fa-user fa-fw'></i>"
+    pre = "<i class='fas fa-user fa-fw'></i>"
     weight = 2
     identifier = "people"
     url = "/people/"
   [[menu.main]]
     name = "Publications"
-    pre = "<i class='fa fa-book fa-fw'></i>"
+    pre = "<i class='fas fa-book fa-fw'></i>"
     weight = 3
     identifier = "publications"
     url = "/publications/"
   [[menu.main]]
     name = "Biorepository"
-    pre = "<i class='fa fa-stethoscope fa-fw'></i>"
+    pre = "<i class='fas 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>"
+    pre = "<i class='fas fa-chart-bar fa-fw'></i>"
     weight = 5
-    identifier = "data"
-    url = "/data"
+    identifier = "sc.data"
+    url = "/sc.data/"
   [[menu.main]]
     name = "Contact"
-    pre = "<i class='fa fa-phone fa-fw'></i>"
+    pre = "<i class='fas fa-phone fa-fw'></i>"
     weight = 6
     url = "/contact"
 
@@ -78,4 +75,11 @@ paginate = 10
   twitter = "strand_lab"
 
   # Techie
-  biohpcgitlab = "StrandLab/"
\ No newline at end of file
+  biohpcgitlab = "StrandLab/"
+
+[deployment]
+  order = [".jpg$", ".gif$"]
+
+  [[deployment.targets]]
+    name = "aws"
+    URL = "s3://www.strandlab.net?region=us-east-2"
\ 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
+draft: false
+type: "custom"
+layout: "contact"
 ---
-<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/henry_g.md

 ---
 title: "Henry_g"
 date: 2019-05-18T21:34:35-05:00
-draft: true
+draft: false
 name: "Gervaise H. Henry"
 degree: "M.S."
 pic: "henry_g.jpg"
-tit: "Research Technician"
+tit: "Computatonal Biologist"
 orcid: "0000-0001-7772-9578"
 weight: "10"
+current: true
 ---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
 
-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
+Gervaise obtained his master's degree at American University in 2015. He joined Dr. Strand's lab in 2015. His previous experience involved the utilization of a diverse set of molecular techniques to investigate cancer biology. He also has a strong background in early-stage drug discovery, including the use of lab robotics. After a very successful fellowship with UT Southwestern Bioinformatics Department's Bioinformatics Core Facility (BICF), he transitioned to a more computational role in the lab. He is responsible for the analysis of sequencing, in particular single-cell RNA-sequencing analysis. He also builds pipelines for automated analysis, and tools for easy data exploration.
\ 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"
+draft: false
+name: "Diya Binoy Joseph"
 degree: "Ph.D."
-pic: "joseph_d.jpeg"
+pic: "joseph_d.jpg"
 tit: "Postdoctoral Researcher"
 orcid: "0000-0002-0587-9558"
 weight: "4"
+current: true
 ---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
 
-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
+Diya joined the Strand lab in January 2019 as a postdoctoral researcher. Prior to this, she received her Bachelor's degree in Biotechnology from the National Institute of Technology, Calicut in India in 2013 and a Ph.D in Cellular and Molecular Biology in December 2018 from the University of Wisconsin-Madison. During her doctoral studies in Dr. Chad Vezina's lab, Diya studied the development of the lower urinary tract with special emphasis on the role of DNA methylating enzymes during prostate development. During her doctoral studies, Diya was part of a collaborative project with Dr. Strand to produce the first cellular anatomy of the normal human prostate at single cell resolution. This collaboration led to her current position as a postdoctoral researcher in the Strand lab where she studies Benign Prostatic Hyperplasia (BPH) and the role of novel club and hillock urethral cell types in BPH growth.
\ No newline at end of file

content/people/malewska_a.md

 ---
 title: "Malewska_a"
 date: 2019-05-18T21:34:09-05:00
-draft: true
+draft: false
 name: "Alicia Malewska"
 degree: "M.S."
 pic: "malewska_a.jpg"
 tit: "Research Technician"
 orcid: ""
 weight: "5"
+current: true
 ---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
 
 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
+draft: false
 name: "Caitlin L. Mcalanis"
 degree: ""
 pic: "mcalanis_c.jpg"
 tit: "STARS Student (2019)"
 orcid: ""
 weight: "15"
+current: false
 ---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
 
-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
+While a senior at North Forney High School, Caitlin joined us in the Strand lab for the summer of 2019.
\ No newline at end of file

content/people/strand_d.md

 ---
 title: "Strand_d"
 date: 2019-05-18T21:33:29-05:00
-draft: true
+draft: false
 name: "Douglas W. Strand"
 degree: "Ph.D."
 pic: "strand_d.jpg"
 tit: "Assistant Professor of Urology"
 orcid: "0000-0002-0746-927X"
 weight: "1"
+current: true
 ---
+<!--Weight: 1=PI 2=Faculty 3=Instructors 4=PostDocs 5=Techs 6=GradStudents 10=Other 15=Interns-->
 
-Doug obtained his Ph.D. with David Rowley at Baylor College of Medicine in the department of Molecular and Cellular Biology. He did a postdoctoral fellowship at Vanderbilt University under Simon Hayward. He joined the faculty of UTSW in 2014.
\ No newline at end of file
+Doug obtained his Ph.D. with David Rowley at Baylor College of Medicine in the department of Molecular and Cellular Biology. He did a postdoctoral fellowship at Vanderbilt University under Simon Hayward. He joined the faculty of UTSW in 2014 and works closely with the clinicians in the Urology department to characterize the cellular pathogenesis of diseases of the human lower urinary tract.
\ No newline at end of file

content/publications/2010_curmolmed.md

 ---
 title: "2010_curmolmed"
 date: 2019-05-19T13:28:53-05:00
-draft: true
+draft: false
 pname: "Perspectives on tissue interactions in development and disease."
 pauthor: "Strand DW. et al"
 pjournal: "Curr. Mol. Med."

content/publications/2011_differentiation.md

 ---
 title: "2011_differentiation"
 date: 2019-05-19T13:24:23-05:00
-draft: true
+draft: false
 pname: "PPARγ: a molecular link between systemic metabolic disease and benign prostate hyperplasia."
 pauthor: "Jiang M. et al"
 pjournal: "Differentiation"

content/publications/2013_amjpathol.md

 ---
 title: "2013_amjpathol"
 date: 2019-05-19T13:20:11-05:00
-draft: true
+draft: false
 pname: "Deficiency in metabolic regulators PPARγ and PTEN cooperates to drive keratinizing squamous metaplasia in novel models of human tissue regeneration"
 pauthor: "Strand DW. et al"
 pjournal: "Am. J. Pathol."