Merge branch 'main' of github.com:irisdyoung/irisdyoung.github.io

.gitignore

@@ -1,3 +1,4 @@
 .jekyll-metadata
+jekyll_serve_cmd
 Gemfile*
 _site/*

Gemfile

@@ -1,4 +1,3 @@
 source "https://rubygems.org"
-gem "github-pages", "~> 225", group: :jekyll_plugins
-
-gem "webrick", "~> 1.7"
+gem "github-pages", group: :jekyll_plugins
+gem "webrick"

Gemfile.lock

@@ -225,13 +225,15 @@ GEM
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.3.6)
+    mini_portile2 (2.8.1)
     minima (2.5.1)
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
     minitest (5.15.0)
     multipart-post (2.1.1)
-    nokogiri (1.13.4-x86_64-darwin)
+    nokogiri (1.13.4)
+      mini_portile2 (~> 2.8.0)
       racc (~> 1.4)
     octokit (4.22.0)
       faraday (>= 0.9)
@@ -276,8 +278,8 @@ PLATFORMS
   x86_64-darwin-21
 
 DEPENDENCIES
-  github-pages (~> 225)
-  webrick (~> 1.7)
+  github-pages
+  webrick
 
 BUNDLED WITH
    2.3.12

_config.yml

@@ -1,5 +1,6 @@
 title: "Iris Young"
-description: "This is my homepage. Hello! I am 70% coffee by volume."
+description: "Personal website for Iris Young"
+url: https://irisdyoung.github.io/
 
 permalink: pretty
 markdown: kramdown

_includes/footer.html

@@ -2,13 +2,13 @@
     <div class="footer">
         <div class="container">
             <ul class="list-inline">
-            <li class="footer-inverse"><a href="https://twitter.com/irisdyoung"><i class="fa fa-twitter fa-2x"></i></a></li>
+            <li class="footer-inverse"><a href="https://struct.bio/@irisvirus"><i class="fa fa-mastodon fa-2x"></i></a></li>
             <li class="footer-inverse"><a href="mailto:irisdyoung@gmail.com"><i class="fa fa-envelope fa-2x"></i></a></li>
             <li class="footer-inverse"><a href="https://github.com/irisdyoung"><i class="fa fa-github-alt fa-2x"></i></a></li>
-            <li class="footer-inverse"><a href="https://cci.lbl.gov/"><i class="fa fa-code fa-2x"></i></a></li>
-	    <li class="footer-inverse"><a href="https://cci.lbl.gov/docs/cctbx/"><i class="fa fa-code fa-2x"></i></a></li>
-	    <li class="footer-inverse"><a href="https://dials.github.io/"><i class="fa fa-code fa-2x"></i></a></li>
-	    <li class="footer-inverse"><a href="https://www.exascaleproject.org/research-project/exafel/"><i class="fa fa-code fa-2x"></i></a></li>
+            <!--<li class="footer-inverse"><a href="https://cci.lbl.gov/"><i class="fa fa-code fa-2x"></i></a></li>
+	        <li class="footer-inverse"><a href="https://cci.lbl.gov/docs/cctbx/"><i class="fa fa-code fa-2x"></i></a></li>
+	        <li class="footer-inverse"><a href="https://dials.github.io/"><i class="fa fa-code fa-2x"></i></a></li>-->
+	        <li class="footer-inverse"><a href="https://www.exascaleproject.org/research-project/exafel/"><i class="fa fa-code fa-2x"></i></a></li>
             </ul>
         </div>
     </div>

_includes/header.html

@@ -14,19 +14,13 @@
     <link href="/static/css/syntax.css" rel="stylesheet">
     <link href="/static/css/custom.css" rel="stylesheet">
 
+    <link rel="icon" type="image/png" href="/favicon.png">
+
+
     {% if page.group == 'blog' or page.group == 'home' %}
     <link rel="alternate" type="application/atom+xml" title="blog feed" href="/blog.xml">
     {% endif %}
 
-    <link rel="icon" type="image/png" href="/static/img/favicomatic/favicon-32x32.png" sizes="32x32" />
-    <link rel="icon" type="image/png" href="/static/img/favicomatic/favicon-16x16.png" sizes="16x16" />
-    <link rel="icon" type="image/png" href="/static/img/favicomatic/favicon-128.png" sizes="128x128" />
-
-    <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
-    <!--[if lt IE 9]>
-      <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-    <![endif]-->
-
     <script>
       (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
       (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),

_layouts/default.html

@@ -1,7 +1,5 @@
 {% include header.html %}
-<div class="container px-2 max-width: 100%">
-    <img class="img-fluid mx-auto d-block" src="/static/img/art/spectrum.png" alt="Rainbow generated from a sequence of sciencey photographs">
-</div>
+<img class="img-fluid max-width:100%" src="/static/img/art/Rainbow_from_photos.png" alt="Rainbow generated from a sequence of photographs">
 
 {{content}}
 

_layouts/home.html

@@ -1,11 +1,13 @@
 {% include header.html %}
 
-<div class="container px-2 max-width: 100%">
-    <img class="img-fluid mx-auto d-block" src="/static/img/art/spectrum.png" alt="Rainbow generated from a sequence of sciencey photographs">
-    <div class="row">
+
+<img class="img-fluid" src="/static/img/art/Rainbow_from_photos.png" alt="Rainbow generated from a sequence of photographs">
+<div class="container-fluid">
+    <div class="row-fluid">
         <div class="jumbotron-fluid">
        	    {{ content }}
         </div>
     </div>
 </div>
+
 {% include footer.html %}

_publications/20230830_diaz.md

@@ -0,0 +1,46 @@
+---
+title: "Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase"
+authors: "Díaz RE, Ecker AK, Correy GJ, Asthana P, **Young ID**, Faust B, Thompson MC, Seiple IB, Van Dyken SJ, Locksley RM, Fraser JS." # use * for co-first
+journal: 'eLife'
+pub_date: '2023-08-30'
+image: '/static/img/pub/2023_diaz.png'
+biorxiv: 2023.06.03.542675
+doi: 10.1101/2023.06.03.542675
+pdbs:
+- 8FG5
+- 8FG7
+- 8GCA
+- 8FRC
+- 8FR9
+- 8FRB
+- 8FRD
+- 8FRG
+- 8FRA
+zenodo:
+- code: 8250616
+  description: Kinetic properties of mAMCase catalytic domain at various pH
+- code: 7967930
+  description: Characterization of mAMCase sugar-binding subsites
+- code: 7905828
+  description: Asp138 orientation correlates with ligand subsite occupancy
+- code: 7905863
+  description: pKa of GH18 chitinases in the inactive and active conformation
+- code: 7758821
+  description: "10 ns Molecular Dynamics simulations of mAMCase at pH 2.0 and 6.5 in complex with GlcNAc6"
+- code: 7967958
+  description: Proposed catalytic mechanism of mAMCase
+- code: 7905944
+  description: Crystallization conditions of apo and holo mAMCase
+- code: 7967978
+  description: Overview of key residues for mAMCase activity
+- code: 7967954
+  description: Protein-ligand interactions between mAMCase and chitin
+- code: 7758815
+  description: Ringer analysis of catalytic triad confirms alternative Asp138 conformations
+labs:
+- fraser: yes
+- locksley: yes
+- seiple: yes
+- thompson: yes
+- vandyken: yes
+---

_publications/_template.md

@@ -56,6 +56,7 @@ labs:
 - hogbom: yes
 - instruct_eric: yes
 - jcap: yes
+- locksley: yes
 - meents: yes
 - messinger: yes
 - mfx: yes
@@ -74,6 +75,7 @@ labs:
 - sawaya: yes
 - schlichting: yes
 - schofield: yes
+- seiple: yes
 - soltis: yes
 - ssrl: yes
 - stan: yes
@@ -82,8 +84,10 @@ labs:
 - tawfik: yes
 - thompson: yes
 - unicat: yes
+- vandyken: yes
 - vierstra: yes
 - wagner: yes
+- wall: yes
 - weik: yes
 - weis: yes
 - wernet: yes

index.md

@@ -6,25 +6,23 @@ group: home
 
 <div class="row">
 <div class="jumbotron h-100">
-<div class="col-sm-5">
+<div class="col-sm-6">
 {: .display-4}
 <br>
 
-![Penrose tiling coffee art](static/img/art/coffee_penrose_03.png){:style="width: auto; max-width: 90%;"}
+![my photogenic cat Rory against a background of art](static/img/art/Rory_headboard_and_art.jpg){:style="width: auto; max-width: 90%; margin:0"}
 </div>
 <div class="col">
 
 Hello! You have found Iris' homepage. It is probably not up to date, but maybe you can find something useful here anyway.
 {: .welcomefont}
 
-Iris works as a project scientist in the [Sauter group](https://biosciences.lbl.gov/profiles/nicholas-sauter/) at [Lawrence Berkeley National Laboratory](https://www.lbl.gov/). He is focusing on two main projects right now, the [(sp)ectral (re)solution of (a)nomalous (d)ispersion (SPREAD)](http://dx.doi.org/10.1107/S2059798320000418) project and the [(exa)scale computing for X-ray (f)ree (e)lectron (l)aser diffraction experiments (ExaFEL)](https://www.exascaleproject.org/research-project/exafel/) project. Essentially, these involve the development of new computational capabilities to meet instrumental demands such as the megahertz pulse rate of LCLS II and to leverage the awesome potential of these experiments.
+Iris works as a project scientist in the [Sauter group](https://biosciences.lbl.gov/profiles/nicholas-sauter/) at [Lawrence Berkeley National Laboratory](https://www.lbl.gov/). He is focusing on two interconnected projects right now, the [(sp)ectral (re)solution of (a)nomalous (d)ispersion (SPREAD)](http://dx.doi.org/10.1107/S2059798320000418) project and the [(exa)scale computing for X-ray (f)ree (e)lectron (l)aser diffraction experiments (ExaFEL)](https://www.exascaleproject.org/research-project/exafel/) project. Essentially, these involve the development of new computational capabilities to meet instrumental demands such as the megahertz pulse rate of LCLS II and to leverage the awesome potential of these experiments.
 {: .welcomefont}
 
-Outside of the lab (and inside too), Iris is a coffee afficionado, student of various languages, avid reader, and companion to a very affectionate cat named Rory. When he has time he also enjoys aikido, pottery, cooking, and hiking. He is queer/trans/nonbinary and uses pronouns he/him, she/her, or they/them.
+Outside of the lab, Iris is a coffee afficionado, student of various languages, avid reader, and companion to a very affectionate cat named Rory. When he has time he also enjoys electronics, fixing stuff, 3d printing, sewing, aikido, pottery, cooking, and hiking. He is queer/trans/nonbinary and uses pronouns he/him, they/them or she/her.
 
-Iris is reachable at [irisdyoung@gmail.com](mailto:irisdyoung@gmail.com). He is also active on [twitter](http://twitter.com/irisdyoung) and has some work on up [github](http://github.com/irisdyoung). Feature requests, bug reports, requests for troubleshooting help, wild ideas, and general inquiries welcome!
-
-<br>
+Iris is reachable at [irisdyoung@gmail.com](mailto:irisdyoung@gmail.com). He is also active on the fediverse via <a rel="me" href="https://struct.bio/@irisvirus">mastodon</a> and has some work on up [github](http://github.com/irisdyoung). All good faith inquiries/requests welcome!
 
 _Fact: Iris is 70% coffee by volume._
 {: .welcomefont}

publications/index.html

@@ -268,6 +268,9 @@ <h5>Core Collaborators and Facilities</h5>
 				{% if lab.jcap %}
 					<li><a href="https://solarfuelshub.org/" alt="JCAP" target="_blank">Joint Center for Artificial Photosynthesis (JCAP)</a></li>
 				{% endif %}
+                {% if lab.locksley %}
+                    <li><a href="https://locksleylab.ucsf.edu/" alt="Locksley lab" target="_blank">Locksley lab @ UCSF</a></li>
+                {% endif %}
 				{% if lab.meents %}
 					<li><a href="https://cid.cfel.de/team/scientific_staff/alke_meents/" alt="Alke Meents" target="_blank">Alke Meents @ DESY/CFEL</a></li>
 				{% endif %}
@@ -322,6 +325,9 @@ <h5>Core Collaborators and Facilities</h5>
 				{% if lab.schofield %}
 					<li><a href="https://schofield.chem.ox.ac.uk/home" alt="Schofield lab" target="_blank">Schofield lab @ Oxford</a></li>
 				{% endif %}
+                {% if lab.seiple %}
+                    <li><a href="https://seiplegroup.ucsf.edu/" alt="Seiple lab" target="_blank">Seiple lab @ UCSF</a></li>
+                {% endif %}
 				{% if lab.slac %}
 					<li><a href="https://www6.slac.stanford.edu/" alt="SLAC" target="_blank">SLAC National Accelerator Laboratory</a></li>
 				{% endif %}
@@ -343,12 +349,18 @@ <h5>Core Collaborators and Facilities</h5>
 				{% if lab.thompson %}
 					<li><a href="https://thompsonlab.science/" alt="Thompson lab" target="_blank">Thompson lab @ UC Merced</a></li>
 				{% endif %}
+                {% if lab.vandyken %}
+                    <li><a href="https://sites.wustl.edu/vandykenlab/" alt="Van Dyken lab" target="_blank">Van Dyken lab @ Washington University in St. Louis</a></li>
+                {% endif %}
 				{% if lab.vierstra %}
 					<li><a href="https://vierstra.genetics.wisc.edu/" alt="Viersrta lab" target="_blank">Vierstra lab @ University of Wisconsin</a></li>
 				{% endif %}
 				{% if lab.wagner %}
 					<li><a href="https://www.diamond.ac.uk/Instruments/Mx/I23/Staff/Wagner.html" alt="Armin Wagner" target="_blank">Armin Wagner @ Diamond</a></li>
 				{% endif %}
+                {% if lab.wall %}
+                    <li><a href="https://public.lanl.gov/mewall/" alt="Michael Wall" target="_blank">Michael Wall @ LANL</a></li>
+                {% endif %}
 				{% if lab.weik %}
 					<li><a href="https://www.ibs.fr/research/research-groups/research-groups/dynamics-and-kinetics-of-molecular-processes-group/?lang=fr" alt="Weik lab" target="_blank">Dynamics and kinetics of molecular processes group (Martin Weik) @ Institut de Biologie Structurale</a></li>
 				{% endif %}