updating to django 1.11.6

.gitignore

@@ -3,3 +3,6 @@
 
 # log
 karrlab/log/
+
+#temporary files
+tmp/

karrlab/core/apps.py

@@ -0,0 +1,14 @@
+""" Core app configuration
+:Author: Jonathan Karr <[email protected]>
+:Date: 2017-10-26
+:Copyright: 2017, Karr Lab
+:License: MIT
+"""
+
+from __future__ import unicode_literals
+from django.apps import AppConfig
+
+
+class CoreConfig(AppConfig):
+    name = 'core'
+    verbose_name = 'core'

karrlab/templates/alumni.html → karrlab/core/templates/alumni.html

@@ -8,10 +8,13 @@
 <div class="bio">
 
 	<h3>Alumni</h3>
+    {% include "people/anwar.html" %}
     {% include "people/barrette.html" %}
     {% include "people/deming.html" %}
 	{% include "people/gossel.html" %}
     {% include 'people/miravet.html' %}
+    {% include "people/rodriguez.html" %}
+    {% include 'people/roy.html' %}
     {% include "people/sun.html" %}
     {% include "people/wu.html" %}
 </div>

karrlab/templates/base.html → karrlab/core/templates/base.html

@@ -46,16 +46,17 @@ <h1 class="title">Karr Systems Biology Lab</h1>
                 <aside class="left-off-canvas-menu">
                     <ul class="off-canvas-list">
                         <li><label>Karr Systems Biology Lab</label></li>
-                        <li><a href="{% url index %}">Home</a></li>
-                        <li><a href="{% url research %}">Research</a></li>
-                        <li><a href="{% url resources %}">Resources</a></li>
-                        <li><a href="{% url publications %}">Publications</a></li>
-                        <li><a href="{% url news %}">News</a></li>
-                        <li><a href="{% url press %}">Press</a></li>
-                        <li><a href="{% url funding %}">Funding</a></li>
-                        <li><a href="{% url people %}">People</a></li>
-                        <li><a href="{% url join %}">Join us</a></li>
-                        <li><a href="{% url contact %}">Contact</a></li>
+                        <li><a href="{% url 'index' %}">Home</a></li>
+                        <li><a href="{% url 'research' %}">Research</a></li>
+                        <li><a href="{% url 'resources' %}">Resources</a></li>
+                        <li><a href="{% url 'publications' %}">Publications</a></li>
+						<li><a href="{% url 'video' %}">Videos</a></li>
+                        <li><a href="{% url 'news' %}">News</a></li>
+                        <li><a href="{% url 'press' %}">Press</a></li>
+                        <li><a href="{% url 'funding' %}">Funding</a></li>
+                        <li><a href="{% url 'people' %}">People</a></li>
+                        <li><a href="{% url 'join' %}">Join us</a></li>
+                        <li><a href="{% url 'contact' %}">Contact</a></li>
                     </ul>
                 </aside>
 
@@ -66,16 +67,17 @@ <h1 class="title">Karr Systems Biology Lab</h1>
                     <div class="top-bar row show-for-medium-up">
                         <div class="small-12 columns">
                             <dl class="sub-nav">
-                                <dd{% if section == "" %} class="active"{% endif %}><a href="{% url index %}">Home</a></dd>
-                                <dd{% if section == "research" %} class="active"{% endif %}><a href="{% url research %}">Research</a></dd>
-                                <dd{% if section == "resources" %} class="active"{% endif %}><a href="{% url resources %}">Resources</a></dd>
-                                <dd{% if section == "publications" %} class="active"{% endif %}><a href="{% url publications %}">Publications</a></dd>
-                                <dd{% if section == "news" %} class="active"{% endif %}><a href="{% url news %}">News</a></dd>
-                                <dd{% if section == "press" %} class="active"{% endif %}><a href="{% url press %}">Press</a></dd>
-                                <dd{% if section == "funding" %} class="active"{% endif %}><a href="{% url funding %}">Funding</a></dd>
-                                <dd{% if section == "people" %} class="active"{% endif %}><a href="{% url people %}">People</a></dd>
-                                <dd{% if section == "join" %} class="active"{% endif %}><a href="{% url join %}">Join us</a></dd>
-                                <dd{% if section == "contact" %} class="active"{% endif %}><a href="{% url contact %}">Contact</a></dd>
+                                <dd{% if section == "" %} class="active"{% endif %}><a href="{% url 'index' %}">Home</a></dd>
+                                <dd{% if section == "research" %} class="active"{% endif %}><a href="{% url 'research' %}">Research</a></dd>
+                                <dd{% if section == "resources" %} class="active"{% endif %}><a href="{% url 'resources' %}">Resources</a></dd>
+                                <dd{% if section == "publications" %} class="active"{% endif %}><a href="{% url 'publications' %}">Publications</a></dd>
+								<dd{% if section == "video" %} class="active"{% endif %}><a href="{% url 'video' %}">Videos</a></dd>
+                                <dd{% if section == "news" %} class="active"{% endif %}><a href="{% url 'news' %}">News</a></dd>
+                                <dd{% if section == "press" %} class="active"{% endif %}><a href="{% url 'press' %}">Press</a></dd>
+                                <dd{% if section == "funding" %} class="active"{% endif %}><a href="{% url 'funding' %}">Funding</a></dd>
+                                <dd{% if section == "people" %} class="active"{% endif %}><a href="{% url 'people' %}">People</a></dd>
+                                <dd{% if section == "join" %} class="active"{% endif %}><a href="{% url 'join' %}">Join us</a></dd>
+                                <dd{% if section == "contact" %} class="active"{% endif %}><a href="{% url 'contact' %}">Contact</a></dd>
                             </dl>
                         </div>
                     </div>

karrlab/core/templates/join.html

@@ -0,0 +1,58 @@
+{% extends "joinJob.html" %}
+
+{% load static %}
+
+{% block head_title %}{{ block.super }} :: Join us{% endblock %}
+{% block page_title %}Join us{% endblock %}
+
+
+{% block job_details %}
+<div class="area">
+  	<h4>Joining our team</h4>
+  	<p>We're always looking for great people to join our team. Please contact Jonathan to explore opportunities to work with us.</p>
+</div>
+
+<div class="area">
+  	<h4>Open positions</h4>
+
+    <!--<p>We do not currently have any open positions.</p>-->
+
+    <p>Currently, we are looking for additional team members to develop whole-cell models and whole-cell modeling tools:
+      <ul class="inpara">
+          <li><a href="{% url 'join20171002Scientist' %}">Postdoctoral Fellow, Scientist, or graduate student in human whole-cell modeling</a> <a href="{% get_static_prefix %}/doc/jobs/2017-10-02-Scientist.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20171002Engineer' %}">Postdoctoral Fellow, Software Engineer, or graduate sudent in online simulation and visualization</a> <a href="{% get_static_prefix %}/doc/jobs/2017-10-02-Engineer.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20171002Undergrad' %}">Undergraduate or Master's Research Assistant</a> <a href="{% get_static_prefix %}/doc/jobs/2017-10-02-Undergrad.pdf"><i class="fi-print" title="PDF"></i></a></li>
+
+          {% comment %}
+          <li><a href="{% url 'join20170812Scientist' %}">Postdoctoral Fellow or Scientist in human whole-cell modeling</a> <a href="{% get_static_prefix %}/doc/jobs/2017-08-12-Scientist.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20170316PostdoctoralFellow' %}">Postdoctoral Fellow</a> <a href="{% get_static_prefix %}/doc/jobs/2017-03-16-Postdoctoral-Fellow.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20170316SoftwareEngineer' %}">Software Engineer</a> <a href="{% get_static_prefix %}/doc/jobs/2017-03-16-Software-Engineer.pdf"><i class="fi-print" title="PDF"></i></a></li>          
+          <li><a href="{% url 'join20170316StudentResearchAssistant' %}">Undergraduate or Master Summer Research Assistant</a> <a href="{% get_static_prefix %}/doc/jobs/2017-03-16-Student-Research-Assistant.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20160622PostdoctoralFellowBacteria' %}">Postdoctoral Fellow in bacterial whole-cell modeling</a> <a href="{% get_static_prefix %}/doc/jobs/2016-06-22-Postdoctoral-Fellow-Bacteria.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20160622PostdoctoralFellowHuman' %}">Postdoctoral Fellow in human whole-cell modeling</a> <a href="{% get_static_prefix %}/doc/jobs/2016-06-22-Postdoctoral-Fellow-Human.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20160622PostdoctoralFellowMethods' %}">Postdoctoral Fellow or Engineer in high-performance whole-cell simulation</a> <a href="{% get_static_prefix %}/doc/jobs/2016-06-22-Postdoctoral-Fellow-Methods.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20160622PostdoctoralFellowGenomics' %}">Postdoctoral Fellow in integrating systems dynamical modeling and genomics/bioinformatics</a> <a href="{% get_static_prefix %}/doc/jobs/2016-06-22-Postdoctoral-Fellow-Genomics.pdf"><i class="fi-print" title="PDF"></i></a></li>      
+          <li><a href="{% url 'join20150317ScientistHuman' %}">Postdoctoral Fellow or Senior Scientist in human whole-cell modeling</a> <a href="{% get_static_prefix %}/doc/jobs/2015-03-17-Scientist-Human.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20150317ScientistBacteria' %}">Postdoctoral Fellow or Senior Scientist in bacterial whole-cell modeling</a> <a href="{% get_static_prefix %}/doc/jobs/2015-03-17-Scientist-Bacteria.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          <li><a href="{% url 'join20150317Engineer' %}">Biomedical Software Developer in whole-cell modeling</a> <a href="{% get_static_prefix %}/doc/jobs/2015-03-17-Engineer.pdf"><i class="fi-print" title="PDF"></i></a></li>
+          {% endcomment %}        
+      </ul>
+    </p>
+</div>
+
+<div class="area">
+  	<h4>Desired skills/experience</h4>
+  	<p>
+      Because whole-cell modeling is highly interdisciplinary, we're looking for people with a broad range of skills and experience. Applicants with related experience are also encouraged to apply.
+    	<ul class="inpara">
+            <li>PhD, MS, or BS in computational biology or related field;</li>
+          	<li>Strong experience dynamical modeling, genome-scale modeling, cell biology, genomics, bioinformatics,</li> biochemistry, physics, mathematics, computer science, and/or software engineering;</li>
+          	<li>Deep commitment to innovation and a strong desire to tackle the most challenging problems;</li>
+          	<li>Abilities to solve challenging problems by thinking creatively, integrating diverse concepts, and pushing through barriers;</li>
+          	<li>Passion for transforming bioengineering and medicine;</li>
+          	<li>Excellent oral and written communication skills; and</li>
+          	<li>Abilities to work independently and within a team.</li>
+      	</ul>
+  	</p>
+</div>
+{% endblock %}

karrlab/core/templates/join/2017-08-12-Scientist.html

@@ -0,0 +1,35 @@
+{% extends "joinJob.html" %}
+
+{% load static %}
+
+{% block head_title %}{{ block.super }} :: Join us :: Postdoctoral Fellow or Senior Scientist in human whole-cell modeling{% endblock %}
+{% block page_title %}Postdoctoral Fellow or Senior Scientist in human whole-cell modeling{% endblock %}
+{% block page_pdf %}<a href="{% get_static_prefix %}/doc/jobs/2017-08-12-Scientist.pdf"><i class="fi-print" title="PDF"></i></a>{% endblock %}
+
+{% block job_details %}
+<div class="area">
+	<h4>Responsibilities</h4>
+  <p>The scientist will help develop the first whole-cell model of a human embryonic stem cell and use the model to gain insights into pluripotency maintenance among other fundamental cell behaviors. This will include aggregating and organizing experimental data to build models, designing models, calibrating models, validating models, analyzing simulation results, and using models to generate new hypotheses. The scientist will also have many opportunities to contribute to the development of new whole-cell modeling methods and tools. The scientist will work closely with our team at Mount Sinai, including our experimental collaborators Profs. Marc Birtwistle <a href="labs.icahn.mssm.edu/birtwistlelab/"><i class="fi-link"></i></a> and Jianlong Wang <a href="http://www.stemcellwanglab.com/"><i class="fi-link"></i></a>.</p>
+</div>
+
+<div class="area">
+	<h4>Desired skills/experience</h4>
+  <p>Whole-cell modeling is a highly challenging and interdisciplinary problem. Consequently, we are looking for creative scientists with strong experience in both computational science and biology who want to work with an interdiscplinary team. The ideal candidate has the following skills and experience. We also encourage applicants with related experience to apply.
+  <ul class="inpara">
+        <li>PhD in computational biology or related field;</li>
+        <li>Strong experience in dynamical and/or genome-scale modeling;</li>
+        <li>Broad knowledge of cell biology, genomics, mathematics, and computer programming;</li>
+        <li>Deep commitment to innovation and desire to tackle the most challenging problems;</li>
+        <li>Abilities to solve challenging problems by thinking creatively, integrating diverse concepts, and pushing through barriers;</li>
+        <li>Passion for transforming bioengineering and medicine;</li>
+        <li>Excellent oral and written communication skills; and</li>
+        <li>Abilities to work independently and within a team.</li>
+    </ul>
+  </p>
+</div>
+
+<div class="area">
+	<h4>Funding and duration</h4>
+  <p>This position is supported by a five-year NIGMS NIGMS Maximizing Investigators' Research Award (MIRA) award.<p>
+</div>
+{% endblock %}

karrlab/core/templates/join/2017-10-02-Engineer.html

@@ -0,0 +1,30 @@
+{% extends "joinJob.html" %}
+
+{% load static %}
+
+{% block head_title %}{{ block.super }} :: Join us :: Postdoctoral Fellow, Software Engineer, or PhD student in online simulation and visualization{% endblock %}
+{% block page_title %}Postdoctoral Fellow, Software Engineer, or PhD student in online simulation and visualization{% endblock %}
+{% block page_pdf %}<a href="{% get_static_prefix %}/doc/jobs/2017-10-02-Engineer.pdf"><i class="fi-print" title="PDF"></i></a>{% endblock %}
+
+{% block job_details %}
+<div class="area">
+	<h4>Responsibilities</h4>
+  <p>To help enable whole-cell models, the candidate will help develop new tools for simulating models and visualizing simulation results online. This will include developing a universal systems biology simulator that is capable of executing a wide range of simulations including steady-state, logical, deterministic kinetic, stochastic kinetic, and spatial simulations; a repository for simulation results; a system for large-scale analysis of simulation results; and tools for visually analyzing simulation results in the context of biologically intuitive diagrams. Importantly, all of these tools will be web-based to enable researchers to collaboratively build and simulate models, as well as to enable journal reviewers and readers to simulate reported models. The candidate will work with our team at Mount Sinai, as well as with our collaborators at the University of Washington (Herbert Sauro <a href="http://sys-bio.org"><i class="fi-link"></i></a> and John Gennari <a href="http://faculty.washington.edu/gennari/"><i class="fi-link"></i></a>), the University of Connecticut Health Center (Ion Moraru <a href="http://facultydirectory.uchc.edu/profile?profileId=Moraru-Ion"><i class="fi-link"></i></a>, Jim Schaff <a href="http://facultydirectory.uchc.edu/profile?profileId=Schaff-James"><i class="fi-link"></i></a>, and Michael Blinov <a href="http://apache.cam.uchc.edu/mblinov/"><i class="fi-link"></i></a>), and the University of Auckland (David Nickerson <a href="https://unidirectory.auckland.ac.nz/profile/dnic019"><i class="fi-link"></i></a>) and our partner journals. The candidate would also have many opportunities to work with our team to build and analyze models.
+</div>
+
+<div class="area">
+	<h4>Desired skills/experience</h4>
+  <p>Whole-cell modeling is a highly interdisciplinary problem. Consequently, we're looking for team members with a broad range of skills and experience. The ideal candidate has the following skills. Applicants with related experience are also encouraged to apply.
+  <ul class="inpara">
+        <li>BS, MS, or PhD in computer science, applied math, or a related field;</li>
+        <li>Strong experience in modeling, software engineering, and/or visualization;</li>
+        <li>Deep commitment to innovation and desire to tackle the most challenging problems;</li>
+        <li>Abilities to solve challenging problems by thinking creatively, integrating diverse concepts, and pushing through barriers;</li>
+        <li>Passion for transforming bioengineering and medicine;</li>
+        <li>Excellent oral and written communication skills; and</li>
+        <li>Abilities to work independently and within a team.</li>
+    </ul>
+  </p>
+</div>
+
+{% endblock %}

karrlab/core/templates/join/2017-10-02-Scientist.html

@@ -0,0 +1,31 @@
+{% extends "joinJob.html" %}
+
+{% load static %}
+
+{% block head_title %}{{ block.super }} :: Join us :: Postdoctoral Fellow, Scientist, or graduate student in human whole-cell modeling{% endblock %}
+{% block page_title %}Postdoctoral Fellow, Scientist, or graduate student in human whole-cell modeling{% endblock %}
+{% block page_pdf %}<a href="{% get_static_prefix %}/doc/jobs/2017-10-02-Scientist.pdf"><i class="fi-print" title="PDF"></i></a>{% endblock %}
+
+{% block job_details %}
+<div class="area">
+	<h4>Responsibilities</h4>
+  <p>The candidate will help develop the first whole-cell model of a human embryonic stem cell and use the model to gain insights into pluripotency maintenance among other fundamental cell behaviors. This will include aggregating and organizing experimental data to build models, designing models, calibrating models, validating models, analyzing simulation results, and using models to generate new hypotheses. The candidate will also have many opportunities to contribute to the development of new whole-cell modeling methods and tools. The candidate will work closely with our team at Mount Sinai.</p>
+</div>
+
+<div class="area">
+	<h4>Desired skills/experience</h4>
+  <p>Whole-cell modeling is a highly challenging and interdisciplinary problem. Consequently, we are looking for creative scientists with strong experience in both computational science and biology who want to work with an interdisciplinary team. The ideal candidate has the following skills and experience. We also encourage applicants with related experience to apply.
+  <ul class="inpara">
+        <li>BS, MS, or PhD in computational biology or related field;</li>
+        <li>Strong experience in dynamical and/or genome-scale modeling;</li>
+        <li>Broad knowledge of cell biology, genomics, mathematics, and computer programming;</li>
+        <li>Deep commitment to innovation and desire to tackle the most challenging problems;</li>
+        <li>Abilities to solve challenging problems by thinking creatively, integrating diverse concepts, and pushing through barriers;</li>
+        <li>Passion for transforming bioengineering and medicine;</li>
+        <li>Excellent oral and written communication skills; and</li>
+        <li>Abilities to work independently and within a team.</li>
+    </ul>
+  </p>
+</div>
+
+{% endblock %}