Merge branch 'main' of https://github.com/tbmorgan/scinet-site

_data/navigation.yml

@@ -83,14 +83,14 @@ primary:
           url: /research/working-groups/ag100pest
         - title: Arthropod Genomics
           url: /research/working-groups/arthropods
+        - title: Breeding AI and ML
+          url: /research/working-groups/breeding
         - title: Geospatial Research
           url: /research/working-groups/geospatial
         - title: Microbiome
           url: /research/working-groups/microbiome
         - title: LTAR Phenology
           url: /research/working-groups/LTARphenology
-        - title: Pollinator
-          url: /research/working-groups/pollinator
         - title: Protein Function and Phenotype Prediction
           url: /research/working-groups/proteinfunction
         - title: Translational Omics
@@ -136,8 +136,10 @@ primary:
         url: /opportunities/fellowships
       - title: AI Innovation Fund
         url: /opportunities/ai-innovation/
-      - title: SCINet and AI-COE fellowship proposals
-        url: /opportunities/scinet-aicoe-fellowships
+      - title: Postdoctoral Fellowship Mentor Proposals
+        url: /opportunities/fellowship-mentors
+      - title: Graduate Student Internship Mentor Applications
+        url: /opportunities/internship-mentors
 #      - title: Open Positions
 #        url: /opportunities/open_positions
 

_data/tables/fellowships.csv

@@ -1,16 +1,5 @@
-Opportunity,Location,Keywords,url
-"Computational Tools & Pipeline Development for Metagenomic Data Analysis Fellowship, USDA-ARS-2022-0027","Ames, IA","Metagenomics, Bioinformatics",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0027
-"High Performance Computing and Prediction of Geospatial Dynamics Fellowship, USDA-ARS-2022-0029",TBD,"Geospatial, Times Series Data",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0029
-"USDA-ARS Remote Sensing of Agro-ecosystems & High-performance Computing Fellowship, USDA-ARS-2022-0031","Beltsville, MD","Geosptial, Remote Sensing, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0031
-"USDA-ARS High Performance Computing Fellowship, USDA-ARS-2022-0071",TBD,"Agro-ecosystem dynamics, Natural Language Processing, Remote Sensing, Geospatial",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0071
-"USDA-ARS SCINet AI Machine Learning in Maize Genomics Postdoctoral Fellowship, USDA-ARS-2022-0158","Dubois, ID","Image Analysis, AI, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0158
-"USDA-ARS SCINet Postdoctoral Fellowship in Machine Learning for Influenza A Virus Pandemic Prevention, USDA-ARS-2022-0162","Ames, IA","Genomics, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0162
-"USDA-ARS SCINet Fellowship for Developing AI and ML Techniques to Advance Understanding of How Dietary Patterns Influence Human Health, USDA-ARS-2022-0369","Beltsville, MD","Human Health, Dietary Patterns, AI, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0369
-"USDA-ARS SCINet Postdoctoral Fellowship in AI Methods for Predicting Protein Function and Disease Susceptibility in Crops, USDA-ARS-2022-0436","Stuttgart, AR","Genomics, AI",https://www.zintellect.com/Opportunity/Details/USDA-ARS-2022-0436
-"USDA-ARS SCINet/AI-COE postdoctoral fellowship in AI/Machining Learning for Animal Behavior Research","Boise, ID","Geospatial, ML, AI",https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINET-2023-0202
-"USDA-ARS SCINet/AI-COE postdoctoral fellowship in Using AI to address large, complex datasets in microbiome-based integrated pest management","Colombia, MO","Microbiome Science, Genetics, AI, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2023-0223
-"USDA-ARS SCINet/AI-COE postdoctoral fellowship in Machine Learning to Distinguish Pest from Non-Pest Weevils","College Station, TX","Genomics, Pest Management, Genomics",https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2023-0224
-"USDA-ARS SCINet/AI-COE postdoctoral fellowship in Food Security Agency in Alaska","Tifton, GA","Geospatial, Remote Sensing, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2023-0228
-"USDA-ARS SCINet/AI-COE postdoctoral fellowship in bridging local measurements to management scales using machine learning","Beltsville, MD","Soil Moisture, Hydrology, AI, Geospatial",https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2023-0229
-"USDA-ARS SCINet/AI-COE postdoctoral fellowship in using AI to develop a cross kingdom gene editing tool kit","Colombia, MO","Genomics, AI, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2023-0245
-"USDA-ARS SCINet/AI-COE postdoctoral fellowship in taxon-specific model training to improve accuracy of variant calling in non-model systems","Hilo, HI","Genomics, AI, ML",https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2023-0260
+Opportunity,Location,Deadline,url
+USDA-ARS Postdoctoral Fellowship in Fish Functional Genomics and Epigenetics,"Auburn, AL",2025-01-03 03:00 PM ET,https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2024-0285
+USDA-ARS SCINet/AI-COE Postdoctoral Fellowship in Comparative Chemosensory Genomics of Stored Product Insects,"Manhattan, KS",2025-07-31 03:00 PM ET,https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2024-0299
+USDA-ARS SCINet/AI-COE Postdoctoral Fellowship to Modernize Hydrologic Models for High-Performance Computing,"Temple, Texas",2025-10-25 03:00 PM ET,https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2024-0307
+USDA-ARS SCINet/AI-COE Postdoctoral Fellowship in Fungal Secondary Metabolomes,"Ithaca, New York",2024-10-25 03:00 PM ET,https://www.zintellect.com/Opportunity/Details/USDA-ARS-SCINet-2024-0308

_data/tables/funded_FY22.csv

@@ -0,0 +1,20 @@
+Title,Mentor,Co-mentor(s)
+Developing tools for the real-time monitoring and query of all the world's publicly available sequence data.,Adam Rivers,
+Determining the structure and function of proteins of foodborne and plant pathogens using Alphafold2 and top-down proteomic analysis,Clifton K. Fagerquist,
+AI-driven phenotype extraction from UAS imagery for crop genetics and breeding,Jacob Washburn,"Alisa Coffin, Max Feldman"
+Machine learning approaches to gain structural and functional insights of genes regulating climate adaptability,Carson Andorf,Taner Sen
+Inferring Protein Function for Enhanced Breeding using Machine Learning and Protein Structure Prediction,Taner Sen,Carson Andorf
+A MATLAB toolbox for dynamic prediction of meteorological drought across Southern Great Plains,Daniel Moriasi,Ali Mirchi
+Optimization of AI-based microscope image analysis with the Blackbird imaging robot,Lance Cadle-Davidson,Yu Jiang
+Automated Detection of Insect Species in Food and Processing Environments using Artificial Intelligence,Paul R Armstrong,Lester Pordesimo
+Improving the accuracy and scope of machine learning tools for camera trap-based ecological data analysis across US grazinglands,Hailey Wilmer,
+"A broadly deployable deep learning workflow for image feature identification, segmentation, and data extraction.",Devin A Rippner,"Jeff Neyhart , Kayla Altendorf, Garett Heineck, Andrew McElrone"
+An AI approach for discovering novel blast disease resistance sources in rice.,Jeremy Edwards,Yulin Jia
+Predicting interspecies transmission of influenza A virus from swine to humans with machine learning,Tavis Anderson,Amy Vincent
+Modeling the Spread and Adaptation of Stored-Product Insect Pests in the Face of Climate Change,Alison Gerken,Rob Morrison
+Using AI to Analyze Climate Effects on Crop Performance,Xianran Li,
+AI/ML and Deep Learning to Enhance Understanding of Dietary Patterns that Promote Human Health,David Baer,Lauren O'Connor
+The evolutionary genomics of Macrophomina phaseolina.,Peter Montgomery Henry,
+Spatial multi-criterion optimization of agricultural ecosystem services at the landscape scale,Sarah Goslee,
+Application of machine learning in livestock genomics,George Liu,
+Determining the pervasiveness of hybridization and introgression in agriculture and the driving mechanisms,Christopher Owen,

_data/tables/funded_FY24.csv

@@ -0,0 +1,6 @@
+Title,Mentor,Co-mentor(s)
+Application of machine learning to reproductive epigenetics for precision aquaculture,Jason Abernathy,
+Secondary Metabolome of Nematode Parasitic Fungi for Biocontrol,Kathryn Bushley,Ted Thannhauser and Catherine Wram
+Developing AI-empowered climate mitigation solutions in agricultural soils,Michael Cosh,
+Integrating Multiple Data Streams into Forecasts of Vector-borne Livestock Disease Emergence and Spread,Amy Hudson,
+Modernizing the Soil and Water Assessment Tool (SWAT+) for use on SCINet computing infrastructure,Kelly Thorp,"Jeff Arnold, Mike White, and Merilynn Schantz"

_includes/collect/components/calendar

@@ -17,9 +17,9 @@
 
 {% if include.filter == "true" %}
 
-{% assign tags = allevents | map: 'tags' | uniq %}
-{% assign types = allevents | map: 'type' | uniq %}
-{% assign providers = allevents | map: 'provider' | uniq %}
+{% assign tags = allevents | map: 'tags' | uniq | compact | sort %}
+{% assign types = allevents | map: 'type' | uniq | compact | sort %}
+{% assign providers = allevents | map: 'provider' | uniq | compact | sort %}
 {% assign sort_list = true %}
 
 {% endif %}
@@ -58,7 +58,7 @@
 
 {% assign sortings = page.sorted %}
 
-<ul class="usa-list usa-list--unstyled">
+<ul class="usa-list usa-list--unstyled margin-bottom-105 padding-bottom-105">
 
       {% if flow == 'normal' %}
         {% for _events in allevents %}
@@ -71,6 +71,6 @@
       {% endif %}
 
   </ul>
-  <br>
+
   {% endif %}
   {% endif %}

_includes/collect/components/session-ul

@@ -44,7 +44,7 @@
     {% endif %}
     {% if session.details %}
     {% for _detail in session.details %}
-    <li>{% include components/link.html url=_detail.url text=_detail.text external=true %}</li>
+    <li>{{_detail.text}}</li>
     {% endfor %}
 {% endif %}
 

_includes/collect/process/event

@@ -29,8 +29,7 @@
 {%- assign materials = session.materials | default: parent.materials %}
 {%- assign details = session.details | default: parent.details %}
 
-{%- capture stags %}{% if include.session['tags'] %}{{ session.tags }} {% endif %}{{ parent.tags }}{% endcapture %}
-{% assign tags = stags | split: ' ' %}
+{% assign tags = session.tags | concat: parent.tags %}
 
 {% if end_date %}
 {% assign end_date = end_date | date: '%s' | plus: 0 %}
@@ -63,6 +62,6 @@
 {% endif %}
 
 
-{% include collect/process/hashed date=date date-start=date-start duration=duration time=time end_date=end_date caldate=cal_date multiday=multiday url=url title=title section=section parenttitle=parenttitle excerpt=excerpt type=type provider=provider registration=registration sessions=sessions prerequisites=prerequisites duration=duration system=system location=location reason=reason assets=assets link=link latest=latest instructor=instructor presenter=presenter lead=lead location=location materials=materials details=details %}
+{% include collect/process/hashed date=date date-start=date-start duration=duration time=time end_date=end_date caldate=cal_date multiday=multiday url=url title=title section=section parenttitle=parenttitle excerpt=excerpt type=type provider=provider registration=registration sessions=sessions prerequisites=prerequisites duration=duration system=system location=location reason=reason assets=assets link=link latest=latest instructor=instructor presenter=presenter lead=lead location=location materials=materials details=details tags=tags %}
 
 {% assign event = hashed %}

_includes/components/table.html

@@ -55,8 +55,12 @@
             {% endfor %}
         </tbody>
     </table>
+    {% if table.sort %}
+    <div class="usa-sr-only usa-table__announcement-region"
+    aria-live="polite" ></div>
+    {% endif %}
     {% if table.announcement %}
-    <div class="usa-table__announcement-region" aria-live="polite">
+    <div>
        {{ table.announcement | markdownify }}
     </div>
     {% endif %}

_layouts/downtime.html

@@ -77,7 +77,7 @@
 <h5>Further detail for each outage is posted in the announcements below if availible.</h5>
 {% endif %}
 
-{% for _down in downtime reversed %}
+{% for _down in downtime %}
   {% include components/collection-downtime.html post=_down %}
 {% endfor %}
 

_layouts/feed.ics

@@ -90,7 +90,7 @@ DURATION:{{ post.duration }}{% elsif post.end_date %}
 DTEND{{ tzid }}:{{ post.end_date | date: "%Y%m%dT%H%M00" }}{{ endtzid }}{% else %}
 DTEND:{{ post.date | date: "%Y%m%d" }}{% endif %}{% if post.rrule %}
 RRULE:{{post.rrule}}{% endif %}
-SUMMARY:{% include feed.html content=fulltitle %}
+SUMMARY:{% include collect/feed.html content=fulltitle %}
 DESCRIPTION:{%- capture mydescription -%}<p>{% if post.cal-text %}{{post.cal-text}}{% elsif post.excerpt %}{{ post.excerpt }}{% else %}{{ post.text }}{% endif %}</p>
 <ul>{% if post.time %}
 <li><b>Outage time:</b> {{ post.time }}</li>{% endif %}{% if post.systems %}

_layouts/nav.html

@@ -8,7 +8,16 @@
 
 <div class="grid-container main-side">
 
-
+{% if page.sidenav_basic %}  
+  {% assign sidenav = page.sidenav_basic %}
+  {% assign bc_sidenav = sidenav %}
+  {% if page.alt_nav %}
+  {% assign alt_nav = page.alt_nav %}
+  {% else %}
+  {% assign firstnav = sidenav | first %}
+  {% assign alt_nav = firstnav.title %}
+  {% endif %}
+{% else %}
   {% if page.sidenav_link %}
     {% assign pagelink = page.sidenav_link %}
   {% else %}
@@ -139,6 +148,8 @@
     {% assign sidenav = bc_sidenav %}
 {% endif %}
 
+{% endif %}
+
 {% if page.sidenav_append %}
   {% assign sidenav = sidenav | concat: page.sidenav_append %}
 {% endif %}

pages/about/about.md

@@ -8,7 +8,7 @@ breadcrumb_title: About
 
 The SCINet initiative is an effort by the USDA Agricultural Research Service to improve the USDA’s research capacity by providing scientists with access to high-performance computing (HPC) clusters, high-speed networking for data transfer, and training in scientific computing.
 
-SCINet supports a growing community of nearly 2,000 USDA research scientists and university partners to accelerate agricultural discovery through advanced computational infrastructure and scientific computing. 
+SCINet supports a growing community of over 2,000 USDA research scientists and university partners to accelerate agricultural discovery through advanced computational infrastructure and scientific computing. 
 
 Current uses of SCINet span multiple disciplines, including genomics, plant breeding, hydrology, crop production, plant and animal disease modeling, and natural resource management. SCINet users include ARS and other federal scientists, as well as partners external to the federal government.
 
@@ -40,4 +40,4 @@ To get started using SCINet, [sign up for an account](/about/signup) and visit o
   </li>
 </ul>
 </div>
-</div>
+</div>

pages/about/organization.md

@@ -130,7 +130,7 @@ SAC-table:
       Term expires: ""
 ---
 
-The ARS Scientific Computing Initiative is led by an Executive Committee comprised of ARS leadership including Dr. Marlen Eve – Acting Associate Administrator for National Programs,  Dr. Brian Stucky – Acting Chief Scientific Information Officer, Rob Butler – Acting SCINet Project Manager, ARS scientists representing IT and security, and users of the HPC systems. SCINet committees report to the Executive Committee, including the Scientific Advisory Committee (SAC), an HPC Policy Committee, and an HPC Software Committee.
+The ARS Scientific Computing Initiative is led by an Executive Committee comprised of ARS leadership including Dr. Jeff Silverstein – Associate Administrator for National Programs,  Dr. Brian Stucky – Acting Chief Scientific Information Officer, Rob Butler – Acting SCINet Project Manager, ARS scientists representing IT and security, and users of the HPC systems. SCINet committees report to the Executive Committee, including the Scientific Advisory Committee (SAC), an HPC Policy Committee, and an HPC Software Committee.
 
 The program runs two high performance computer clusters and a storage unit.  The Ceres cluster is housed at the National Animal Disease Center in Ames, IA and operated by Iowa State University. The Atlas cluster is located and ran by Mississippi State University in Starkville, MS, and the Juno storage unit is located at the National Agricultural Library in Beltsville, MD. 
 
@@ -141,7 +141,7 @@ User support at SCINet is provided by the  Virtual Support Research Core (VSRC)
 {: .usa-table .usa-table--compact }
 Person | Position
 ---|---
-Dr. Marlen Eve | Acting Associate Administrator for National Programs
+Dr. Jeff Silverstein | Associate Administrator for National Programs
 Dr. Brian Stucky | Acting Chief Scientific Information Officer, ARS
 
 ## Executive Committee
@@ -151,7 +151,7 @@ The ARS Scientific Computing Initiative is led by an Executive Committee.
 {: .usa-table .usa-table--compact }
 Person | Position
 ---|---
-Dr. Marlen Eve | Acting Associate Administrator for National Programs
+Dr. Jeff Silverstein | Associate Administrator for National Programs
 Dr. Brian Stucky | Acting Chief Scientific Information Officer, ARS
 Ms. Lorna Drennen | Assistant Chief Information officer
 Mr. Stan Kosecki | Deputy Assistant Chief Information Officer
@@ -212,7 +212,7 @@ Rob Butler | Acting SCINet Project Manager
 
 The software committee evaluates requests by users to add or delete software to/from one of the HPCs. This committee is composed of scientific experts in the use of HPCs from across agricultural disciplines, and that represent our two HPCs. Users can make software requests by completing the [Software Request Form]({{ site.baseurl }}/support/request#software-request). 
 
-
+{% comment %}
 <!---------------------------------------------------------------------------------------
 WAITING FOR A FEW DEVELOPMENTS IN THE SCINET PROGRAM TO OCCUR, THEN NEED TO EDIT THE title BELOW AND REPLACE THE INFORMATION ON THIS PAGE ENTIRELY
 ## Executive Committee
@@ -257,3 +257,4 @@ Steven Schroeder
 #Scientific Points of Contact (SPOCs)
 Each ARS location also has at least one designated point of contact for the ARS Scientific Computing Initiative. These representatives are occasionally contacted by the various committees when information from many locations is required for decision making. For more information, including how to participate, please contact Stan Kosecki.
 -->
+{% endcomment %}

pages/home.md

@@ -4,11 +4,12 @@ permalink: /
 type: future
 description: SCINet is a USDA initiative to provide agricultural scientists access to high performance computing, networking and training.
 
-#alerts:
-#  - alert:
-#    title: Atlas Update
-#    type: warning
-#    text: There have been several changes to the Atlas compute cluster.  <a href="/announcements/2024-05-03-altas" class="usa-link">Read more about these updates here.</a>
+# alerts:
+#   - alert:
+#     title: Ceres Update
+#     type: success
+#     title: Ceres maintenance completed
+#     text: Ceres' new storage system is now fully deployed and available for use!  <a href="/announcements/2024-10-16-ceres" class="usa-link">Read more about these updates here.</a>
 
 layout: scinet_home
 

pages/news/newsletter.md

@@ -17,6 +17,8 @@ Research highlights from researchers who use SCINet resources are added quarterl
 
 <br>
 
+### [USDA ARS SCINet Newsletter: October 2024](/assets/pdf/newsletters/SCINet-Newsletter-October-2024.pdf){:target="_blank"}
+
 ### [USDA ARS SCINet Newsletter: July 2024](/assets/pdf/newsletters/SCINet-Newsletter-July-2024.pdf){:target="_blank"}
 
 ### [USDA ARS SCINet Newsletter: April 2024](/assets/pdf/newsletters/SCINet-Newsletter-April-2024.pdf){:target="_blank"}