Merge pull request #24 from opensciencegrid/master

merging with upstream

.github/workflows/build-client-container.yml

@@ -19,7 +19,7 @@ jobs:
     steps:
     - name: make date tag
       id: mkdatetag
-      run: echo "::set-output name=dtag::$(date +%Y%m%d-%H%M)"
+      run: echo "dtag=$(date +%Y%m%d-%H%M)" >> $GITHUB_OUTPUT
 
   build:
     runs-on: ubuntu-latest
@@ -29,7 +29,7 @@ jobs:
       fail-fast: False
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Generate tag list
       id: generate-tag-list
@@ -43,26 +43,26 @@ jobs:
           tag_list+=($registry/$docker_repo:release-$TIMESTAMP)
         done
         IFS=,
-        echo "::set-output name=taglist::${tag_list[*]}"
+        echo "taglist=${tag_list[*]}" >> $GITHUB_OUTPUT
 
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
+      uses: docker/setup-buildx-action@v2.7.0
 
     - name: Log in to Docker Hub
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2.2.0
       with:
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
 
     - name: Log in to OSG Harbor
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2.2.0
       with:
         registry: hub.opensciencegrid.org
         username: ${{ secrets.OSG_HARBOR_ROBOT_USER }}
         password: ${{ secrets.OSG_HARBOR_ROBOT_PASSWORD }}
 
     - name: Build and push Client Docker images
-      uses: docker/build-push-action@v2.2.0
+      uses: docker/build-push-action@v4
       with:
         push: true
         tags: "${{ steps.generate-tag-list.outputs.taglist }}"

.github/workflows/build-sw-container.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     if: startsWith(github.repository, 'opensciencegrid/')
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Generate tag list
       id: generate-tag-list
@@ -28,26 +28,26 @@ jobs:
         # This causes the tag_list array to be comma-separated below,
         # which is required for build-push-action
         IFS=,
-        echo "::set-output name=taglist::${tag_list[*]}"
+        echo "taglist=${tag_list[*]}" >> $GITHUB_OUTPUT
 
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v1
+      uses: docker/setup-buildx-action@v2.7.0
 
     - name: Log in to Docker Hub
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2.2.0
       with:
         username: ${{ secrets.DOCKER_USERNAME }}
         password: ${{ secrets.DOCKER_PASSWORD }}
 
     - name: Log in to OSG Harbor
-      uses: docker/login-action@v1
+      uses: docker/login-action@v2.2.0
       with:
         registry: hub.opensciencegrid.org
         username: ${{ secrets.OSG_HARBOR_ROBOT_USER }}
         password: ${{ secrets.OSG_HARBOR_ROBOT_PASSWORD }}
 
     - name: Build and push Docker images
-      uses: docker/build-push-action@v2.2.0
+      uses: docker/build-push-action@v4
       with:
         context: .
         push: true

.github/workflows/validate-caches.yml

@@ -10,9 +10,9 @@ jobs:
     if: startsWith(github.repository, 'opensciencegrid/')
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9.15
       - name: Compare StashCache config lists

.github/workflows/validate-code.yml

@@ -6,9 +6,9 @@ jobs:
     name: Validate Topology code
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9.15
       - name: Install packages

.github/workflows/validate-data.yml

@@ -7,9 +7,9 @@ jobs:
     name: Validate Topology data
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9.15
       - name: Install packages

mappings/project_institution.yaml

@@ -10,6 +10,7 @@ BNL: "Brookhaven National Laboratory"
 BU: "Boston University"
 BYUI: "Brigham Young University Idaho"
 Caltech: "California Institute of Technology"
+CedarsSinai: "Cedars-Sinai Medical Center"
 Cincinnati: "University of Cincinnati"
 Clarkson: "Clarkson University"
 Coe: "Coe College"
@@ -39,6 +40,7 @@ Mines: "Colorado School of Mines"
 MIT: "Massachusetts Institute of Technology"
 Mizzou: "University of Missouri"
 MMC: "Meharry Medical College"
+MSKCC: "Memorial Sloan Kettering Cancer Center"
 MSU: "Montana State University"
 MTU: "Michigan Technological University"
 NCSU: "North Carolina State University"
@@ -49,9 +51,11 @@ NMSU: "New Mexico State University"
 NOAA: "National Oceanic and Atmospheric Administration"
 Northeastern: "Northeastern University"
 NSHE: "Nevada System of Higher Education"
+OHSU: "Oregon Health & Science University"
 OSU: "The Ohio State University"
 Pitt: "University of Pittsburgh"
 PortlandState: "Portland State University"
+PSI: "Planetary Science Institute"
 PSU: "Pennsylvania State University"
 Repertoire: "Repertoire Immune Medicines"
 Rochester: "University of Rochester"
@@ -84,6 +88,7 @@ UMCES: "University of Maryland Center for Environmental Science"
 UMiss: "University of Mississippi"
 UNL: "University of Nebraska - Lincoln"
 USD: "University of South Dakota"
+USDA: "United States Department of Agriculture"
 USheffield: "University of Sheffield"
 UTEP: "University of Texas at El Paso"
 UTulsa: "University of Tulsa"

projects/BNL_Venugopalan.yaml

@@ -0,0 +1,7 @@
+Description: >
+  We investigate the dynamics of strongly interacting field theories through a variety of numerical methods, 
+  ranging from classical lattice simulations to tensor network projects.
+Department: Physics
+FieldOfScience: Physics
+Organization: Brookhaven National Laboratory
+PIName: Raju Venugopalan

projects/BrighamAndWomens_ Baratono.yaml

@@ -0,0 +1,5 @@
+Description: Studying how atrophy and connectivity to atrophy impacts cognitive and psychological outcomes in patients with a variety of neurodegenerative disorders
+Department: Neurology
+FieldOfScience: Biological and Biomedical Sciences
+Organization: Brigham and Women's Hospital
+PIName: Sheena R Baratono

projects/CSUN_Jiang.yaml

@@ -0,0 +1,9 @@
+Description: >
+  Wildfire Prediction for California using various remote sensing data from the past decades. 
+  This is a computation intensive research project that involves applying machine learning models for data analysis and prediction, 
+  and also computation-intensive work for data visualization. 
+  This project will involve collaborations from both internal and external students at California State University, Northridge.
+Department:  Computer Science
+FieldOfScience: Computer and Information Sciences
+Organization: California State University, Northridge
+PIName: Xunfei Jiang

projects/CSU_Buchanan.yaml

@@ -0,0 +1,5 @@
+Description: Modeling of magnetorheological elastomers
+Department: Physics
+FieldOfScience: Physics
+Organization: Colorado State University
+PIName: Kristen Buchanan

projects/CedarsSinai_Meyer.yaml

@@ -0,0 +1,10 @@
+Description: >
+  The Platform for Single-Cell Science is a tool for improving both the reproducibility and accessibility of analytical 
+  pipelines developed for single-cell multiomics. Researchers will be able to upload their data, create an analysis pipeline
+  using our javascript designer, and link their results to a publication. The raw data, analysis, and results will be made 
+  available for interactive exploration or download when users are ready to publish. We are hoping to understand if there 
+  is a way we can use OSG by sending jobs that are prepared on our website hosted on AWS to the OSG for execution.
+Department: Computational Biomedicine
+FieldOfScience: Biological and Biomedical Sciences 
+Organization: Cedars-Sinai Medical Center
+PIName: Jesse Meyer

projects/Emory_Pesavento.yaml

@@ -0,0 +1,16 @@
+Department: Economics
+Description: >
+  The goal of our research project is to develop a new technique to estimate
+  impulse response functions in Time-varying-parameters vector autoregressive models
+  (in short: TVP-VARs). TVP-VARs are particularly useful because, unlike traditional
+  VAR models, they accounts for changing economic conditions by allowing parameters
+  to change over time. Estimating impulse responses (one of the main tools in
+  macroeconomic analysis) in a TVP-VAR requires the implementation of Markov Chain
+  Montecarlo algorithms (such as Gibbs sampling). This is a computationally demanding
+  task in a TVP-VAR framework, due to the huge number of parameters to estimate.
+  However, we could substantially ease such task by using parallel computing
+  techniques. In this way, we could provide policy makers with a more realistic
+  and flexible framework use to perform macroeconomic policy evaluation."
+FieldOfScience: Economics
+Organization: Emory University
+PIName: Elena Pesavento

projects/Etown_Wittmeyer.yaml

@@ -0,0 +1,9 @@
+Description: I am interested in examining experience-dependent neuroplasticity and individual differences in humans as it pertains to learning and memory.  In particular, I analyze structural magnetic resonance imaging (sMRI) data from various neuroimaging data-sharing platforms to explore changes in gray matter across learning and/or correlate learning performance with various cognitive and demographic factors.
+Department: Psychology
+FieldOfScience: Psychology and Life Sciences
+Organization: Elizabethtown College
+PIName: Jennifer Legault Wittmeyer
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/FIU_Guo.yaml

@@ -0,0 +1,9 @@
+Description: >
+  My research in experimental nuclear physics requires large amounts of 
+  simulations. These simulations are independent of one another and the OSPool is 
+  very well suited for these tasks. Access to the OSG computing resources would be 
+  a useful asset for my research.
+Department: College of Arts and Science
+FieldOfScience: Physics
+Organization: Florida International University
+PIName: Lei Guo

projects/IIT_Zhong.yaml

@@ -0,0 +1,9 @@
+Description: We conduct research on scientific machine learning, especially related to how machine learning can be used to learn and understand dynamical systems from observation data.  Right now, we are developing models to understand synchronization, i.e. how oscillators can be put in sync with spatial patterns.
+Department: Appleid Mathematics
+FieldOfScience: Appleid Mathematics
+Organization: Illinois Institute of Technology
+PIName: Ming Zhong
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/MSKCC_Chodera.yaml

@@ -0,0 +1,5 @@
+Department: MSKCC
+Description: We are developing a system to enable high throughput free energy calculations.
+FieldOfScience: Bioinformatics
+Organization: Memorial Sloan Kettering Cancer Center
+PIName: John Chodera

projects/NCSU_Gray.yaml

@@ -0,0 +1,9 @@
+Description: >
+  Map and characterize global change, and to understand the consequences of these changes for the Earth system and society. 
+  Anthropogenic changes to vegetation (e.g. cropping systems, deforestation, etc.) are of particular interest. 
+  Example research questions include: How can we feed a growing population without running out of water? 
+  Have tropical deforestation mitigation policies been effective? How is vegetation phenology changing in response to a changing climate?
+Department: Center for Geospatial Analytics
+FieldOfScience: Geosciences
+Organization: North Carolina State University
+PIName: Josh Gray

projects/NCSU_Staff.yaml

@@ -0,0 +1,7 @@
+Description: >
+  Continue my access to the OSPool after the OSG School to further 
+  support potential users and workflows for NC State University
+Department: Research Facilitation Service
+FieldOfScience: Other
+Organization: North Carolina State University
+PIName: Christopher Blanton

projects/NMSU_Lawson.yaml

@@ -0,0 +1,9 @@
+Description: >
+  I am requesting an OSPool project for my postdoctoral research investigating 
+  drivers of population decline for the American Kestrel, a raptor species that breeds 
+  across North America. I plan to use OSG resources to compile my environmental data 
+  and fit statistical models.
+Department: Fish, Wildlife, and Conservation Ecology  
+FieldOfScience: Ecological and Environmental Sciences
+Organization: New Mexico State University
+PIName: Abigail Lawson

projects/OHSU_Katamreddy.yaml

@@ -0,0 +1,14 @@
+Description: >
+  Cardiovascular disease occurs due to environmental factors like diet, 
+  exercise but also due to genetic predisposition. 
+  I want to work on finding genetic pathways that underlie the genesis cardiovascular disease. 
+  Please find link to my previous work on cardiovascular disease and medicine. ‪
+  Adarsh Katamreddy‬ - ‪Google Scholar‬
+Department: Cardiovascular Medicine
+FieldOfScience: Medical Sciences
+Organization: Oregon Health & Science University
+PIName: Adarsh Katamreddy
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/PSI_Kaib.yaml

@@ -0,0 +1,8 @@
+Description: >
+  I will be using computer simulations to model the orbital evolution of comets and asteroids over the 
+  lifetime of the solar system. In addition, I will be studying the stability of the solar system and Kuiper belt as
+  it is subjected to close flybys of other stars in the Milky Way. https://www.psi.edu/about/staffpage/nkaib
+Department: Planetary Science Institute
+FieldOfScience: Astronomy and Astrophysics
+Organization: Planetary Science Institute
+PIName: Nathan Kaib

projects/RIT_Tu.yaml

@@ -0,0 +1,5 @@
+Description: Study on Solid State Battery Cathode Optimization 
+Department: Mechanical Engineering
+FieldOfScience: Mechanical Engineering
+Organization: Rochester Institute of Technology
+PIName: Howard Tu

projects/SIUE_Quinones.yaml

@@ -0,0 +1,5 @@
+Description: Research in Computer Vision, Digital Image Processing, and Multi-Agent Simulation.
+Department: Computer Science
+FieldOfScience: Computer Science
+Organization: Southern Illinois University Edwardsville
+PIName: Rubi Quinones

projects/UCI_Sheng.yaml

@@ -0,0 +1,6 @@
+Department: Paul Merage School of Business
+Description: 'Research on the US housing market and transactions with the aim of comprehending
+  how housing prices move and are correlated with each other. '
+FieldOfScience: Economics
+Organization: University of California, Irvine
+PIName: Jinfei Sheng

projects/UMiss_Gupta.yaml

@@ -0,0 +1,6 @@
+Department: LIGO
+Description: 'We are studying the evolution of binary black holes and it would be
+  great to try out the OS Pool facility through the AP40 cluster. '
+FieldOfScience: Astronomy and Astrophysics
+Organization: University of Mississippi
+PIName: Anuradha Gupta

projects/UNI_Staff.yaml

@@ -0,0 +1,5 @@
+Description: Will be using OSPool to evaluate and develop training for UNI users.
+Department: Information Technology, Network & Infrastructure Services
+FieldOfScience: Training
+Organization: University of Northern Iowa
+PIName: Wesley Jones

projects/UNL_Hebets.yaml

@@ -0,0 +1,5 @@
+Description: Assess spider web structure by training and tracking models using SLEAP
+Department: Biological Sciences
+FieldOfScience: Biological Sciences
+Organization: University of Nebraska-Lincoln
+PIName: Eileen Hebets

projects/USDA_Andorf.yaml

@@ -0,0 +1,8 @@
+Description: >
+  The research is part of the Maize Genetics and Genomics Database (MaizeGD) to utilize protein structure models to improve maize functional genomics.
+  The project will generate new protein structure models to improve functional classification, canonical isoform detection, 
+  gene structure annotation, and assigning confidence scores to point mutations based on the likelihood to change function.    
+Department: Midwest Area, Corn Insects, and Crop Genetics Research Unit
+FieldOfScience: Biological and Biomedical Sciences
+Organization: United States Department of Agriculture
+PIName: Carson Andorf

projects/UTEP_Moore.yaml

@@ -0,0 +1,5 @@
+Description: We are developing portable containers for deep-learning frameworks and applications
+Department: Computer Science
+FieldOfScience: Computer and Information Services
+Organization: University of Texas at El Paso
+PIName: Shirley Moore

projects/UTSA_Anantua.yaml

@@ -0,0 +1,8 @@
+Description: >
+   I am using Monte Carlo ray-tracing code GRMONTY to create and
+   compare two different emission models R-Beta and Critical-Beta
+   of M87 and Sgr A*. https://richardanantua.com/spectra/
+Department: Department of Physics and Astronomy
+FieldOfScience: Astronomy and Astrophysics
+Organization: The University of Texas at San Antonio
+PIName: Richard Anantua

projects/UWMadison_Ericksen.yaml

@@ -0,0 +1,5 @@
+Department: Small Molecule Screening Facility
+Description: Molecule docking as part of drug discovery research (http://hts.wisc.edu/)
+FieldOfScience: Health
+Organization: University of Wisconsin-Madison
+PIName: Spencer Ericksen

projects/UWMadison_Kwan.yaml

@@ -0,0 +1,5 @@
+Department: Pharmacy
+Description: 'Bioactive molecules from cultured and uncultured bacteria (https://kwanlab.github.io/)'
+FieldOfScience: Health
+Organization: University of Wisconsin-Madison
+PIName: Jason Kwan

projects/UWMadison_Li.yaml

@@ -0,0 +1,5 @@
+Description: Multiscale modeling, computational materials design, mechanics and physics of polymers, and machine learning-accelerated polymer design.
+Department: Mechanical Engineering
+FieldOfScience: Engineering
+Organization: University of Wisconsin-Madison
+PIName: Ying Li

projects/UWMadison_Pool.yaml

@@ -1,5 +1,5 @@
-Department: Genetics
-Description: http://www.genetics.wisc.edu/user/338
+Department: Genomics & Genetics
+Description: 'Population Genomics and the Genetic Basis of Adaptive Evolution - http://www.genetics.wisc.edu/user/338'
 FieldOfScience: Biological Sciences
 Organization: University of Wisconsin-Madison
 PIName: John Pool