updated centers

Author: jeevangelista

script/ingestion/centers.py

@@ -53,6 +53,11 @@
 	DELETE FROM center_publications;
 ''')
 
+cur.execute('''
+	DELETE FROM center_outreach;
+''')
+
+
 cur.execute('''
 	DELETE FROM centers;
 ''') 

src/pages/centers/CWIC.md

@@ -5,8 +5,14 @@ short_label: CWIC
 project_title: The CFDE Cloud Workspace
 grant_num: OT2OD037936
 principal_investigators:
-- name: John M. Fonner PhD
-  url: https://tacc.utexas.edu/about/staff-directory/john-fonner/
+- name: James Carson, PhD
+  url: https://tacc.utexas.edu/about/staff-directory/james-carson/
+- name: Anton Nekrutenko, PhD
+  url: https://www.huck.psu.edu/people/anton-nekrutenko
+- name: Michael Schatz, PhD
+  url: https://engineering.jhu.edu/faculty/michael-schatz/
+- name: Shava Smallen, PhD
+  url: https://profiles.ucsd.edu/shava.smallen
 institution:
 - name: University of Texas at Austin
   url: https://tacc.utexas.edu/
@@ -16,8 +22,4 @@ press_release:
 layout: '@/layouts/Center.astro'
 short_description: The CFDE Cloud Workspace enables researchers to analyze, integrate, and share data with powerful tools, fostering collaboration and accelerating discoveries through free computational resources and training.
 ---
-The CFDE Cloud Workspace is designed to provide researchers with an accessible and collaborative environment for data analysis. It allows users to import and integrate data with Common Fund datasets while utilizing a wide range of analysis tools, workflows, and pipelines. The Cloud Workspace Implementation Center (CWIC) streamlines deployment by leveraging key partnerships: TACC’s high-performance computing resources, Galaxy’s open-source interface for data analysis, and CloudBank’s tools for simplified cloud access and billing. 
-
-This workspace supports both novice and expert users by offering training, outreach, and cost-management tools to optimize resource usage. Users will have access to a variety of tools developed by CFDE, Galaxy, and other partners, with the flexibility to incorporate custom or third-party tools. By providing free storage and compute resources, the Cloud Workspace lowers barriers to entry, enabling researchers to work with large datasets and complex analyses.
-
-By fostering data sharing, collaboration, and ease of access, CWIC accelerates biomedical research and supports a broader scientific community in tackling high-priority challenges. This initiative represents a significant step toward expanding access to advanced computational resources and empowering researchers to drive innovation in the field.
+The CFDE Cloud Workspace is designed to provide researchers with an accessible and collaborative environment for data analysis. It allows users to import and integrate data with Common Fund datasets while utilizing a wide range of analysis tools, workflows, and pipelines. The Cloud Workspace Implementation Center (CWIC) streamlines deployment by leveraging key partnerships: TACC’s high-performance computing resources, Galaxy’s open-source interface for data analysis, and CloudBank’s tools for simplified cloud access and billing. <br/><br/>This workspace supports both novice and expert users by offering training, outreach, and cost-management tools to optimize resource usage. Users will have access to a variety of tools developed by CFDE, Galaxy, and other partners, with the flexibility to incorporate custom or third-party tools. By providing free storage and compute resources, the Cloud Workspace lowers barriers to entry, enabling researchers to work with large datasets and complex analyses.<br/><br/>By fostering data sharing, collaboration, and ease of access, CWIC accelerates biomedical research and supports a broader scientific community in tackling high-priority challenges. This initiative represents a significant step toward expanding access to advanced computational resources and empowering researchers to drive innovation in the field.

src/pages/centers/ICC.md

@@ -31,8 +31,4 @@ icon: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/icc-logo.png
 layout: '@/layouts/Center.astro'
 short_description: The CONNECT ICC enhances CFDE research by streamlining operations, improving data sustainability, and fostering collaboration through expert leadership, Agile management, and innovative evaluation metrics.
 ---
-The CONNECT Integration and Coordination Center (ICC) is dedicated to advancing biomedical research within the Common Fund Data Ecosystem (CFDE) by enhancing efficiency, transparency, and innovation. Led by Prof. Jake Chen at UAB, alongside Profs. Casey Greene, Sean Davis, Peipei Ping, and Wei Wang, the ICC integrates three key cores—Administrative, Evaluation, and Sustainability—to drive its mission forward.
-
-The Administrative Core, led by Prof. Chen, ensures seamless coordination and project management across CFDE entities. Utilizing Agile methodologies and collaboration tools like U-BRITE, it optimizes communication and accelerates scientific progress. The Evaluation Core, led by Profs. Greene and Davis, focuses on continuous quality improvement, developing evaluation metrics and feedback mechanisms to assess and enhance CFDE initiatives. Meanwhile, the Sustainability Core, led by Prof. Ping with support from Prof. Wang, ensures the long-term accessibility and reusability of CF program data through strategic data management practices and repository planning.
-
-By integrating these efforts, the CONNECT ICC fosters collaboration, accelerates biomedical discoveries, and strengthens CFDE’s long-term impact. Through innovative methodologies and expert leadership, it is positioned to drive transformative advancements in biomedical research.
+The CONNECT Integration and Coordination Center (ICC) is dedicated to advancing biomedical research within the Common Fund Data Ecosystem (CFDE) by enhancing efficiency, transparency, and innovation. Led by Prof. Jake Chen at UAB, alongside Profs. Casey Greene, Sean Davis, Peipei Ping, and Wei Wang, the ICC integrates three key cores—Administrative, Evaluation, and Sustainability—to drive its mission forward.<br/><br/>The Administrative Core, led by Prof. Chen, ensures seamless coordination and project management across CFDE entities. Utilizing Agile methodologies and collaboration tools like U-BRITE, it optimizes communication and accelerates scientific progress. The Evaluation Core, led by Profs. Greene and Davis, focuses on continuous quality improvement, developing evaluation metrics and feedback mechanisms to assess and enhance CFDE initiatives. Meanwhile, the Sustainability Core, led by Prof. Ping with support from Prof. Wang, ensures the long-term accessibility and reusability of CF program data through strategic data management practices and repository planning.<br/><br/>By integrating these efforts, the CONNECT ICC fosters collaboration, accelerates biomedical discoveries, and strengthens CFDE’s long-term impact. Through innovative methodologies and expert leadership, it is positioned to drive transformative advancements in biomedical research.

src/pages/centers/TC.md

@@ -7,16 +7,14 @@ grant_num: OT2OD037922
 principal_investigators:
 - name: LaFrancis Gibson PhD
   url: https://reporter.nih.gov/search/qIgnXbJ7VEOtA3dq-K2mPg/projects
+- name: Jennifer Burnette PhD
+  url: https://reporter.nih.gov/search/hpsdHO3ruEuSAogyVN1SFw/projects
+- name: Allissa Amanda Dillman PhD
+  url: reporter.nih.gov/search/MeqtiJAacUyN2AXUvGlWQA/projects
 institution:
 - name: Oak Ridge Associated Universities
   url: https://orau.org/
 layout: '@/layouts/Center.astro'
 short_description: The CFDE Training Center will expand data accessibility by providing tailored training, mentoring, and outreach, fostering a diverse learning community to enhance biomedical research and data use.
 ---
-The CFDE Training Center (TC) will ensure that Common Fund Data Ecosystem (CFDE) data, tools, and resources are findable, accessible, interoperable, and reusable (FAIR). Serving as the central hub for training development, coordination, and evaluation, the TC will expand the CF data user base, enhance dataset usage, and increase awareness of CFDE resources.
-
-Team ORAU will achieve this through targeted training programs, outreach initiatives, and a collaborative learning community. The TC will design customized training materials for a diverse audience, with a focus on postgraduate students and early-career investigators. A CFDE Mentoring Program will pair learners with experienced bioinformaticians to provide technical and professional guidance, fostering careers in bioinformatics and data science. Additionally, the TC will ensure diversity, equity, inclusion, and accessibility (DEIA) through targeted recruitment, a Diversity Committee, and an inclusive learning environment.
-
-To support collaboration, the TC will establish a CFDE Trainers Working Group to share best practices, a CFDE Landing Page for centralized training resources, and a Virtual Community of Learners for engagement and ongoing support. Development will be informed by a comprehensive landscape analysis, including gap assessments, literature reviews, and stakeholder input. Ongoing evaluation will guide program improvements and ensure alignment with CFDE and NIH goals.
-
-Led by a skilled team from Oak Ridge Associated Universities (ORAU) and BioData Sage LLC, the TC will be managed through structured project controls, ensuring effective, flexible coordination with NIH and CFDE stakeholders. Through these efforts, the TC will build a strong, supportive ecosystem for training biomedical researchers in data-driven science.
+The CFDE Training Center (TC) will ensure that Common Fund Data Ecosystem (CFDE) data, tools, and resources are findable, accessible, interoperable, and reusable (FAIR). Serving as the central hub for training development, coordination, and evaluation, the TC will expand the CF data user base, enhance dataset usage, and increase awareness of CFDE resources.<br/><br/>Team ORAU will achieve this through targeted training programs, outreach initiatives, and a collaborative learning community. The TC will design customized training materials for a diverse audience, with a focus on postgraduate students and early-career investigators. A CFDE Mentoring Program will pair learners with experienced bioinformaticians to provide technical and professional guidance, fostering careers in bioinformatics and data science. Additionally, the TC will ensure diversity, equity, inclusion, and accessibility (DEIA) through targeted recruitment, a Diversity Committee, and an inclusive learning environment.<br/><br/>To support collaboration, the TC will establish a CFDE Trainers Working Group to share best practices, a CFDE Landing Page for centralized training resources, and a Virtual Community of Learners for engagement and ongoing support. Development will be informed by a comprehensive landscape analysis, including gap assessments, literature reviews, and stakeholder input. Ongoing evaluation will guide program improvements and ensure alignment with CFDE and NIH goals.<br/><br/>Led by a skilled team from Oak Ridge Associated Universities (ORAU) and BioData Sage LLC, the TC will be managed through structured project controls, ensuring effective, flexible coordination with NIH and CFDE stakeholders. Through these efforts, the TC will build a strong, supportive ecosystem for training biomedical researchers in data-driven science.

src/pages/centers/drc.md

@@ -25,7 +25,4 @@ layout: '@/layouts/Center.astro'
 video_tutorial: https://www.youtube.com/watch?v=TAnKcNp2kdY
 short_description: The CFDE Workbench provides data and information portals, that enables users to access CF data, query biological entities, and engage with standardized, FAIR, AI-ready resources for biomedical research collaboration.
 ---
-The CFDE Data Resource Center (DRC) was tasked with developing two web-based portals: an **Information Portal** to serve information about the CFDE and a **Data Portal** to host harmonized metadata and processed data contributed by participating CF Data Coordination Centers (DCCs) and other sources. By combining the data and information portals, the **CFDE Workbench** is a comprehensive resource where users can collect both information and data from CFDE and CF resources, as well as query disease, gene, drug, and other biological entities across standardized data formats from each CF DCC. The CFDE Workbench consolidates efforts toward making CF programs funded resources harmonized, FAIR, and AI-ready.
-To achieve these goals, the DRC team works collaboratively with the other CFDE newly established centers, the participating CFDE DCCs, the CFDE NIH team, and relevant external entities and potential consumers of these three software products. These interactions will be achieved via face-to-face meetings, virtual working groups meeting, one-on-one meetings, Slack, GitHub, project management software, and e-mail exchange. Via these interactions, we will establish standards, workstreams, feedback and mini projects towards accomplishing the goal of developing a lively and productive Common Fund Data Ecosystem.
-
-The **Data Portal** of the CFDE Workbench catalogs several types of uniformly processed data and metadata filesand other digital objects from each participating DCC. The **Information Portal** provides relevant information about each DCC and on overarching consortium activities that include training and outreach events, brief descriptions of CFDE partnership projects, and detailed community-established protocols.
+The CFDE Data Resource Center (DRC) was tasked with developing two web-based portals: an **Information Portal** to serve information about the CFDE and a **Data Portal** to host harmonized metadata and processed data contributed by participating CF Data Coordination Centers (DCCs) and other sources. By combining the data and information portals, the **CFDE Workbench** is a comprehensive resource where users can collect both information and data from CFDE and CF resources, as well as query disease, gene, drug, and other biological entities across standardized data formats from each CF DCC. The CFDE Workbench consolidates efforts toward making CF programs funded resources harmonized, FAIR, and AI-ready.<br/><br/>To achieve these goals, the DRC team works collaboratively with the other CFDE newly established centers, the participating CFDE DCCs, the CFDE NIH team, and relevant external entities and potential consumers of these three software products. These interactions will be achieved via face-to-face meetings, virtual working groups meeting, one-on-one meetings, Slack, GitHub, project management software, and e-mail exchange. Via these interactions, we will establish standards, workstreams, feedback and mini projects towards accomplishing the goal of developing a lively and productive Common Fund Data Ecosystem.<br/><br/>The **Data Portal** of the CFDE Workbench catalogs several types of uniformly processed data and metadata filesand other digital objects from each participating DCC. The **Information Portal** provides relevant information about each DCC and on overarching consortium activities that include training and outreach events, brief descriptions of CFDE partnership projects, and detailed community-established protocols.

src/pages/centers/kc.md

@@ -7,7 +7,7 @@ grant_num: OT2OD036440
 principal_investigators:
 - name: Jason Flannick PhD
   url: https://www.broadinstitute.org/bios/jason-flannick
-- name: Noël Burtt PhD
+- name: Noël Burtt
   url: https://www.broadinstitute.org/bios/no%C3%ABl-burtt
 - name: Kyle Jeffrie Gaulton PhD
   url: https://profiles.ucsd.edu/kyle.gaulton
@@ -21,8 +21,4 @@ icon: https://cfde-drc.s3.us-east-2.amazonaws.com/assets/img/cfde_kc_logo.svg
 layout: '@/layouts/Center.astro'
 short_description: The CFDE KC aims to present scientifically valid knowledge produced by CF projects through both (a) careful knowledge extraction, by ensuring that each edge in the KG is either a primary experimental finding or the result of an expert-applied analysis, and (b) careful knowledge presentation, by building a portal that de-emphasizes general-purpose graph traversal in favor of single-purpose visualizations.
 ---
-Making NIH Common Fund (CF) datasets FAIR is just the first step in unlocking their potential in the era of big data. Scientific progress depends on accessible knowledge, yet non-computational researchers often struggle with interpreting knowledge graphs (KGs) due to their logic-based reasoning, which can overlook scientific context and uncertainty, leading to invalid inferences.
-
-Our CFDE Knowledge Center (KC) will focus on presenting scientifically valid knowledge from CF projects in a KG format aligned with CFDE and external curation efforts. To ensure accuracy, we will emphasize careful knowledge extraction—ensuring each KG edge is based on primary experimental findings or expert analysis—and thoughtful knowledge presentation, using tailored visualizations instead of general graph traversal.
-
-Leveraging our experience from four large-scale NIH-funded projects, we will develop a user-friendly portal that enhances data accessibility and scientific validity, empowering a diverse range of researchers to engage with CF-generated knowledge.
+Making NIH Common Fund (CF) datasets FAIR is just the first step in unlocking their potential in the era of big data. Scientific progress depends on accessible knowledge, yet non-computational researchers often struggle with interpreting knowledge graphs (KGs) due to their logic-based reasoning, which can overlook scientific context and uncertainty, leading to invalid inferences.<br/><br/>Our CFDE Knowledge Center (KC) will focus on presenting scientifically valid knowledge from CF projects in a KG format aligned with CFDE and external curation efforts. To ensure accuracy, we will emphasize careful knowledge extraction—ensuring each KG edge is based on primary experimental findings or expert analysis—and thoughtful knowledge presentation, using tailored visualizations instead of general graph traversal.<br/><br/>Leveraging our experience from four large-scale NIH-funded projects, we will develop a user-friendly portal that enhances data accessibility and scientific validity, empowering a diverse range of researchers to engage with CF-generated knowledge.