CFDE Information Portal

CFDE Workbench

Information PortalData Portal

Home

CF Programs

Partnerships

Training & Outreach

Publications

Webinars

Documentation

What's New?

CFDE Workbench

CFDE Webinar Series

Join us on the last Friday of each month from 1-2 PM Eastern Time to learn more about how the CFDE is harmonizing and discovering new knowledge by integrating datasets, tools and other resources from a collection of NIH Common Fund programs.

Upcoming Webinars

More details will be added soon

Past Webinars

Friday, Nov 22, 2024

Introduction to Communication and Outreach to Maximize Product Adoption (COMPA)
Bernard de Bono
PI, COMPA
Summary
In this lecture, Dr. Bernard de Bono presented information on the CFDE Communication and Outreach to Maximize Product Adoption (COMPA) partnership. He explained COMPA’s strategic approaches for user profiling, outreach activities, and gap analysis aimed to promote CFDE-developed products.
Data-Driven Strategies for Developing and Marketing Scientific Information Resources
Stephen Larson
CEO, MetaCell
Summary
In this lecture, Dr Stephen Larson, the CEO of Metacell presented strategies for driving user engagement to scientific tools. Metacell works with the COMPA CFDE partnership. He explained the challenges of user adoption, and effective user engagement strategies, and shared their experiences on various methods of outreach activities. He also shared the survey about user behaviors and tendencies toward scientific products.

Friday, Oct 25, 2024

Comprehensive Multi-Species, Multi-Omic, Multi-Tissue Insights into Exercise Molecular Responses
David Jimenez-Morales, PhD
Bioinformatics Lead, MoTrPAC
Summary
In this lecture, Dr. David Jimenez-Morales presents a seminar titled: MoTrPAC - Comprehensive Multi-Species, Multi-Omic, Multi-Tissue Insights into Exercise Molecular Responses. Dr. Jimenez-Morales is a Bioinformatics Lead at Stanford University and member of the NIH Common Fund Molecular Transducers of Physical Activity Consortium (MoTrPAC) program (https://motrpac.org/) Data Coordination Center (DCC). In the lecture, Dr. Jimenez-Morales introduces the MoTrPAC DCC and explains their published and future studies on the molecular changes that occur during acute and long term aerobic and weight exercise in humans and rats.
The MoTrPAC Data Hub
Jimmy Zhen
Software Developer, MoTrPAC
Summary
In this lecture, Jimmy Zhen, a software developer at the Molecular Transducers of Physical Activity Consortium (MoTrPAC) Data Coordination Center (DCC) explains and demonstrates the MoTrPAC Data Hub (https://motrpac-data.org/). He covers various features of the data hub including the data download, analysis tools, and interactive visualizations, as well as the backend architecture supporting these features.

Friday, Sep 27, 2024

Tools and methods for discovering disease-causing gene regulatory variants from WGS data, with application to Congenital Heart Disease
Keyang Yu
Genboree Research Assistant, exRNA
Summary
This lecture by Keyang Yu, a member of ERCC (https://exrna.org/) DCC, was about tools and methods for discovering disease-causing gene regulatory variants from WGS data, with application to congenital heart disease. To overcome the limitations of genome-wide association studies (GWAS), Keyang Yu introduced a framework for the discovery of pathogenic non-coding variants. The framework uses point-wise mutual information (PMI) models and aggregates regulatory information using the CFDE Link Data Hub (CFDE LDH; https://genboree.org/cfde-gene/ui/).

Friday, Aug 30, 2024

Overview of Acute to Chronic Pain Signatures Consortium - Part 1
Martin Lindquist, MSc, PhD
PI, A2CPS DRIC
Summary
Dr. Martin Linquist, the PI of the Data Integration and Resource Center for Acute to Chronic Pain Signatures (A2CPS), presented an overview of the Acute to Chronic Pain Signatures consortium.
Overview of Acute to Chronic Pain Signatures Consortium - Part 2
Ari Kahn, PhD
PI, A2CPS DCC and a member of A2CPS DIRC, TACC
Summary
Ari Kahn, a PI for the A2CPS DCC, and a member of DIRC, TACC, covered how A2CPS manages and processes the data and the release plan.
An A2CPS Use Case with Cloud Infrastructure
Seth Berke
Post-Bacc Researcher, Acute to Chronic Pain Signatures Consortium
Summary
Seth Berke, a Post-Bacc researcher explains a use case leveraging cloud infrastructure including Docker containers and CAVATICA to analyze data across various DCCs.

Friday, Jul 26, 2024

A Tour of the Human Reference Atlas v2.1
Katy Börner and Bruce Herr
Cyberinfrastructure for Network Science Center (CNS)
Summary
A Tour of the Human Reference Atlas (HRA) v2.1 was delivered by Katy Börner, Center Director for the Cyberinfrastructure for Network Science Center (CNS), and Bruce Herr, Technical Director for CNS. They explain the history and goals of HuBMAP and the concept of the Vascular Common Coordinate Framework (VCCF).

Friday, Jun 28, 2024

Illuminating the Druggable Genome (IDG) History and Background
Jeremy Yang, Ph.D
Research Associate Professor, UNM SoM, DoIM, TI Division
Summary
Jeremy Yang, PhD, provides a brief overview of the workshop and the history and background of the IDG DCC. He explains the network of institutions and collaborators involved and introduces the IDG portal and Pharos data portal. He then covers how they categorize targets into four target development levels (TDLs).

Relevant resources that will be discussed:
IDG portal: https://druggablegenome.net/
Pharos: https://pharos.nih.gov/
Illuminating the Druggable Genome (IDG) Importance and Impact
Anna Waller, Ph.D
Scientist & Project Manager, UNM SoM, Dept of Pathology
Summary
Anna Waller, PhD introduced the importance and impact of the IDG program. She explains the collaborative efforts within the IDG consortium. She then covered the research output, global collaborations, and outreach initiatives that have advanced the understanding of understudied proteins and their potential for clinical therapeutics.
DrugCentral, Exemplar and Featured IDG Knowledge Base
Jayme Holmes
Sr Engineer & Lead Developer, UNM SoM, DoIM, TI Division
Summary
Jayme Holmes, a lead programmer for DrugCentral, introduced the features and growth of DrugCentral including the demonstration of an AI-powered Avatar, designed to assist DrugCentral users.

Relevant resources that will be discussed:
DrugCentral: https://drugcentral.org/
Pharos, the IDG Data Portal
Timothy Sheils
Sr Engineer & Project Manager, NIH NCATS
Summary
Timothy Sheils, a senior engineer at NIH NCATS, introduced the Pharos resource, covering how Pharos aggregated 78 data resources, the Pharos user-interface, filters, and ways to download and interact with the data using APIs.

Relevant resources that will be discussed:
Pharos: https://pharos.nih.gov/

Friday, May 31, 2024

Improved Methods to Query the LINCS L1000 Data
Avi Ma'ayan, PhD
LINCS Data Coordination Center and the CFDE Data Resource Center
Summary
The Library of Integrated Network-Based Cellular Signatures (LINCS) was an NIH Common Fund program that was established to catalog how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and gene expression signatures. The presentation will cover LINCS datasets, tools, and a newly developed method to query the LINCS L1000 data for better prioritization of drugs, small molecules and single gene perturbations.

Relevant resources that will be discussed:
Rummagene: https://rummagene.com/
SigCom LINCS: https://maayanlab.cloud/sigcom-lincs/
Playbook Workflow Builder: https://playbook-workflow-builder.cloud/
Automatic Mining of Human and Mouse Gene Sets from GEO
Giacomo Marino
LINCS Data Coordination Center and the CFDE Data Resource Center
Summary
RummaGEO is a web server application that enables gene expression signature search against thousands of human and mouse RNA-seq studies deposited into GEO. To enable such a search engine, an offline automatic process was established to identify the experimental conditions from uniformly aligned GEO studies available from ARCHS4. Once conditions are identified, differential expression signatures are computed to extract gene sets from these signatures. In total, RummaGEO currently contains 135,264 human and 158,062 mouse gene sets from 23,395 GEO studies. Overall, RummaGEO provides an unprecedented resource for the biomedical research community enabling hypothesis generation for many future studies.

Relevant resources that will be discussed:
RummaGEO: https://rummageo.com/
ARCHS4: https://maayanlab.cloud/archs4/

Friday, Apr 26, 2024

Overview of the Common Fund Data Ecosystem
George Papanicolaou, PhD
NIH, CFDE Program Leader
Christy Kano, PhD
NIH, CFDE Program Officer
Metabolomics Workbench/National Metabolomics Data Repository
Shankar Subramaniam, PhD and Mano Maurya, PhD
Metabolomics Workbench DCC and CFDE Data Resource Center
CFDE and the Biomedical Research Community
Noël Burtt and Kyle Gaulton, PhD
CFDE Knowledge Center

CFDE Workbench

Consortium

Ecosystem

Assets

@CFDE Workbench 2024

The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.

Consortium

Ecosystem

Assets

CFDE Workbench

The CFDE Workbench is actively being developed and maintained by the CFDE Data Resource Center (DRC).The DRC is funded by OT2OD036435 from the Common Fund at the National Institutes of Health.

@CFDE Workbench 2024