CFDE Webinar Series

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.<br/><br/>Relevant resources that will be discussed: <br/>**Rummagene**: https://rummagene.com/ <br/>**SigCom LINCS**: https://maayanlab.cloud/sigcom-lincs/ <br/>**Playbook Workflow Builder**: https://playbook-workflow-builder.cloud/

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

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).<br/><br/> Relevant resources that will be discussed:<br/> **IDG portal**: https://druggablegenome.net/<br/> **Pharos**: https://pharos.nih.gov/

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.

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.<br/><br/> Relevant resources that will be discussed:<br/> **DrugCentral**: https://drugcentral.org/<br/>

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.<br/><br/> Relevant resources that will be discussed: <br/> **Pharos**: https://pharos.nih.gov/

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).

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.

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.

Seth Berke, a Post-Bacc researcher explains a use case leveraging cloud infrastructure including Docker containers and CAVATICA to analyze data across various DCCs.

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/).

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.

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.

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.

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.

In this lecture, Giacomo Marino, a Bioinformatics Software Engineer in the Ma'ayan Lab at the Icahn School of Medicine at Mount Sinai, describes a new platform for assembling, augmenting, combining, visualizing, and analyzing gene sets. The platform utilizes LLMs to form hypotheses from datasets produced by NIH Common Fund programs.

The workshop thoroughly discussed the Common Fund Data Ecosystem (CFDE), an open-access resource enabling the broad use of NIH Common Fund Data. We cover navigating and using CFDE data, analysis tools, and knowledge and how CFDE can accelerate common and rare human disease research and basic biological discoveries.

The 4D Nucleome consortium aims to understand the underlying principes of nuclear organization across space and time. Dr. Peter Park went over the infrastructure that 4DN have developed, the data they generated, as well as their published work over the course of ten years.

Julie Jurgens from the Knowledge Center presented on scientific updates from the Knowledge Center, including the novel method, PIGEAN.

Dr. Allissa Dillman from the Training Center presented on Hackathons with Impact: Data-Driven Projects with CFDE.

The Integration and Coordination Center presented about Sustainability and Evaluation Within the Common Fund Data Ecosystem.

NIH HuBMAP JumpStart Fellow Dr. Andreas Bueckle presented 'Multiscale Virtual Reality Exploration of the 3D Human Reference Atlas Provides Novel Insights into Health, Aging, and Disease.'