www.uab.edu/ccts [email protected] 205.934.7442 U-BRITE : a biocomputing infrastructure to enable collaborative genomic data science SUPPORT CONTACT To start a project Contact Dr. Jake Y. Chen ([email protected] ) Technical Support Contact Jelai Wang ([email protected] ) Visit the U-BRITE web site at http://ubrite.informatics.uab.edu/ . INTRODUCTION U-BRITE (UAB Biomedical Research Information Technology Enhancement) assembles HIPAA-compliant, clinical informatics and bioinformatics tools layered on top of high-performance computing infrastructure. We aim to help researchers better manage and analyze genomic medicine data sets in a new “translational research commons” environment. U-BRITE will facilitate and enable interdisciplinary team science across geographic locations. • Equip translational biomedical researchers with cutting- edge data science tools • Facilitate computational method development for integrated genomic medicine studies • Build an online workspace and enable data-intensive scholarly communication for interdisciplinary study teams Aims ARCHITECTURE OVERVIEW BENEFITS • Access clinical data from Clinical Data Repository to build cohorts. • Integrate multi-omics data from local databases or remote API inside the Omics Data Repository. • Prototype in Jupyter Notebook and deploy to UAB’s Cheaha supercomputer without leaving the Analysis Gateway. • Develop team-based or open-source coding via the Source Code Repository. • Achieve and ship reproducible research workflow with Binder supported by U- BRITE. • Streamline NIH-compliant genomic data sharing with scholarly communication using Expo Gallery. • Self-help or gain full support from data scientists in the UAB Informatics Institute. CASE STUDY Case Study: A Multiethnic Longitudinal Study in SLE A significant unmet need was the inability to easily integrate these existing datasets to drive further discovery research into the biological basis for disease development and progression. Accordingly, supported by U-BRITE, Dr. Jeff Edberg’s team developed a master database of IDs associated with each participant (study ID for clinical data, genotyping IDs for experimental results). Using a Jupyter Notebook allowed us to merge data elements from our phenotypic and genotypic resources. We have also built an interface that allows us to derive real-time clinical data from the EMR through U-BRITE’s Clinical Data Repository. This foundational infrastructure allows us to more easily integrate our WES data for analysis. Key questions to be addressed will be genotype-phenotype relationships with SLE development in minorities (African-Americans) and genotype-disease severity (such as renal disease) relationships based on up-to-date clinical data. Finally, with integration of our specimen biobank, we will be able to easily determine availability of specimens for mechanistic studies as follow-up to the genetic findings with further linkage to EHR data to determine patient availability for collection of new specimens. Statistical analysis of 62 WGS of Lupus patients with rapid-onset renal failure (partial chr 1) Recruited patients by genotype & visit time 0% 3% 1% 5% 0% 32% 59% Linked Donors /Patients 1+ year ago next-year Pre-1900 Pre-2000 prev-month StartOfTime NA's USE CASE SCENARIOS Jelai Wang, Jake Y. Chen, and the UAB Informatics Institute U-BRITE team http://ubrite.informatics.uab.edu A genomic medicine research team can take advantage of multiple components of the U-BRITE infrastructure to perform team-based biomedical data science.

ubrite.informatics.uab• Prototype in Jupyter Notebook and deploy to UAB’s Cheaha supercomputer without leaving the Analysis Gateway . • Develop team-based or open-source coding

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Page 1: ubrite.informatics.uab• Prototype in Jupyter Notebook and deploy to UAB’s Cheaha supercomputer without leaving the Analysis Gateway . • Develop team-based or open-source coding

www.uab.edu/[email protected] 205.934.7442

U-BRITE : a biocomputing infrastructure to enable collaborative genomic data science

SUPPORT CONTACTTo start a projectContact Dr. Jake Y. Chen ([email protected])

Technical SupportContact Jelai Wang ([email protected])

Visit the U-BRITE web site at http://ubrite.informatics.uab.edu/.

INTRODUCTION

U-BRITE (UAB Biomedical Research Information TechnologyEnhancement) assembles HIPAA-compliant, clinical informaticsand bioinformatics tools layered on top of high-performancecomputing infrastructure. We aim to help researchers bettermanage and analyze genomic medicine data sets in a new“translational research commons” environment. U-BRITE willfacilitate and enable interdisciplinary team science acrossgeographic locations.

• Equip translational biomedical researchers with cutting-edge data science tools

• Facilitate computational method development for integratedgenomic medicine studies

• Build an online workspace and enable data-intensivescholarly communication for interdisciplinary study teams

Aims

ARCHITECTURE OVERVIEW

BENEFITS• Access clinical data from Clinical Data

Repository to build cohorts.• Integrate multi-omics data from local

databases or remote API inside the Omics Data Repository.

• Prototype in Jupyter Notebook and deploy to UAB’s Cheaha supercomputer without leaving the Analysis Gateway.

• Develop team-based or open-source coding via the Source Code Repository.

• Achieve and ship reproducible research workflow with Binder supported by U-BRITE.

• Streamline NIH-compliant genomic data sharing with scholarly communication using Expo Gallery.

• Self-help or gain full support from data scientists in the UAB Informatics Institute.

CASE STUDYCase Study: A Multiethnic Longitudinal Study in SLEA significant unmet need was the inability to easily integrate these existingdatasets to drive further discovery research into the biological basis fordisease development and progression. Accordingly, supported by U-BRITE, Dr.Jeff Edberg’s team developed a master database of IDs associated with eachparticipant (study ID for clinical data, genotyping IDs for experimentalresults). Using a Jupyter Notebook allowed us to merge data elements fromour phenotypic and genotypic resources. We have also built an interface thatallows us to derive real-time clinical data from the EMR through U-BRITE’sClinical Data Repository. This foundational infrastructure allows us to moreeasily integrate our WES data for analysis. Key questions to be addressed willbe genotype-phenotype relationships with SLE development in minorities(African-Americans) and genotype-disease severity (such as renal disease)relationships based on up-to-date clinical data. Finally, with integration of ourspecimen biobank, we will be able to easily determine availability ofspecimens for mechanistic studies as follow-up to the genetic findings withfurther linkage to EHR data to determine patient availability for collection ofnew specimens.

Statistical analysis of 62 WGS of Lupus patients with rapid-onset renal failure (partial chr 1)

Recruited patients by genotype &

visit time

0%3%1% 5%

32%59%

Linked Donors/Patients

1+ year agonext-yearPre-1900Pre-2000prev-monthStartOfTimeNA's

USE CASE SCENARIOS

Jelai Wang, Jake Y. Chen, and the UAB Informatics Institute U-BRITE team

http://ubrite.informatics.uab.edu

A genomic medicine research team can take advantage of multiple components of the U-BRITE infrastructure to perform team-based biomedical data science.

mailto:[email protected]

http://ubrite.informatics.uab.edu/