Topic : Introduction to Single Cell Analysis Workflows

Speaker : John Lafin, PhD

John is a Computational Biologist in the Strand Lab in the Department of Urology at UT Southwestern. The Strand Lab’s focus is developing a deep understanding of the cellular components and functions of the human lower urinary tract, and how these aspects change during both benign and malignant urological disease. In pursuit of this goal, Dr. Lafin’s work is focused on the production and analysis of single cell genomics and spatial transcriptomics data. These datasets and pipelines will be released as public references following FAIR (Findable, Accessible, Interoperable, Reusable) principles. 

Abstract: Single cell transcriptomics is a powerful tool which allows for an examination of transcriptional changes at cellular resolution. However, analysis of these datasets can be challenging due in part to a lack of a standard analysis pipeline and steep computational and/or expertise requirements. As part of the BioHPC Fellowship program, Dr. Lafin has developed Astrocyte workflows to provide a user-friendly interface for single cell analysis and interactive visualization. In this session, he will introduce these workflows, discuss their use, and demonstrate a single cell visualization workflow. The collection of Strand Lab single cell Astrocyte workflows is available for any BioHPC user and can be accessed here.  

Topic : ATAC-seq Workflow Development

Speaker : Achisha Saikia, M.S. , Felix Perez , M.S.

Achisha is a Computational Biologist in Lee Lab within the Department of Bioinformatics at UT Southwestern Medical Center. Her work focuses on genomics and analyzing Next Generation Sequencing data, along with building pipelines using workflow management systems. As part of BioHPC, Achisha developed an astrocyte workflow with Felix Perez to analyze ATAC-seq data. 

Felix is a Computational Scientist in BioHPC within the Department of Bioinformatics at UT Southwestern Medical Center. He was brought onto the Astrocyte Workflow Platform project team to develop new astrocyte workflows for frequently used bioinformatics pipelines and to containerize the software stacks utilized by existing workflows. His current work has been developing the ATAC-seq workflow, and a containerized version of the ChIP-seq Analysis workflow. 

 Abstract: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a cutting-edge technique for probing chromatin accessibility across the genome, providing insights into regulatory elements and chromatin structure. By integrating the ENCODE ATAC-seq pipeline, we have established a robust and reproducible workflow on the Astrocyte platform to process and analyze ATAC-seq data. Astrocyte facilitates advanced computational workflows for the UT Community, ensuring standardized, high-quality data processing. This integration enables researchers to elucidate chromatin dynamics and regulatory landscapes with precision and efficiency. The workflow's documentation and guidelines are accessible on the Astrocyte platform, providing a comprehensive resource for effective ATAC-seq data analysis. 

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BioHPC provides high-performance computing (HPC) infrastructure & services to the UT Southwestern community. It was conceptualized by and is housed within the Lyda Hill Department of Bioinformatics. The BioHPC team covers all aspects of HPC for users, from technical jobs like system expansion and maintenance to carrying out collaborative work on computational aspects of research projects. BioHPC also provides support to current UTSW PhD students and PostDocs interested in applying computer science to their ongoing biomedical research projects.

This event will be held in a hybrid format.