{"id":5409,"date":"2024-08-23T01:49:24","date_gmt":"2024-08-23T06:49:24","guid":{"rendered":"https:\/\/info.hsls.pitt.edu\/molbio\/?p=5409"},"modified":"2025-01-06T16:02:20","modified_gmt":"2025-01-06T21:02:20","slug":"fall-2024-bioinformatics-workshops","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2024\/08\/23\/fall-2024-bioinformatics-workshops\/","title":{"rendered":"Fall 2024 CRC Bioinformatics Workshops"},"content":{"rendered":"

The fall Bioinformatics Workshop Series<\/a> from the Center for Research and Computing (CRC)<\/a> is designed to address practical issues often encountered in bioinformatics work. These workshops are designed to help users understand and work with the CRC clusters. Some basic understanding of R or Python programming and the Linux environment will be advantageous, but is not required unless specified for a particular workshop.<\/p>\n

Free and open to everyone at University of Pittsburgh and its affiliates.<\/p>\n

Workshops in this series will be offered in-person only.<\/p>\n

Register for the Bioinformatics Workshop Series<\/a><\/p>\n

<\/p>\n

Spatial Transcriptomics – Workshop 1<\/strong><\/h3>\n

Sep. 30, Monday, 1:00pm – 4:00pm<\/p>\n

10X Spatial Transcriptomics (Visium)-\u00a0<\/strong>Sample requirements, evaluate sample quality, tissue optimization, sample and library preparation, and library QC and sequencing. Presented by\u00a0Amanda Poholek<\/strong><\/p>\n

Demo on 10X genomics cloud analysis<\/strong>: From FASTQs to biological information with Space Ranger<\/p>\n

Running Space Ranger using the CRC cluster:<\/strong>\u00a0For fresh frozen samples and formalin fixed paraffin embedded samples Presented by\u00a0Dhivyaa Rajasundaram<\/strong><\/p>\n

 <\/p>\n

Spatial Transcriptomics – Workshop 2<\/strong><\/h3>\n

Oct. 1, Tuesday, 1:00pm – 4:00pm<\/strong><\/p>\n

Introduction to 10X Visium and Visium HD Data Analysis –\u00a0<\/strong>Step by step analysis to correct batch effects between datasets, pre-processing spatial transcriptomics data, identification of spatial features, and spatially variable genes identification.<\/p>\n

Basic R knowledge required. Presented by\u00a0Silvia Liu<\/strong><\/p>\n

 <\/p>\n

Spatial Transcriptomics – Workshop 3<\/strong><\/h3>\n

Oct. 2, Wednesday, 1:00pm – 4:00pm<\/strong><\/p>\n

Exploring Visium data: Deconvolution and Mapping Methods:\u00a0<\/strong>Integrating scRNA-seq and spatial data.\u00a0<\/strong>Cell-type deconvolution of the spatially resolved transcriptome and visualization.<\/p>\n

Basic R knowledge required. Presented by\u00a0Jiefei Wang<\/strong><\/p>\n

 <\/p>\n

Spatial Transcriptomics – Workshop 4<\/strong><\/h3>\n

Oct. 3, Thursday, 1:00pm – 4:00pm<\/strong><\/p>\n

Cell-Cell Communication Analysis:\u00a0<\/strong>Uncover cell-cell communications for spot-based spatially resolved transcriptomics data. Spatially informed ligand-receptor and ligand-receptor-target analysis.<\/p>\n

Basic R knowledge required.\u00a0 Presented by\u00a0Dhivyaa Rajasundaram<\/strong><\/p>\n

 <\/p>\n

Spatial Transcriptomics – Workshop 5<\/strong><\/h3>\n

Oct. 4, Friday, 1:00pm – 4:00pm<\/strong><\/p>\n

Gene Co-expression Network Estimation for Spatial Transcriptomics:\u00a0<\/strong>Cover basics of WGCNA and \u00a0perform co-expression network analysis on spot-based spatial transcriptomics data.<\/p>\n

Basic R knowledge required. Presented by\u00a0Jishnu Das<\/strong><\/p>\n

 <\/p>\n

Spatial Transcriptomics – Workshop 6<\/strong><\/h3>\n

Oct. 7, Monday, 1:00pm – 4:00pm<\/strong><\/p>\n

The Single-Cell Spatial Transcriptomics Analysis (ScSTA) Cookbook<\/strong><\/p>\n

This workshop aims to provide attendees with comprehensive knowledge and hands-on experience in the data analysis of sub-cellular resolution single-cell spatial transcriptomics (ScST) technologies such as Nanostring CosMx and 10X Genomics Xenium. We will start with an introduction to the components of ScST, including image registration, cell segmentation, cell type identification, spatial gene expression analysis, and more. A hands-on guided tutorial using real-world lung adenocarcinoma and COVID-19 datasets will follow. Presented by\u00a0Arun Das<\/strong><\/p>\n

 <\/p>\n

Spatial Transcriptomics – Workshop 7<\/strong><\/h3>\n

Oct. 8, Tuesday, 1:00pm – 4:00pm<\/strong><\/p>\n

10X Genomics Xenium data analysis<\/strong><\/p>\n

The hands-on session will provide a solid foundation for handling and analyzing 10x Genomics Xenium datasets. We will begin with the Xenium onboard analysis ranger to conduct initial data exploration and quality assessment. Following this, we will move on to a downstream analysis pipeline using the Seurat workflow, which includes data import, quality control, dimension reduction and clustering, visualization and integration. We will also briefly cover advanced topics including cell segmentation, cell type deconvolution and integration with single cell data. Presented by\u00a0Dhivyaa Rajasundaram<\/strong><\/p>\n

 <\/p>\n

Monai for biomedical image analysis<\/strong><\/h3>\n

Nov. 14, Thursday, 1:00pm – 4:00pm<\/strong><\/p>\n

This workshop will explore Project MONAI, a set of open-source, freely available collaborative frameworks built for accelerating research and clinical collaboration in Medical Imaging. The goal of MONAI is to accelerate the pace of innovation and clinical translation by building a robust software framework that benefits nearly every level of medical imaging, deep learning research, and deployment.
\nPrerequisite:\u00a0Introductory deep learning knowledge, with comfort with PyTorch and transfer learning preferred. Intermediate Python experience, including object-oriented programming and libraries. Presented by\u00a0Yassin Khalifa<\/strong><\/p>\n

 <\/p>\n

Leveraging large language models for single-cell and biomedical research<\/strong><\/h3>\n

Dec. 10, Tuesday, 1:00pm – 4:00pm<\/strong><\/p>\n

This workshop will introduce emerging large language models (LLMs), including GPT-4 developed by OpenAI. We will discuss \u201cprompt engineering\u201d techniques to efficiently and effectively use these LLMs for biomedical research, such as cell type annotation for scRNA-seq data and the inference of gene-gene regulatory mechanisms and gene-drug relationships using scientific publications. Attendees will have hands-on experience with open-source LLMs and prompt engineering using CRC clusters. Presented by\u00a0Yu-Chiao Chiu<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

The fall Bioinformatics Workshop Series<\/a> from the Center for Research and Computing (CRC)<\/a> is designed to address practical issues often encountered in bioinformatics work. These workshops are designed to help users understand and work with the CRC clusters.<\/p>\n

Read more…<\/a><\/p>\n","protected":false},"author":46,"featured_media":5432,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[48],"tags":[],"class_list":["post-5409","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-september-2024"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/5409","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/users\/46"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/comments?post=5409"}],"version-history":[{"count":4,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/5409\/revisions"}],"predecessor-version":[{"id":5435,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/5409\/revisions\/5435"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media\/5432"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=5409"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=5409"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=5409"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}