Bioinformatics workshops - Fall 2023
We continuously organize basic and advanced workshops on a wide range of bioinformatics topics. These workshops are designed to address practical issues often encountered in bioinformatics work. They are designed to help users understand and work with the CRC clusters.
These workshops have hands-on components that require the following requirements be set up before a workshop begins.
- Participants should have an account on the HTC cluster, which is the cluster we will use for demonstration purposes. (page 1 of this documentation)
- This workshop also requires that participants either be on a Pitt network (hard-line) or behind a VPN. (page 2 of this documentation)
- You can submit jobs, i.e., your group's account has not expired, and your group's service units (CPU-hours) have not been exhausted entirely (page 4 of this documentation)
As a general rule, we offer no troubleshooting for technical setup issues at the workshops themselves! Therefore, be aware that if you do not set up the workshop's technical prerequisites well in advance, you may not be able to participate fully in its hands-on activities.
Please note: workshops will be presented in a hybrid format with up to 20 in-person participants. If you register for an in-person session and the in-person session is full, you will be alerted and receive a video conferencing link via the e-mail address you provide. CRC will continue to follow University guidelines regarding COVID-19 precautions, so other changes could be possible depending on those guidelines.
Register for all workshops: Fall 2023 bioinformatics workshops
Multi-Omics Data Analysis
Tuesday, Sep. 26, 2023, 1:00 pm - 4:00pm
The course will provide an overview, and the theoretical foundation of the methods for multi-modal integration, with a focus on omics data. In the practical session, participants will learn how to select the most appropriate methods and apply it to bulk and/or single cell multi-omics data sets. The workflow will include pre-processing and data management, method performance assessment, choice of tuning parameters, interpretation of the models, data visualization and interactive exploration. Solid experience with R is required. Presented by Dhivyaa Rajasundaram
Introduction to electronic health record (EHR) data analysis
Tuesday, Oct. 10, 2023, 1:00pm - 4:00pm
The lecture will introduce the EMR data structures, data analysis and paper discussion, focusing on medication use and patient outcome prediction with machine learning/deep learning approaches. Presented by LiRong Wang
Best practices for rigor and reproducibility in bioinformatics - Documentation
Tuesday, Oct. 17, 2023, 1:00pm - 2:30pm
This workshop gives an introduction to bioinformatics documentation essentials and research reproducibility guidelines. Utilizing methodologies used by the Genomics Analysis Core, the workshop will provide recommendations and directions with real-world examples of documentation to promote reproducibility for bioinformatics research projects. By the end of the workshop, participants will have a framework to follow to document their own bioinformatics projects with tools such as R markdown, HackMD, Github Wiki, and file management systems. In addition, reproducible pipelines with technologies such as nfcore and Docker will also be discussed. Presented by Uma Chandran
An Introduction to Computational Systems Immunology
Tuesday, Oct. 24, 2023, 1:00pm - 4:00pm
We will provide a high-level conceptual introduction to machine learning and network approaches used to analyze multi-omic datasets (e.g., scRNA-seq, scATAC-seq, bulk RNA-seq, bulk ATAC-seq, proteomic/cytokine) routinely generated in systems immunology studies. The workshop will also include hands-on demos for some of these techniques. Moderate R and/or Python proficiency is required. Presented by Jishnu Das
Introduction to R Shiny App
Tuesday, Nov. 7, 2023, 1:00pm - 4:00pm
I will briefly introduce Shiny, a popular R package, to build highly interactive web applications without needing any other programming languages. I will introduce two R packages, based on reusable components created using Shiny modules, to build a Shiny app for interactive mining of health science data. I will summarize the options to deploy Shiny web apps in production. Presented by Fangping Mu
An Introduction to Functional magnetic resonance imaging (fMRI) data analysis
Wednesday, Nov. 29, 2023, 12:30pm - 3:30pm
In recent times, there has been a surge in neuroimaging research utilizing functional Magnetic Resonance Imaging (fMRI). This research has generated a vast amount of complex fMRI data characterized by intricate spatiotemporal patterns. This workshop aims to guide attendees through the complex preprocessing steps and the subsequent statistical analysis of task-based and resting-state fMRI data. Additionally, we will discuss some latest trending research topics in human brain mapping via fMRI. Presented by Tingting Zhang