Workshops
Scientific Workshops
Core Bioinformatics Workshops
The Bioinformatics Core team at NYUAD organized a series of workshops during AY 23-24, which were open to the entire NYUAD community, including undergraduates, graduates, postdocs, researchers, and faculty. These workshops were conducted in collaboration with the NYUAD Library and the Office of Graduate and Postdoctoral Support. Each workshop attracted significant interest, consistently resulting in at least 10 individuals on the waiting list, with some sessions having up to 80 people waiting to participate.
The topics covered included:
- Metagenomics
- Python for Beginners
- Intermediate Python
- Introduction to R & RShiny
- Code Rigor and Reproducibility in R
- Single Cell RNAseq Analysis
- Variant Detection & Annotation
- De novo Transcriptome Assembly and Annotation
Metagenomics Data Analysis Workshop
A hands-on training course titled "Metagenomics data analysis" was conducted by Research Scientist Muhammad Arshad of the Core Bioinformatics team. The training focused on analyzing the metagenomics shotgun sequencing data where participants submitted their data on Dalma HPC. They were navigated through the complete data analysis workflow using an internally developed BioSAILs workflow management system.
Introduction to BioSAILs Workshops
The Core Bioinformatics team delivered 2 training workshops titled "Introduction to BioSAILs." The workshop was a hands-on tutorial on how to use BioSAILs, NYUAD's bioinformatics workflow management system, and an introduction to WMS. It also provided an opportunity for participants to discuss their research needs and how to tailor analysis workflows using BioSAILs for their needs.
Deep Sequencing Workshop
This hands-on, 5-day training workshop aimed to introduce the concepts of performing high throughput bioinformatics analysis on the NYUAD HPC (Dalma), using the workflows/pipelines developed by the Core Bioinformatics. It addressed De novo genome assembly, De novo metagenomic analysis, RNA-seq analysis, Single Cell RNAseq analysis, CHIP-seq analysis, variant detection (SNPs/Indels), and data visualization. This workshop aimed to prepare and train participants on performing these types of analysis in a high-performance- computing environment; the Bioinformatics team used this opportunity to train participants in the usage of BioSAILs. Before attending this workshop, participants completed two online courses that introduced Linux & the command line interface and the R statistical language. The workshop included short introduction talks/presentations on each subject, followed by hands-on data analysis. The Deep Sequencing Analysis Book Camp was organized and jointly delivered between NYU-AD and NYU-NY. The topics covered included:
- How the HPC is organized and partitioned
- SLURM commands
- The NYUAD Core Bioinformatics workflows/pipelines
- NGS data and formats
- Data quality checking and quality trimming
- Sequence alignment, software, methods & file formats
- De novo metagenomics analysis, software, and methods
- De novo genome analysis, software, and methods
- RNA-seq analysis (Expression profiling and Differential gene expression), software, methodology, and file formats
- Single-cell RNAseq analysis using the popular R package “Seurat”
- Variant detection & variant annotation (SNPs & Indels), software, methodology, and file formats
- CHIP-seq analysis
- Data visualization for Variant detection as well as RNAseq data exploration and plotting
Hands-on Workshop in Bioinformatics: Introduction to Bioinformatics
The Bioinformatics workshop was designed to cover key bioinformatics concepts and tools required to analyze genomic data sets. Participants were exposed to the most recent trends in the field and gained experience in data analysis for DNA and RNA expression datasets. This workshop included several hands-on sessions, research presentations, and an opportunity for participants to discuss their projects and ideas.
Biology Exchange
The Center for Genomics and Systems Biology, the NYUAD Core Technology Platforms, and the NYUAD Science Division co-organized the NYUAD Biology Exchange (BioEx). NYUAD Researchers gathered at BioEx to discuss and share their expertise on techniques and core platforms, including sequencing, bioinformatics, and microscopy.
Career Development Workshops
Applying for Faculty Positions Workshop
A panel discussion for postdoctoral associates and research scientists delivered by Stéphane Boissinot, Kirsten Sadler Edepli from New York University Abu Dhabi alongside Amandine Cornille from The National Center for Scientific Research, and Ikram Blilou from King Abdullah University of Science and Technology. This workshop offered NYUAD researchers valuable insights into best practices and effective strategies for applying to faculty positions.
Applying for Faculty Positions Workshop
A panel discussion for postdoctoral associates and research scientists delivered by Stéphane Boissinot, Claude Desplan, Kirsten Sadler Edepli from New York University Abu Dhabi, and Michael Dorrity from The European Molecular Biology Laboratory. This workshop provided NYUAD researchers the opportunity to learn the best practices and processes for applying for faculty positions.
Applying for Faculty Positions Workshop
A panel discussion for postdoctoral associates and research scientists led by Justin Blau and NYUAD standing faculty, provided NYUAD Researchers the opportunity to learn the best practices and processes for applying for faculty positions.
How to Give an Effective Research Workshop?
Justin Blau conducted 'How to Give an Effective Research Workshop?' to NYUAD Researchers. This workshop provided Researchers the opportunity to improve their communication skills, gain expert knowledge, and the confidence to discuss their research in public.
Grant Writing for Researchers and Junior Faculty
'Grant Writing for Researchers and Junior Faculty,' presented by Justin Blau, taught participants how to write a successful grant proposal.