2021
Orchestra: A cloud platform for hosting hands-on computational workshop environments
Orchestra is a cloud platform for hosting hands-on computational workshop environments. In this talk, I review the detailed use case of Bioconductor Workshops and then proceed to a shallow dive into Kubernetes infrastructure that powers Orchestra.
Bioinformatics, HPC and AI
These are just introductor slides for a panel discussion at the Supercomputer21 conference.
GenomicSuperSignature: Interpretation of RNA-Seq Experiments through Robust, Efficient Comparison to Public Databases
Millions of transcriptomic profiles have been deposited in public archives, yet remain underused for the interpretation of new experiments. Existing methods for leveraging these public resources have focused on the reanalysis of existing data or analysis of new datasets independently. We present a novel approach to interpreting new transcriptomic datasets by near-instantaneous comparison to public archives without high-performance computing requirements. All necessary data and functions to apply our approach to existing or new data are included in our software available as part of the Bioconductor project.
2020
Big Data Approaches
Introduction What Big Data problem are we trying to solve? Class 1: Need only part of data, so extract from the whole and then operate on extracted data; eg., extracting a few dozen genes of interest, finding all intervals that overlap with a chromosomal region, Class 2: Need to operate on all the data, but can operate independently on parts; eg., computing over 1Mb bins on the genome, modeling over independent studies Class 3: Need to operate on all the data, but need to work on all at once (may be for performance reasons, also); eg.
2019
Howard County Community College STEM Career Panel
This is a career panel for students interested in STEM fields.
Bioconductor: Tools for interpreting high-throughput biological data
In this talk, I give a high-level overview of the Bioconductor project.
ATAC-Seq workshop
This workshop introduces ATAC-Seq, quality control approaches, isolating nucleosome compartments, and profile plots and heatmaps.
Statistical Methods in Functional Genomics
In a series of talks and exercises, I cover introduction to R, Bioconductor, genomic ranges, container classes, annotation of genes and …
2018
Practical Data Science and Informatics Training
This talk compares and contrasts four formats for data science and informatics education. The discussion will highlight some approaches …
Bioconductor: software for interpreting high-throughput biological data
This talk presents a very quick overview of the Bioconductor project, focusing on its values of reproducibility, reuse, and openness.
The cancer data ecosystem: data and cloud resources for cancer genomic data science
In this talk, I motivate the need for cloud-based cancer data resourdces. I provide an overview of the NCI Genomic Data Commons and how …
Accessing and Using Public Data Resources with Bioconductor
Workshop Description The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources including the Gene Expression Omnibus GEO, Sequence Read Archive SRA, the Genomic Data Commons GDC, and Bioconductor-hosted curated data resources for metagenomics, pharmacogenomics PharmacoDB, and The Cancer Genome Atlas.
Instructor names and contact information Levi Waldron (City University of New York, New York, NY, USA) Benjamin Haibe-Kains (Princess Margaret Cancer Center, Toronto, Canada) Sean Davis (Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA) Pre-requisites Basic knowledge of R syntax Familiarity with the ExpressionSet and SummarizedExperiment classes Basic familiarity with ‘omics technologies such as microarray and NGS sequencing
The NCI SevenBridges Cancer Genomics Cloud Resource
I demonstrate the use of the SevenBridges Cancer Genomics Cloud Resource to run RNA-seq and DNAse-seq workflows on cloud resources.
Tutorial: Using the NCI SevenBridges Cancer Genomics Cloud Resources
In this guided workshop, we will use the SevenBridges Cancer Genomics Cloud Resource to run simple RNA-seq workflow on cloud resources.
Cancer Bioinformatics Primer -- Papillary Renal Cell Carcinoma Hackathon
More than 150 researchers, engineers and data enthusiasts gathered at Salesforce in San Francisco for an intense weekend of exploration …
2017
Bioconductor: orchestrating high-throughput biological data analysis
Progress in biotechnology is continually leading to new types of data, resulting in data sets that are rapidly increasing in volume, …
Thoughts on an Agricultural Data Ecosystem
The USDA and the Agricultural Research Service (ARS) hosted a workshop to develop their ten year plan for genomics and phenotype. These …