This seminar will focus on using publicly available DNA and RNA sequencing datasets to investigate biological hypotheses, taking breast cancer as a case example. To start, we will formulate the hypothesis for this case study, then discuss how to tailor the publicly available datasets for a preliminary exploration of the chosen topic and briefly…
Computational biology has undergone a significant transformation since the advent of high-throughput sequencing, a pivotal breakthrough that democratized large-scale genomic analyses for researchers. However, even prior to this technological advancement, several of the most widely utilized tools in the field prioritized reliable software…
The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake, although evidence of recent selection is lacking. Here, using 94 long-read haplotype-resolved…
Although the CHM13 reference represents a complete human genome, it lacks the full diversity of human haplotypes present in Africa. Analysis pipelines which map sequencing reads to a single linear reference may suffer from “reference genome bias”, where unmapped reads bias downstream analysis. The impact of reference genome bias in the clinical…
Dockstore.org is a repository of reusable bioinformatics analyses shared by the research community. Tools and workflows registered in Dockstore are written using languages that combine containers to reproduce the exact compute environment with a precise description of each step of a computational analysis.…
This workshop will provide an overview of the Gen3 Data Commons Framework. We will describe the core microservices used to create a data service that can be used to harmonize data, facilitate access, and assist new research projects to identify relevant data and will provide a demonstration using two of our current data commons.
Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate. This interactive workshop on Terra will teach you the skills you need to know to start working and collaborating securely in Terra. Specifically, you’ll learn about the architecture of Terra as…