The OmicIDX is an ecosystem that treats omics metadata as data. We collect metadata from omics repositories, process it into computable forms, and make it available for search, analysis, bulk processing, and for integration with additional data resources.

Build and deploy an NCBI GEO metadata fetch API

Build, containerize, and then deploy a simple serverless web API that returns json-formated metadata for any GEO accession.

Symposium: Participants Share Data 2019

The NCI organized a symposium to broadly assess the landscape of personal control of genomic data. We focused the meeting on the patient, research participant, and personal perspectives. The Symposium drew 200 in-person participants and over 300 online.

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 regions, ATAC-Seq data analysis, and an introduction to machine learning.

Using google cloud registry for private docker images

In this post, I will quickly build a docker image containing the sra-toolkit and a key for dbGaP downloads. Because the key file is private, I will be using the secure Google Container Registry to store the image for later use in genomics workflows. Background Container technologies like docker enable quick and easy encapsulation of software, dependencies, and operating systems. One or more containers can render entire software ecosystems portable, enhance reproducibility and reusability, and facilitate sharing of software, tools, and even infrastructure.