Skip to content

BioDepot Training

Welcome to the BioDepot training portal!

Overarching goal of Biodepot: To develop accessible, interactive and cloud-enabled methods and tools to facilitate reproducible and scalable analyses across diverse data types.

BioDepot-workflow-builder (Bwb)is a software tool that allows users to create and interactively execute reproducible bioinformatics workflows using a drag-and-drop interface. Graphical widgets control Docker containers executing a modular task.

Bwb is open source with extensive documentation at https://github.com/BioDepot/BioDepot-workflow-builder

Open in GitPod

Available workshops

We have the following workshops available. Episodes 2 to 5 are independent, so you can watch them in any order. Episodes labeled as “advanced” are optional. The estimated time to complete each workshop is provided.

Episodes 1 to 4 are based on the cloud-based GitPod environment so that no local set up on your computer is needed. No prior programming experience or technical skills are required unless otherwise noted.

Basic training

Image title

Episode 1: Basic training (60 minutes)

Start Episode 1: Basic Training

Executing workflows on your data

Image title

Episode 2: Executing workflows on your data

Start Episode 2

Cutosmizing workflows

Image title

Episode 3: Customizing workflows

Start Episode 3

Running the Biodepot-workflow-builder (Bwb)

Image title

Episode 4: Running the Biodepot-workflow-builder (Bwb)

Start Episode 4

Applications

Under construction

MorPhiC Logo

Episode 5: Applications. Example: Bulk RNA-seq workflow for the NIH MorPhiC program (30 minutes)

Start Episode 5

How to cite Biodepot-workflow-builder (Bwb)

Building containerized workflows using the BioDepot-workflow-Builder (BwB). Ling-Hong Hung, Jiaming Hu, Trevor Meiss, Alyssa Ingersoll, Wes Lloyd, Daniel Kristiyanto, Yuguang Xiong, Eric Sobie, Ka Yee Yeung. Cell Systems volume 9, issue 5, pages 508-514.E3 (2019).

Publications that use the Biodepot-workflow-builder

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data. Shishir Reddy, Ling-Hong Hung, Olga Sala-Torra, Jerald Radich, Cecilia CS Yeung, Ka Yee Yeung. BMC Genomics 22, Article number: 626 (2021).

Cloud-enabled Biodepot workflow builder integrates image processing using Fiji with reproducible data analysis using Jupyter notebooks. Ling-Hong Hung, Evan Straw, Shishir Reddy, Robert Schmitz, Zachary Colburn, and Ka Yee Yeung. Scientific Reports 12: 14920 (2022).

Accessible, interactive and cloud-enabled genomic workflows integrated with the NCI Genomic Data Commons. Ling-Hong Hung, Bryce Fukuda, Robert Schmitz, Varik Hoang, Wes Lloyd, Ka Yee Yeung. Pre-print bioRxiv 10.1101/2022.08.11.503660..

Rapid detection of myeloid neoplasm fusions using Single Molecule Long-Read Sequencing. Olga Sala-Torra, Shishir Reddy, Ling-Hong Hung, Lan Beppu, David Wu, Jerald Radich, Ka Yee Yeung, Cecilia CS Yeung. PLOS Global Public Health 3(9): e0002267 (2023).

Funding Acknowledgement

We are very grateful for funding support from NIH grants U24HG012674, R21CA280520, R21CA280520-01S1, and R03AI159286.