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
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.
Running the Biodepot-workflow-builder (Bwb)
Episode 4: Running the Biodepot-workflow-builder (Bwb)
Applications
Under construction
Episode 5: Applications. Example: Bulk RNA-seq workflow for the NIH MorPhiC program (30 minutes)
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.