BioC 2018: Where Software and Biology Connect

When: July 25 (Developer Day) 26 and 27, 2018
Where: Victoria University, University of Toronto, Toronto, Canada
Twitter: #bioc2018

Developer Day Schedule (Tentative)

Logistics:

• Lightning talks – sign up! Include authors, affiliation, title.
• Start your course AMI
• Join the bioc-community slack
• Provide interactive feedback on sli.do #bioc2018

8:30 - 9:00 – Registration and breakfast, VC second floor foyer

9:00 - 9:40 – Welcome

Orientation & project updates – slides – VC 213 Chapel

9:40 - 10:00 – Peter F. Hickey

Lessons from switching to on-disk storage using DelayedArray containers – slides – VC 213 Chapel

10:00 - 10:30 – Lightning talks I

Lightning talk platforms will be available to all Developer Day attendees – VC 213 Chapel

• Qian Liu*, Hervé Pagès, Martin Morgan, Roswell Park Comprehensive Cancer Center. DelayedDataFrame: an on-disk data representation in DataFrame metaphor.
• Aedin Culhane*, Dana Farber Cancer Institute. TCGA immune subtypes.
• Wolfgang Huber*, Susan Holmes, EMBL. Short preview of our new book “Modern Statistics for Modern Biology”.
• Lori Shepherd*, Roswell Park Comprehensive Cancer Center. Submitting packages to Bioconductor
• Martin Morgan*, Roswell Park Comprehensive Cancer Center. Ad hoc workshops – alternative activities during workshop / BoF sessions.

10:30 - 11:00 – Break

11:00 - 12:00 – Birds-of-a-feather I / Workshops I

• BoF: Stephanie Hicks, Statistical Analysis and Comprehension of the Human Cell Atlas in R/Bioconductor – VC 206
• Workshop: Nitesh Turaga, Maintaining your Bioconductor package – VC 212
• Impromptu: tidyverse and Bioconductor – VC 211

12:00 - 1:00 – Lunch – VC Foyer & Alumni Hall

1:00 - 1:30 – Lightning talks II

VC 213 Chapel

• Aedin Culhane*, Dana Farber Cancer Institute. Update in Bioconductor meet ups.
• Lori Shepherd*, Roswell Park Comprehensive Cancer Center. BiocFileCache
• Qian Liu*, Martin Morgan, Roswell Park Comprehensive Cancer Center. VariantExperiment: A RangedSummarizedExperiment container for VCF/GDS data with GDS back-end.
• Nitesh Turaga*, Bioconductor Core Team. Scalable Computing in Bioconductor: from cores to clusters.
• Levi Waldron*, CUNY. Creating the Bioc2018 workshop book and AMIs.
• Daniel Van Twisk*, RPCI. Organism.dplyr: A dplyr compatible Annotation Resource Interface.

1:30 - 2:30 – Birds-of-a-feather II / Workshops II

• BoF: Levi Waldron, New Data Structures for Bioconductor – VC 206
• Workshop: Peter Hickey, Effectively using the DelayedArray framework to support the analysis of large datasets – VC 212
• Impromptu: unit tests – VC 211

2:30 - 3:00 – Break

3:00 - 3:30 – Lightning talks III

VC 213 Chapel

• Michael Steinbaugh*, HSPH. Bioconductor tricks for dealing with genome annotations. slides
• Charlotte Soneson*, UZH; Kevin Rue-Albrecht, Uni Oxford; Federico Marini, Uni Mainz; Aaron Lun, CRUK: iSEE: Interactive SummarizedExperiment Explorer
• Nathan Sheffield*, UVA, Managing genomic project metadata
• Shian Su*, WEHI: BiocExplorer
• Vincent Carey*, S Gopaulakrishnan, S Pollack, BJ Stubbs, A Culhane. Harvard Medical School/Harvard School of Public Health. Recent cloud-scale innovations in Bioconductor.
• Tim Triche, USC: Sesame: a simple way/to analyze a methylation array

3:30 - 4:30 – Community activities

VC 213 Chapel

• Tracking down a bug: rownames and SummarizedExperiment. issue
• Toward a better support site. notes
• Designing PharmaGX data representations. demo code
• Collaborative opportunities: Biocverse package discovery. slides

4:30 - 5:00 – Panel discussion: project directions and opportunities

VC 213 Chapel