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Developer Day 2013

Developer Day is part of the Bioconductor annual conference; Developer Day is on July 17,

  1. This page is under active development, and will be until July 17!

Tentative schedule

8:45 - 12:00 Morning

  • 8:45 - 9:00 Welcome and orientation

  • 9:00 - 9:45 Core team project highlights.

    VariantAnnotation light-weight functions and performance improvements; filterVcf, showHeadLines, showTailLines, better paired end input [Valerie]

    keys, cols, and ranges in the select interface of *Db packages. AnnotationHub. [Marc]

    Single Package Builder; package reviews [Marc, Dan, L].

    Work flows, BiocStyle. Github integration [Dan, Martin].

    BiocGenerics. sequenceLayer [Herve].

    Cloud-aided computation, e.g., ensemblVEP; AnnotationHub [Martin]

    Mentored projects [L, Valerie]. Google Summer of Code: displayR [Marc / Shawn]; BiocParallel [Michel, Michael, Martin].

  • 9:45 - 10:30 Small group team-building activities.

    Quick fix – Brainstorm about and implement a missing but useful feature to be shared by Bioconductor packages. [Martin, Valerie, Herve]

    Unit tests coming and going – Brainstorm and implement tests describing a new feature; fix buggy code with test. [Paul, Laurent, Dan, Marc]

  • 10:30 Break

  • 10:50 - 12:00 Variants:

    Presentation by Paul Pyl, EMBL, rhdf5-supported variant calling; Additional presentations and open discussion on variant calling and down-stream analysis.

12:00 - 1:00 Lunch

1:00 - 5:00 Afternoon

  • 1:00 - 1:50 Participant flashlight presentations (short talks).

    Adrian Alexa, Illumina, BaseSpaceR; Davide Rambaldi, flowFit for use in stem cell research; Tengfei Yin, Updates on ggbio; Bioc Asia; Brian Bot, Synapse.

  • 1:50 - 2:40 Developer workshops – Suggestions:

    knitr [Yihui]; Packages, incl. DESCRIPTION [Paul, Laurent]; S4 classes, methods, NAMESPACEs, BiocGenerics, documentation [Val, Herve]; h5vc [Paul];

  • 3:00 break

  • 3:20 - 4:00 Tackling Big Data with R: new features and concepts for handling large and streaming data in practice

  • 4:00 - 4:40 Developer workshops

    Writing work flows for domain experts [Marc, Dan]; Profiling and debugging R, C code [Dan, Martin]; Elements of parallel programming [Simon]; Rcpp [Laurent, Val].

  • 4:40 - 5:10: Developer Day address: Joe Cheng / RStudio