Monthly Archives: September 2015

DIB jclub, Better reporting for better research: a checklist for reproducibility

By: Lisa Cohen, Camille Scott, Tamer Mansour, Sherine Awad, C. Titus Brown Cross-posted: http://ivory.idyll.org/blog/2015-jclub-etc-on-reproducibility.html Note: at the Lab for Data Intensive Biology, we’re trying out a new journal club format where we summarize our thoughts on the paper in a … Continue reading

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iPlant – Advanced workshop

“API for scalable science” – Matt Vaughn, John Fonner https://pods.iplantcollaborative.org/wiki/display/Events/2015+09+21+iPlant+Workshops+at+UC+Davis https://github.com/iPlantCollaborativeOpenSource/Advanced_iPlant slides: https://docs.google.com/presentation/d/1RioNnjvL2qyRPQHSQ2-MG04m_LwNzf9gGqHwsSpCguM/edit?usp=sharing Install Docker (I’m running OSX. See other instructions for Linux and Windows, although there were challenges with Windows users in the workshop). Docker is solution to binaries and configurations, etc. specific … Continue reading

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iPlant – Intermediate workshop

UCDavis, 9/22 http://dib-training.readthedocs.org/en/pub/2015-09-iplant.html https://pods.iplantcollaborative.org/wiki/display/Events/2015+09+21+iPlant+Workshops+at+UC+Davis https://etherpad.mozilla.org/iplant-ucdavis-sep2015 Harold Pimentel, PhD student in CS at UC Berkeley “Algorithms for RNAseq – from raw reads to differential expression analysis” slides Not all reads are created equal! Number reads proportional to length of transcript, normalize to correct … Continue reading

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Past Year as a Junior Bioinformatician in Perspective

Starting a new chapter in life this week attending grad school (again) towards a PhD. Before moving on, wanted to put into perspective and share a few notes on what I’ve learned over the past year working as a junior bioinformatician … Continue reading

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Erich Schwarz, talk on conserved unknowns

UC Davis, Genome Center 9/17/2015 “Using C. elegans to discover functions of conserved unknown human genes.” http://ivory.idyll.org/lab/talks/2015-09-17-conserved-unknowns.html Titus: Erich is “not content with just a description of a genome”, goes deep into the conservation of gene families How much of … Continue reading

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