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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
Posted in reproducibility, science
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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
Posted in Linux, workshops
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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 https://www.flickr.com/photos/lpcohen/21605321126/in/dateposted-public/ Not all reads are created equal! Number reads proportional to length of transcript, normalize to … Continue reading
Posted in workshops
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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
Posted in Bioinformatics, Data Analyses, Personal, Sequencing
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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
Posted in talks
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Lisa K. Johnson 