Intermediate Bioinformatics Training¶
Who: Titus Brown and many others (see below).
When: February 8 through 12, 2016
Where: Bodega Marine Lab at Bodega Bay
Please contact Jessica Mizzi with any questions.
Description¶
We will be running a week-long set of Carpentry-style tutorials on intermediate to advanced genomics techniques from Feb 8-12, 2016, at the Bodega Marine Lab. We’ve done this before and it went pretty well.
Twitter hashtag: #bodega16
Daily schedule¶
Time period | Activity |
---|---|
8am-8:45am | Breakfast, at housing cafeteria |
9:15am | First tutorial |
noon-3pm | Break for lunch, excursions, relaxation |
3pm-6pm | Second tutorial |
6pm-6:45pm | Dinner, at housing cafeteria |
7pm+ | Unplanned time (down by housing) |
Schedule of presentations¶
Monday:
(starting at 1:30pm in the main lab)
- Titus, introductions; reminding everyone of Amazon Web Services stuff
- 3pm: Quick tour of things.
- Amanda Charbonneau, Michigan State University
- Collaborative authoring with overleaf
Tuesday:
- Will Trimble, Argonne National Lab
- Jon Badalamenti, University of Minnesota
Evening:
- Attendee research presentations
Wednesday:
- Byron Smith, University of Michigan
- Luiz Irber, UC Davis.
- April Wright, Iowa State
Thursday:
- Kevin Murray, Australian National University
- Jane Charlesworth, University of Oxford
Evening activity:
- Docker & drinks in the lounge (starting at 8 pm)
- Titus Brown, Docker / Jupyter / mybinder.org
Friday:
Additional Materials¶
Books¶
Practical Computing for Biologists
This is a highly recommended book for people looking for a systematic presentation on shell scripting, programming, UNIX, etc.
RNAseq¶
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Trapnell et al., Nat. Protocols.
One paper that outlines a pipeline with the tophat, cufflinks, cuffdiffs and some associated R scripts.
Statistical design and analysis of RNA sequencing data., Auer and Doerge, Genetics, 2010.
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nookaew et al., Nucleic Acids Res. 2012.
Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments Vijay et al., 2012.
Computational methods for transcriptome annotation and quantification using RNA-seq, Garber et al., Nat. Methods, 2011.
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments., Bullard et al., 2010.
A comparison of methods for differential expression analysis of RNA-seq data, Soneson and Delorenzi, BMC Bioinformatics, 2013.
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples., Wagner et al., Theory Biosci, 2012. Also see this blog post explaining the paper in detail.
Computing and Data¶
- A Quick Guide to Organizing Computational Biology Projects, Noble, PLoS Comp Biology, 2009.
- Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results, Wicherts et al., PLoS One, 2011.
- Got replicability?, McCullough, Economics in Practice, 2007.
Also see this great pair of blog posts on organizing projects and research workflow.
Resources¶
-
A high quality question & answer Web site.
-
A discussion and information site for next-generation sequencing.
-
A large number of open and reusable tutorials on the shell, programming, version control, etc.
Blogs¶
http://www.genomesunzipped.org/
Genomes Unzipped.
-
Titus’s blog.
-
Blue Collar Bioinformatics
-
Mass Genomics
-
Next Genetics
http://gettinggeneticsdone.blogspot.com/
Getting Genetics Done
http://omicsomics.blogspot.com/
Omics! Omics!
-
Nick Loman’s lab notebook
LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.