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ropensci/wishlist: A Google Docs-Rmarkdown GUI

March 10, 2015
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ropensci/wishlist: A Google Docs-Rmarkdown GUI

ropensci/wishlist: A Google Docs-Rmarkdown GUI: Wishlist for rOpenSci tools I’ve just added A Google Docs-Rmarkdown GUI to the rOpenSci ‘wishlist’. (GUI = graphical user interface). Thought I may as well reproduce it below: Summary: Use Google Docs for ease of drafting, aiming to output Rmarkdown to increase the use of reproducible documents Add some special codes to...

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A modular Rmarkdown workbook in action I’m now using a…

March 4, 2015
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A modular Rmarkdown workbook in action

I’m now using a…

A modular Rmarkdown workbook in action I’m now using a properly modular Rmarkdown workbook, and really quite chuffed with it! I’ve seen discussion of electronic lab notebooks for bioinformatics with only mention of org-mode for emacs users, IPython (now the Jupyter project) and the likes of Evernote/Word etc., so I’m sharing the basic...

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One weird trick to compile multipartite dynamic documents with Rmarkdown

February 28, 2015
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One weird trick to compile multipartite dynamic documents with Rmarkdown

This afternoon I stumbled across this one weird trick an undocumented part of the YAML headers that get processed when you click the ‘knit’ button in RStudio. Knitting turns an Rmarkdown document into a specified format, using the rmarkdown package’s render function to call pandoc (a universal document converter written in Haskell). If you...

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Ants, snakes, and the hydrophobic-polar model

December 1, 2014
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Ants, snakes, and the hydrophobic-polar model

The other night I was reading Lesk’s Introduction to Protein Science, when I came across this diagram: A lattice model represents the structure of a protein as a connected set of points distributed at discrete and regular positions in space, with simplified interaction rules for calculating the energies of different conformations. For small lattice polymers, it is...

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The National Centre for Biotechnology Information (NCBI) is part…

November 25, 2014
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The National Centre for Biotechnology Information (NCBI) is part…

The National Centre for Biotechnology Information (NCBI) is part of the National Institutes of Health’s National Library of Medicine, and most well-known for hosting Pubmed, the go-to search engine for biomedical literature - every (Medline-indexed) publication goes up there. On a separate but related note, one thing I’m constantly looking to do is get DOIs for papers on...

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A bioinformatics walk-through: Accessing protein-protein interaction interfaces for all known protein structures with PDBe PISA

September 28, 2014
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A bioinformatics walk-through: Accessing protein-protein interaction interfaces for all known protein structures with PDBe PISA

If this summer’s posting became a little infrequent, part of the blame lies with computational research I’ve been working on, regarding the systems biology of chromosomal translocations and the ensuing chimeric proteins at the Medical Research Council Laboratory of Molecular Biology in Cambridge. A sizeable part of bioinformatics ‘dry lab’ work falls into what has been described in the 

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