Monkeyshines

Category: Scholarly Thoughts

  • CEB Journal Club: Price et al. (2012)

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    James
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    Members of the Computational and Evolutionary Biology (CEB) group at the University of Manchester participate in a monthly journal club, where a paper of broad interest is discussed. Here, I briefly describe the paper and its context, and summarize our conclusions about the methodology and results presented. (I have attempted to represent the discussion and…

  • Formal Grammars

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    James
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    Throughout the course of my PhD I have found it useful to write summaries of the various aspects of phylogenetics and biology that I have learned. That these will be useful to others is perhaps a vain hope, in both senses of the word, but I thought I might as well publish some of them…

  • LyX: LaTeX, the Easy(ish) Way

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    James
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    Introduction I’ve resisted learning TeX/LaTeX for years; I appreciate the principle, but I baulk at the idea of learning another language, particularly one which requires a bunch of opaque commands at the top of each file. I like a nice GUI, and Word, for all its faults, does give you lots of control if you…

  • Tree Comparison

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    James
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    Throughout the course of my degree I have found it useful to write summaries of the various aspects of phylogenetics and biology that I have learned. That these will be useful to others is perhaps a vain hope, in both senses of the word, but I thought I might as well publish some of them…

  • The War-and-Peace-O-Meter

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    James
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    Some years ago I asked for War and Peace by Leo Tolstoy for Christmas; a new translation had just been published, and that seemed as good a reason as any to tackle this metaphorically and literally immense book. I do a lot of my reading on the bus, which has tended to put me off…

  • T1DBase: gene models

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    James
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    I recently wrote an overview of T1DBase, an online resource for the type 1 diabetes (T1D) research community (Hulbert et al. 2007; Burren et al. 2011). I shall now describe one of the more interesting of my contributions to the project, calculating and graphically displaying gene models. In the month since I first started writing…

  • CEBlog

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    James
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    The “department-sized grouping of researchers” among whom I work, the Computational and Evolutionary Biology (CEB) group at the University of Manchester, have started a blog about our journal club (at which I have presented in the past).

  • MASAMB XXI (Part 2)

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    James
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    Photographic evidence that I did, indeed, attend the latest MASAMB conference.

  • MASAMB XXI, in Vienna

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    James
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    I was pleased to be invited to present some of my work at the MASAMB conference in Vienna recently (11-12th April 2011). My talk was titled “Quantifying the effect of evolution and genomic alignment on de novo RNA gene prediction”. I have a similarly themed manuscript in preparation, so won’t go into detail here. But…

  • Whelan Lab Journal Club: Seemann et al. (2011)

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    James
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    Members of Simon Whelan’s lab at the University of Manchester participate in a regular journal club, where a paper with an evolutionary/phylogenetic slant is discussed. Here, I briefly describe a paper that I recently presented, and summarize our conclusions about the methodology and results. (I have attempted to represent the discussion and consensus of the…