Monkeyshines

Category: Biology

  • 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…

  • 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).

  • 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…

  • CEB Journal Club: Andam et al. (2010)

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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…

  • T1DBase: type 1 diabetes, and my part in its downfall

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    James
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    Apropos of a new T1DBase publication (Burren et al. 2011) (in which I am kindly acknowledged), I thought I’d write a bit about some of the work I did there (Hulbert et al. 2007). I envisage this being the first of maybe three instalments, so before going into detail about the specific projects that I…

  • A most excellent black-and-white bear

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    James
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    On the day that the Giant Panda genome is released, I was surprised to discover that the animal was unknown in Europe until 1869. The best bit is the quote by Armand David, the zoologist priest who first scientifically recorded its existence, describing it as a “most excellent black-and-white bear”.