• The Google Scholar preprint bug redux

    Regular readers of my blog will know that I regularly complain about Google Scholar’s handling of preprints, see e.g. here or here. Well, this week, I had the opportunity to raise my concerns to Anurag Acharya, the co-founder of Google Scholar. His initial response and the subsequent discussion have clarified several things. We now know:

    1. The bug exists
    2. The Scholar team is aware of it
    3. They don’t know how to fix it
    4. They don’t think it’s a particularly pressing problem
    5. For any given paper, the problem will go away eventually, after several months or more
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  • How to not mess up your bibliographies with Bibtex

    Bibtex is the reference manager for Latex. I have used it for 20 years, I have written over 100 papers with it, and I think it works really well. I have also rarely met anybody who could use it without messing up their bibliography in some way. Bibtex is an archaic program, written 30 years ago by a graduate student and never substantively changed or updated since. It uses an awkward database format for storing bibliographic entries and an atrocious, poorly-documented programming language for describing how bibliographic entries should be formatted. In fact, the most complete description of bibtex’s inner workings is aptly called Tame the BeaST. (This document is well worth the read for anybody using bibtex with some regularity.) To help ordinary mortals succeed with using Bibtex, I’m providing here a set of best practices and useful guidelines that help you steer clear of the worst pitfalls of Bibtex.

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  • Avoiding the official style

    Nobody turns into a good writer over night. Writing well takes a lot of dedicated practice, as well as mastery of many different topics, including grammar, punctuation, word choice, and document organization. However, if I had to name one single skill that likely makes the biggest difference in a person’s ability to write well, I would point to recognizing and avoiding the official style. This style, named so by professor of rhetoric Richard Lanham [1], makes heavy use of passive voice, prepositional phrases, and complex, wordy expressions with little content. And it permeates the scientific literature.

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  • Goodbye Squarespace, Hello Github

    After having hosted my blog on Squarespace for about two years, I have decided to move it over to Github pages. Squarespace was a reasonable and easy solution for me two years ago when I knew nothing about web hosting and web design, but I’ve increasingly grown frustrated and feel that I’m constantly having to fight with Squarespace to get it to do what I want it to do. I originally chose Squarespace because I didn’t want to maintain my own article database and I didn’t like the design and feature set of most popular blogging platforms such as WordPress or Blogger. In the mean time, I have learned about static page generators, and I now think that they are superior to most other options for basic blogs and other simple web pages. So I’ve redesigned my site using Jekyll for page generation, Bootstrap as CSS and JS framework, Google fonts and Font Awesome for typograpy and icons, and Disqus for comments.

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  • Safety projects

    If you’ve been in science long enough, eventually you’ll have reached a point where you needed a safety project, either for yourself or for a student. A safety project is a project whose success is all but guaranteed, that doesn’t require much in terms of critical thinking or properly aligned stars. All that is required to complete a safety project is proper execution of the work.

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  • cowplot R package now available on CRAN

    This week, I finally took the time to clean up the code for my cowplot R package and submit it to CRAN. While the code had been up on github for a while, and I had blogged about it previously, nobody had really taken notice as far as I can tell. However, this time, with an official release and better documentation, people seem to like it a lot. The response on Twitter was overwhelming.

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  • Beyond bar and line graphs

    PLOS Biology recently published a nice article on data visualization:

    Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLOS Biol 13(4): e1002128. doi:10.1371/journal.pbio.1002128

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  • PLOS ONE publishes analysis of grant writing costs and benefits

    PLOS ONE just published an article providing a cost-benefit analysis of grant writing:

    von Hippel T, von Hippel C (2015) To Apply or Not to Apply: A Survey Analysis of Grant Writing Costs and Benefits. PLoS ONE 10(3): e0118494.

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  • Teaching a new introductory class in computational biology and bioinformatics

    This semester, I’m teaching a new introductory class in computational biology and bioinformatics. The class is primarily targeted at undergraduates, and it is split approximately 50:50 between R and python. The R component emphasizes effective data analysis and visualization, using packages such as ggplot2 and dplyr. The python component will introduce students to basic programming concepts, and it will also cover some typical bioinformatics applications.

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  • What constitutes a citable scientific work?

    There was a lively discussion on Twitter the other day regarding what constitutes a citable piece of scientific work. In particular, Matthew Hahn was concerned about where to draw the line, and he felt that unless something is traditionally published there’s no need to cite it. When reading this dicussion, I felt it was muddled by the lack of clear criteria separating citable works from other forms of scientific communication. In my mind, there is a clear distinction between preprints, which I consider to be citable works, and presentation slides or tweets, which are not. To formalize this distinction, I would like to propose four conditions that need to be satisfied for a document to be considered a citable piece of scientific work. The document needs to be: (i) uniquely and unambiguously citable; (ii) available in perpetuity, in unchanged form; (iii) accessible to the public; (iv) self-contained and complete.

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  • Post-publication review of the PLOS ONE paper comparing MS Word and LaTeX: How not to compare document preparation

    PLOS ONE just published a paper comparing MS Word with LaTeX, which argues that LaTeX has little benefits over MS Word and should not be allowed by scientific journals:

    Knauff M, Nejasmic J (2014) An Efficiency Comparison of Document Preparation Systems Used in Academic Research and Development. PLoS ONE 9(12): e115069.

    In my mind, this paper makes extremely strong claims based on a rather flawed and thin analysis. I am sure there are useful things to be said about MS Word vs. LaTeX. However, this paper does not make much of a contribution to this question.

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  • Perfectly smooth transition between fixed and variable positioning of HTML elements using CSS and Javascript

    The last couple of days I have been working on a new webpage. In doing so, I wanted to create a design where the menu bar initially resides at the bottom of the page and moves upwards as the user scrolls down. However, once the menu bar hits the top edge of the viewport, it should remain fixed there. A bit of googling quickly revealed a solution for this problem, using a combination of CSS and Javascript. However, I wasn’t happy with the solution, because it created a visible jump in the layout every time the menu bar hit the top edge of the screen. In fact, this jump is quite common among most web pages that use this design trick. For example, check out a profile page on Google Scholar: As you scroll down, the heading above the publication list stays fixed as soon as it hits the top edge of the screen. And if you scroll slowly, you’ll see that the layout jumps the moment the element hits the top edge. I didn’t like this effect at all, so I devised a way to work around it.

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