How to do science with a computer: workflow tools and OpenSource philosophy

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I have two excellent things on my desk, a Linux Journal article by Andy Wills, and a newly published book by Stefano Allesina and Madlen Wilmes. They are: Computing Skills for Biologists: A Toolbox by Stefano Allesina and Madlen Wilmes, Princeton University Press. Open Science, Open Source, and R, by Andy Wills, Linux Journal Why … Continue reading How to do science with a computer: workflow tools and OpenSource philosophy


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A really good computer setup

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I’ve reached a very nice resting point in the ongoing effort to develop a very useful, powerful, stable, and cool computer setup. This started a while back when I built a computer. In particular, this computer. There are several advantages to building a computer. You can save money or get more bang for your buck … Continue reading A really good computer setup


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Mechanical Keyboards: What are they and which one do you want?

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Once upon a time there was the Northgate OmniKey Keyboard, most notably the OmniKey Plus. It was the best keyboard ever. It was sturdy, mechanical, and proffered a plethora of function keys. It was heavy, meaty, robust. You could pound on it an it would stay in place on your desk and just take it. … Continue reading Mechanical Keyboards: What are they and which one do you want?


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Writing Software for Writers

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This is especially for writers of big things. If you write small things, like blog posts or short articles, your best tool is probably a text editor you like and a way to handle markdown language. Chances are you use a word processor like MS Word or LibreOffice, and that is both overkill and problematic … Continue reading Writing Software for Writers


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Logitech Ultrathin Touch Mouse: Apple Magic Mouse Replacement

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Problems with the Apple Magic Mouse I had been using the stock Apple Magic Mouse on an iMac. The right click often didn’t work properly. Also, selecting and dragging files in Finder, or the Finder replacement I use (PathFinder) often failed. I figured the former was related to the mouse but assumed the latter was … Continue reading Logitech Ultrathin Touch Mouse: Apple Magic Mouse Replacement


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Ubuntu Linux 15.04 Vivid Vervet Beta Mate Flavor

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Ubuntu Linux 15.04 will be released in April. There is not a lot new for the average desktop user in the new release, as far as I can tell. One good “change” is a feature called “locally integrated menus.” This is where the menus are, by default, where they are supposed to be, instead of, … Continue reading Ubuntu Linux 15.04 Vivid Vervet Beta Mate Flavor


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10 or 20 things to do after installing Ubuntu Mate (14.10)

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See here to see why you might want to install the Mate flavor of Ubuntu 14.10. Then, install it and consider doing these things. Get your system up to date. Yes, yes, you just installed it but that install image was old(ish). Update and upgrade now: First, you probably want to open the Software Center, … Continue reading 10 or 20 things to do after installing Ubuntu Mate (14.10)


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Scrivener on Linux: Oh Well…

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UPDATE (January 2, 2016): The makers of Scrivener have decided to abandon their Linux project. Kudos for them for giving it a try. The Scrivener on Linux users were not many, and almost nobody donated to the project, and as far as I can tell, the project was not OpenSource and thus could not have … Continue reading Scrivener on Linux: Oh Well…


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NSA Claims That Linux Journal Is A Forum for Radical Extremists? THIS MAY BE FAKE (Updated)

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When I first became a regular user of Linux, several years ago, I tried out different text editors and quickly discovered that emacs was my best choice. By coincidence, about that time I ran into an old emacs manual written by Richard Stallman in the dollar section of a used booksore. In that edition, near … Continue reading NSA Claims That Linux Journal Is A Forum for Radical Extremists? THIS MAY BE FAKE (Updated)


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Best applications to install on your new Mac

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What are the best applications, free or cheap, to install on your iMac for basic tasks and productivity? This post is to guide you in the careful and considered upgrade to your newly acquired iMac or other Mac OSX machine, especially for non-Mac experts. For each of the categories of work you may want to … Continue reading Best applications to install on your new Mac


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