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Tag Archives: tools
Tools of the Trade: Timestamps and Text Editors
Quoting people accurately is a mundane but crucial task in my daily work. Over the years, I’ve tried a variety of approaches, but I think I’ve finally evolved the most efficient system for handling it. When I’m conducting an interview … Continue reading
Tools of The Trade: Zotero
If you read a lot of scientific papers, or do any other kind of academic study, you need a way to manage the mess. I’m talking about the piles of photocopies, books, and notes – or these days, gigabytes of … Continue reading
Tools of The Trade: Stand-Up Desk
This is the first of what might turn into a series of posts about tools and tricks I’ve found handy for my work. I figured I’d start with the thing most people would notice first on walking into my office: … Continue reading
Cell Is for Cellulose
Cultured cells are a mainstay of modern biomedical research, but they’re very limiting. Growing the cells in a flat monolayer on a petri dish is the easiest way to control and study them, but it doesn’t represent their normal in … Continue reading
Stick It In Your Ear, Then Slap Your Forehead
Ever see some new device, and say “wow, why didn’t anyone think of that before?” I mean, really say it and mean it – not sarcastically, and not as part of a hackneyed marketing phrase, but because you really, truly … Continue reading
Wikipedia for Proteins
Genome Biology just published an interesting paper by a group of prominent protein chemists, plus Jimmy Wales, the creator of Wikipedia. In a nutshell, these folks have developed a new wiki-based protein annotation system, which seems like a wise way … Continue reading
Crossing Over
I’ve been struggling with a tricky problem in Web design lately: how to preview my sites in Internet Explorer. For my personal site, I largely ignore that buggy browser’s bizarre behaviors (see my archived tirade for details). But lately, I’ve been working on a Web redesign for a nonprofit group, and they need their site to be accessible. There’s no current version of Explorer for the Mac, and my old copy of IE5 doesn’t capture a lot of the more recent bugs the folks in Redmond have added. It seemed like the only reasonable option was to install Windows on my Intel Mac, paying hundreds of dollars to Microsoft to get a copy of their operating system, and then install Explorer. I have a moral objection to that, though, as it would mean enriching Microsoft, not in spite of, but because of their very worst habits.
Thankfully, the good folks at Codeweavers have come to my rescue. Instead of sending a big payment to Bill Gates, I can now send a measly $60 to this small company that helps support the Open Source movement. That’s the registration price for Crossover, a product very similar to the more popular Parallels. While both applications allow one to run Windows applications on the Mac, with Parallels you still have to shell out for a copy of Windows itself. Crossover eliminates that by using the open source Wine emulator instead. Now, back to hacking these stylesheets. Continue reading
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Tagged browsers, computers, mac, operating systems, tools, web development
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The Joy of Text
Over the past several months, I did one of the hardest things for a professional writer: I switched to a new word-processing application. This is the third time in my ten-year writing career that I’ve done this. Shortly after leaving the lab, I migrated my work from a “borrowed” copy of Microsoft Word (The Worst Word Processor Ever Created) to the vastly underrated AppleWorks application. When Apple abandoned that product, I moved to the supremely elegant Nisus Writer. I’ve heard that for some writers, this application was their main reason for buying a Mac. While I have other excuses, I can understand that thinking perfectly. From its uncluttered, easily configurable menus and tool drawer to its open, nonproprietary file format, Nisus is truly a writer’s tool.
If I were not such an extreme geek, I would have stuck with that decision, and I still recommend Nisus Writer to aspiring and practicing journalists who aren’t especially technical. Besides its aesthetic advantages, having all of your notes and past stories in text-based files (specifically Rich Text Format, or RTF) ensures that your archive will remain accessible for years to come. You can’t say that about many other formats.
About a year ago, though, I started to re-learn computer programming after a 20-year hiatus, and it changed my perspective on “word processing” completely. You wouldn’t know it to read their emails, but in their regular work, computer programmers are the most diligent copyeditors on the planet. As a result, they’ve developed text-handling systems that make even an elegant word processor like Nisus Writer look like a dull #2 pencil. If you’re a technically-minded writer, especially if you work for “new media” outlets on the Web, keep reading. Continue reading
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Tagged computers, emacs, smultron, text editors, tools, writing
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Just Say "No" to Microsoft Word
Microsoft Word, one of the worst pieces of software ever to enter widespread use, has been a thorn in my side for years. As a writer, it offends my aesthetics. As a techie, it offends my sense of good design. And when it comes to digital security, it just plain offends. There are plenty of other tirades against Word on the Web (such as this, this, and this), and reams of information showing how this application seriously hinders regulatory compliance and technical development for all sorts of organizations. When Microsoft finally lost the ISO standards war on this issue, many people hoped that Word’s corrosive influence on the world would soon come to an end.
No such luck. Continue reading
Hacking the Tree of Life
Continuing the merger between open source software and bioinformatics, researchers are starting to adopt not only the philosophy, but also the work habits of the open source community. The Phyloinformatics Hackathon, going on this week in North Carolina, mimics the group work sessions of other free software projects:
Leading programmers from as far away as Japan and New Zealand have come to NESCent to build the missing pieces of glue software. Participants include developers of specific phylogenetic software packages, on the one hand, and experts in designing glue software toolkits such as BioPerl and BioJava. “The participants are learning a lot from each other,” says computational biologist Arlin Stoltzfus of the National Institute of Standards and Technology. “The phylogeneticists know what the cutting edge phylogenetic methods are and what users need, while the toolkit developers have lots of experience working with standards that allow different software packages to communicate”. Continue reading