The Futile Cycle

The internet allows people to produce some amazing things. Go see! Twitter as it was meant to be seen.

I’ve found a bunch of tools recently that have made organizing my life a lot easier, especially with integrating labwork into the rest of my life.

First up is Remember the Milk, which is a free, online to-do list manager. It’s simple, but very useful. I can create multiple lists, tag each list item, and create smart lists based on searches. It’s all done very well, including lots of AJAX-y goodness and keyboard shortcuts to boot. For FireFox users, it has nice integration with Google Gears for offline access. It also integrates into Gmail and Google Calendar, though I’ve used those features less. The only caveat I have with RTM is that I wish its keyboard shortcuts mimicked those in Gmail. Gmail’s shortcuts seem much more intuitive than RTM’s, such as using “x” instead of “i” to select or deselect items.

Having an online tool is really handy, as sometimes I don’t have my computer with me, especially in lab. My To-Do list, however, is only an internet connection’s away.

Next is Gmail. Yes, many people use Gmail, but I especially like to use Gmail to shuttle little bits of data back and forth as attachments on drafts of letters to myself. Very handy! And Gmail’s recent introduction of IMAP has made it a lot easier to keep track of my email from both my home computer as well as a lab computer.

Another amazingly useful tool is Google Calendar. It’s very handy to be able to check my schedule from any computer, but the main problem is that I like the way iCal is integrated into the rest of my system! It picks up dates and times from email read in Apple Mail, it integrates with the Address Book, and alerts are simple to create, making it so much easier to manage my time at my home computer.

So I use BusySync. The 2.0 beta (as I write this) includes Google Calendar synchronization, which is an absolute godsend. The synchronization is seamless!

RTM combined with Google Calendar + BusySync + iCal is a killer combination for me; I can keep track of experiments, time points, appointments, meetings, seminars, classes, and even the rest of my life regardless of what computer I’m on! And now that I use an electronic lab notebook published online (though under a password), I can access data and procedures from home, too, so that I can plan out experiments or process data and record it wherever I am. It’s glorious!

Alas, the only thing I can’t do is pipette my reactions or maintain cell culture from home…Hey Honda, any chance you might come out with an ASIMO Laboratory Rat model?

Annoyed that if you see a song in an iTunes playlist and you hit “delete”, it’ll only disappear from the playlist and not the library? Dislike having to go and hunt for the file in your actual library to delete it?

My expanding iTunes library has made me write this Applescript (oh, the horror!) that’ll delete the original songs from the iTunes library if you select a song in a playlist. Installation and usage instructions are in the Readme file, and I’ve zipped the whole thing.

Note, of course, that this script only works on Macs…

UPDATE: Apparently, there’s a not-well-documented keyboard shortcut for deleting songs from the library straight from the playlist. Instead of hitting “delete”, the keystroke is Opt-delete. Thanks to manduca for the tip!

Looks neat and slick! Very much in keeping with the new iPod aesthetics.

I was really interested in the new gesturing features that Apple included on the trackpad, but looking at the website, I’m very very confused about the user interface. It’s backwards!

Consider our current setup (on MacBooks and MacBook Pros). With two-finger scrolling, moving the fingers up scrolls up, moving the fingers down scrolls down. The way to think about it is that you’re moving the scrollbar. That’s fine; it’s a nice generalization of using the mouse pointer.

But with these new gestures, there’s some sort of inconsistency. For the new pinch and rotate gestures, the fingers move as if you’re manipulating the objects on the screen. But for the new swipe gestures, you move left to see left, move right to see right. You’re not manipulating the pictures anymore, you’re back to moving the scrollbar! On the iPhone, on the other hand, swiping left moves you to the right, because you’re moving the stuff on the screen to the left (take a book and swipe left on the right-hand page; you’ve just turned to the next page, right?). So it gets confusing; what’re you moving? When are you moving what? Are you scrolling, pointing, manipulating, what?

Another example. Take Coverflow. On my MacBook Pro, when I use two finger scroll and move them to the right, the scrollbar moves right, which means the icons move left. That’s fine, I’m used to it. On the iPhone, if I swipe my finger to the right in Coverflow mode, the icons move right; that’s fine, because I’m swiping the pictures right, and so they should move right. What if, now on the MacBook Air, I were to swipe right on the trackpad? I’ll be back to moving the icons left! Confusing? It is!

So, in a way, I’m a little disappointed by the trackpad gestures (of course, their use is optional), as they seem to break consistency with the other products in Apple’s lineup. Ah, for the days when Apple’s Human Interface Guidelines were brilliant innovations in computer-human interaction.

For all of you geneticists out there, here’s a nice quip from David Botstein, a yeast and former bacterial geneticist:

In Microsoft Word’s “Track Changes” and Endnote are synthetic lethals.

For the non-geneticists, a synthetic lethal pair of genes are two gene variants that alone are fine, but when combined into the same organism, cause it to die.

For those of you who program in Mac OS X, once you upgrade to Leopard, you may have to resolve problems with duplicate man pages. I came across this issue when I noticed that hitting ls -l in Terminal started giving me this unfamiliar “@” symbol after the permissions column of some of the files (I had seen “+” there before, but not “@“)

Unfortunately, the man pages didn’t help, and it took me a little time to figure out that for some reason, the old man pages from Tiger were still around, and the system preferentially reads from those rather than the new Leopard ones. A simple Ruby script found here does the trick in removing the old man pages. This problem only appears to those who did an “Upgrade” installation of Leopard instead of a clean install or an “Archive and Install.”

The new Leopard man pages, of course, explain the “@” symbol. (It denotes that the file has extended attributes from the new metadata system. To see the attributes on a specific file, try typing xattr -l filename.)

It’s common sense, but strangely a lot of people don’t seem to get this:

“Linux is only free if your time has no value.” — Jamie Zawinski

From The Introduction to Software Carpentry.

I installed Leopard this past week.

The pictures of Leopard boxes don’t really do it justice. There’s a weird hologram-ish thing in the background of the “X” that makes it look like it’s floating in the middle of space. No really, go check out a box in a computer store (or an Apple Store). It’s pretty nifty.

Overall, I like it a lot! Spotlight and the Finder are considerably more snappy, which is always a great quality of life improvement (yes, it’s sad, much of my life is spent on my computer). QuickLook is excellent. Spring-Loaded Dock folders are also very useful. The new ability to create Dashboard widgets from Safari is quite handy; I’ve set up weather.com and PhD comics widgets. I don’t know what else I’d use it for, though. On the programming side, I’m looking forward to automatic memory management in Objective-C.

I’m not bothered by the UI changes as much as other people seem to be. I don’t like high-contrast backgrounds anyway, so the transparent menu bar isn’t a problem, and I’m just not nit-picky enough about the dock to worry about the angle it’s at. On the other hand, I’m having trouble getting used to the over-saturated colors on little bits of the system (like the menu highlight color), and the rounded corners on everything. It’s still jarring to me that my top menu-bar isn’t white, or at least grey; I keep thinking that I’ve engaged “Exposé.”

The UI change that bothers me most is that the icons in the “Stacks” on the bottom of my computer are pictures of the contents, which means that I have to move my mouse along to hunt for the correct folder, as rarely are the mismash of icons very informative.

A note to those who use DoubleCommand and Logitech software: installing Leopard will cause problems. Logitech’s programmers have decided to try to hack OS X in ways Apple has explicitely told them not to in order to make their hardware work, instead of writing proper drivers. DoubleCommand, for some reason, causes hangups of the system during shutdown, so I’ve had to manually go through and remove every trace of it.

Confused about what the EMBL database is? What about MGD, MTB, or SNPSTR? Maybe you’re intrigued by TIGRFAM, U12DB, or VNTRDB? Do you find KNDBSPRAL frustrating?

Ok, I made that last one up. But seriously, there are a ton of biology databases these days, and I find it hard to wrap my mind around all of them. This issue of Nucleic Acids Research is pretty helpful as a starting point, though. There are some obscure databases on there, too, but they hit several of the major ones. And every article in the issue is open access!

I use Papers to organize all of my, well, papers. I read a lot of journals regularly, because I have a lot of interests; without a good workflow, I’d get buried under a pile of PDFs (admittedly, not that heavy, but >1,000 PDFs is hard to manage, no matter what the organization folder system).

The new version is much better. It integrates with more search services, such as Google Scholar, Scopus, and Web of Science, and the organization system just got a lot easier. The search integration with Spotlight is much snappier now, there is now even better BiBTeX integration, and lots of bugs seem to have been fixed, as it hasn’t crashed for me yet. There are still some small nitpicky issues (like not being able to specify a Smart Collection that gathers all papers imported in the last month), but overall this is a much more stable and useable release. Worth the price, especially with the student discount!