“A great deal of computation is required to perform a Hartree-Fock SCF calculation for a many electron atom. Hartree did several SCF calculations in the 1930s when electronic computors were not in existence. Fortunately Hartree’s father, a retired engineer enjoyed numerical calculation as a hobby and helped his son. Nowadays computers have replaced Hartree’s father.” Quantum Chemistry – Ira Levine

This makes me picture a little old man sitting in a room with all the world’s physicists and chemists sending him equations to solve.

Though more seriously, things like this make me appreciate the tools we have available now. I don’t think I’d be able to handle the things we’re covering in this class if I didn’t have a computer program to do the math for me. A similar feeling goes with a lot of the other things we use in the lab all the time. I just got a new plasmid a little while back that I need to make some point mutations then insert it into a new construct, then I’ll be expressing a human protein in E. coli. IT wouldn’t have been too long ago that just doing that part would have been a serious research project. Now, though the practical aspects are making me jump through some hoops right now, the concepts are fairly trivial and taught to undergrads. Sometimes it’s too easy to take some of the things we use constantly for granted.

• Kile: an all-in-one program that makes it easy to compose documents in LaTeX format, browse and modify output templates, and print to a variety of formats. I wrote my candidacy exam in LaTeX via Kile, and while I’m forced to use Word files usually (because it’s what my boss knows), I still think I write much more efficiently and create prettier output under a real publishing system instead of a word processor.
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• Amarok: The best music playing program I’ve ever used, bar none. If only it could buy songs from the iTunes store, I’d never need anything else. It manages my music, syncs my iPod, fetches lyrics and band info on the fly, and generally just gets the job done. I love background music, and I love Amarok.
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• hugin: A great automated program for stitching together photos (even badly taken, non-tripod, handicam photos) into beautiful panoramas. The extent of its ability to figure out which photos align together and seamlessly mesh them is phenomenal.
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• Yakuake: This is just a little terminal emulator program, but it’s incredibly convenient– At any time, hit F12 and it scrolls down onto the screen. Then, when you hit F12 again, it folds back away– but doesn’t close the session, so you can leave commands running or whatever. Seeing how much I love the shell (see below), it’s a great time saver.
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• Firefly Media Server: This daap server lets me stream my music across my network– be it to amarok or iTunes. It sets up very easily, doesn’t put much strain on my server, and works great.
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• Crossover Office: Sometimes I still need a windows program. No, it’s true! And when that happens, I can’t beat the convenience of Crossover Office. Default wine may technically be able to run everything, but the auto-configuration, creation of independent “bottles” to store different programs, and guaranteed performance on programs I use (like MS Office 2000, the last good version) make it a winner. I’m actually an advocate for some scientific software for them.
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• An actual Shell: Making this list was a lot harder than I expected it would be. I realized that most of my favorite Linux programs are installed by default (even Amarok, above, but also VNC functionality, Kate, and tons more), or small little scripts, code snippets, or essentially command line programs (ssh, sed (truly, truly, do I love sed)) that just make life easier for me. So I guess I can sum that up and say that what I really love is a full-featured shell environment. It makes me more productive, and let’s my customize the computing experience to meet my needs, rather than adapting myself to Windows.

So, here’s a smattering of programs cross-platform or Windows-only programs that I think are worth spreading the gospel of:

• GmailAssistant - I like to have a systray notification of new Gmail messages, but I don’t always want to be signed into google talk, as in the default Gmail notifier. Gmail Assistant is a little java program that alerts you to new email; and it’s VERY configurable. You can set it to only tell you about messages with certain labels, and whether it should display a pop-up or beep, or… well, there’s a lot of configuration options. Nice. Oh, and it can track multiple Gmail accounts at once, if that’s your thing.
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• Prism - Although still a beta, Mozilla Prism is a tool to turn web applications (like Gmail) into stand-alone applications on your desktop. With it, I can have a separate window that’s just Gmail, which always remembers my settings, and can be docked into the system tray, and runs an independent browser– so if Firefox crashes on some crappy flash site, my web app is still fine in it’s own window. Neat.
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• Knotes -Alright, so KNotes isn’t a windows application, but it has lots of equivalent Windows versions (like Sticky Notes, Stickies for Windows, or NoteZilla). It lets you put persistent sticky notes up on your desktop. I use it to remind me of chores, fun tasks (like updating this site), and other things I don’t want to forget.
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• NotePad++ - The built-in windows textpad is just… bad. NotePad++ replaces it (even for things like looking at HTML source, etc), and does a much better job. It can detect and color-code programming schemes, you can have tabs with more than I file at once, and more. It’s great.
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• Inkscape - My preferred diagram and schematic creation software is cross-platform, and very good at what it does. It’s like Adobe Illustrator, but free and funky.
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• Audacity – Again, a freeware solution, Audacity will handle every need you ever have for audio editing. I’ve used to make cell phone ringtones, break a large audiobook up into chapters, make sound effects for games, and a friend uses it to convert books on cassette tape to mp3s for his iPod.

If you take away leveling (experience gain) and the constant need for better gear (varying equipment), what’s left in an MMORPG experience? You’re left with a game:

• that is multiplayer, with thousands of players
• but divides those players into instanced maps
• interesting scenery and fluff
• Clans and organized player group, both casual and hardcore
• and lots of chatting

Well…. that sounds a lot like Team Fortress 2 (or other online, team-based multiplayer FPS games).

Additionally, a common complaint about MMORPGs is that time played is the major controller of success, with player skill being only a small fraction of success. In TF2, most success is skill-based: not only aiming and dodging (much more satisfying than the “click and go get a snack” combat found in most MMORPGs), but knowledge of maps, teamwork, knowing when to switch classes to balance your team, and reacting to changing circumstances.

The only things it lacks are the ability to customize your character and the ability to explore. With the plethora of custom maps available, the exploration concern might be partly alleviated. And with the upcoming unlockables and achievements, the ability to differentiate your character will become even more feasible. Plus, in a skill-based setting, your differentiation is primarily reflected in your skill and your personality on voice chat. Maybe they could release custom faces for TF2, which confer no advantage?

There we go, sent out for posterity.

Sordid crash details: Abbreviated version of my drive crash: it was old. Slightly less abbreviated version: my drive was worn down (it’s something like 7 years old), and had started giving Buffer I/O errors, and sometimes randomly causing a stop error (i.e. the computer randomly shut off). Still, I was oblivious and busy, so I kept putting off changing it. Oops! One morning, it just wouldn’t boot– it said the bootloader was missing. So I use a Kubuntu CD to boot up, and write a new boot section for GRUB on my Linux disk. Problem was, Linux wouldn’t even mount the crashed drive anymore, and it was making ominous noises and heating up fast. Fast-forward hours of researching and discussions with friends. I took the windows drive out, put it in an external USB enclosure, cooled it in the freezer for an hour (it works, don’t knock it), and hooked it up to a Windows PC. Windows saw the USB device, but said the drive had no volumes (partitions, for those of us outside of windows lingo-land), and if you tried to read the volume info– errored out the whole computer. But I found a great little utility called testdisk which was able to see the drive and rebuild the bugged partition table. I could then mount the hard drive under Linux and copy files across– still getting horrible I/O errors, but Linux is good at recovering around that. So, my data is saved, but the drive is kaput.

The Plunge: So now, my computer is running great, I have all my data, but I don’t have Windows on my computer at all. I have an install CD for Windows XP Pro, but… I’m not that eager to try installing it just yet. Linux is doing everything I need– in fact, it does most things better than windows (it loads faster, it’s easier to update and manage, it has a much more organized interface, it has free access to lots and lots and lots of quality programs, etc). What it didn’t have was MS Office or my favorite computer games. But wait! There’s a linux programming effort called Wine that lets you run some windows programs on linux. Would it work for me? Yes. Yes, it would. Using a special, paid version of Wine called Crossover Office (I bought it a year ago, so I don’t even have the latest version), MS Office XP installed and works without a hitch. Heck, it loads large documents faster than under windows. And games? My current favorite game is Oblivion. Wine (just the normal one) worked for it, though it did take more work than just putting in the CD and pressing play. Now, I just need to see if I can get HalfLife working, and I’ll be golden.

What isn’t Linux doing for me? For some reason, I’m having trouble getting Teisha’s windows computer to access the printer hooked up to my computer. This isn’t really a problem, as I wanted to buy a print server anyway… but it is weird, since over Samba (the Linux version of the windows file sharing protocol), she can access my files. Huh. Beyond that, the last big sticking point is… iTunes. I’ve bought quite a few CDs over iTunes, I think it’s a neat program (though the similar linux program Amarok is almost as good) and service. But iTunes doesn’t work under Linux, and so neither do the songs I bought on iTunes. I’ll have to look into this more. But I knew iTunes was a Linux-unfriendly program when I made the decision to use it. Oh well.

The two sites are often compared with one another (in fact, some members of their respective communities have a big rivalry going on… myself, I see them as different resources, each with a very different emphasis and demographic).

SlashDot bills itself as “News for Nerds. Stuff that matters.”, and that is a fairly apt summation. It features a lot of geek-talk about computers, technology, politics, and science. The average reader (or at least, the average person who joins in the discussion) is a bit older, mostly people involved in information technology or science. This means (importantly), that on SlashDot, the stories don’t matter. If you read SlashDot and just look at the little article blurbs posted, you’re missing the point. SlashDot has some amazingly intelligent and cogent commentary on the articles, as well as a complex (and effective) moderation system to ensure that insightful comments are displayed prominently. I urge you, if you ever look at SlashDot– read the comments, not the article. I occasionally comment when I have something worth saying… You can see a record of my latest comments.

Digg, in contrast, has the most useless and juvenile “community” I’ve ever encountered. It’s a great site to visit to see the latest New Thing ™, and to see interesting, out of the way news. But under no circumstances should one read the commentary on their links. It will cause loss of sanity and faith in human nature. The owners of Digg are trying to change this, I think, by introducing some better moderation tools… but it will be an uphill climb for them. So, visit Digg, but don’t read the commentary. Just click on the links and see the latest and greatest the internet has to offer. Oh, you can see a list of stories I recently “dugg” (that is, found interesting) on my profile page.

Enjoy wasting some time!