1. I’ll just retype the docs into this email for you.

and gets even better through sixteen more responses.

Anyone who has served as a software maintainer will appreciate this post.

The biggest problems? There is a looming shortage of qualified data scientists. In addition, managers need to become more data-literate as data-driven business decisions become more important. Third, privacy and security issues may limit the amount of available data. Finally, legacy data is often stored in formats that are not easily converted.

There is no such thing as too much desktop, as far as I’m concerned. In my experience, all software developers can increase their productivity with a second (and even a third) monitor. Data analysts and scientists can also increase their productivity with a second monitor.

At work, I leave my 1920 x 1200 laptop screen open to serve as a second monitor, and for work at home I bought a second 1680 x 1050 monitor a few years ago. What windows do I place on my main monitor? My IDE’s window and the web page I’m currently working on. What windows do I place on my secondary monitor? My email program, my journal document where I track what I’m working on, and my primary Cygwin console window from which I launch additional mintty windows. I often also need to make space for a spreadsheet window and a bioinformatics tool window. If I had a third monitor, I know where those extra windows would end up!

More seriously, however, chromatic in an earlier post rages against Linux vendors who are still including Perl 5.8.8 as the system Perl installation. This holds back the development of CPAN modules, which must maintain backwards compatibility with Perl 5.8.8 and thus cannot take advantage of new functionality that has appeared in Perl 5.10, 5.12, and now 5.14.

Mac OS X 10.6 (Snow Leopard) is almost as bad; it comes with Perl 5.10.0, which was released in December, 2007. That means OS X is delivered with a Perl version that is now more than three years old.

[Updated 15-May-2011]

The release prompted a discussion on Slashdot, which, as always, brought out the trolls who claim that no one uses Perl anymore.

I have one piece of advice (based on a recent experience while reading résumés) for Perl developers who are looking for a new job: Ask someone to read your résumé to make sure you have spelled Pearl Perl correctly. (Damn you, autocorrect!)

This is a list of online resources for Perl, mainly for my reference.

Perl

Perl Programming Language: A comprehensive site with links to everything in the Perl world.

Perl Programming Documentation: The complete documentation for Perl.

Modern Perl

Enlightened Perl Organization: “Enlightened Perl is a membership organization which is built around a movement within the Perl community. Its goals are complementary to the Perl Foundation. Specifically, we support certain Perl development efforts that ensure perl’s future as an enterprise-grade development platform.”

Modern Perl Books: A modern Perl blog, by chromatic.

Catalyst: The Perl MVC Framework.

Moose: A postmodern object system for Perl.

CPAN

CPAN: Comprehensive Perl Archive Network: The place to go when you need a Perl module.

CPAN Testers Reports: “Find CPAN testers reports for all the modules on CPAN.”

CPAN Testers Wiki: “This wiki is the online reference for everything related to CPAN Testing. HowTos, Tutorials, FAQs and Notes are all here to help both beginners and experienced CPAN testers. If there is any aspect of CPAN Testing missing from this site you are encourage to update it.”

The timing of Friedberg’s post is fortuitous for me because I’ve been teaching myself Python recently, and now I’m able to read and understand Friedberg’s entire script without having to refer to a book. The Weasel program would make a nice homework assignment in a programming course.

John: Lots of people now are working in dynamic languages—Ruby, JavaScript, Python, stuff like that.

Dan: What do you work in, most days? Can you say that? ’Cause I know that—

John: I work in Perl. That will flip people out, but believe it or not, people still do that.

…

Dan: Can you read your own Perl once you write it?

John: Of course I can.

Dan: Okay. Most people can’t.

John: Not true.

Via John Gruber’s Daring Fireball, I learned that Tim Ricchuiti at the elaborated has written a long and informative post describing what the dimensions of a retina display would be for different computing devices.

The term “retina display” was invented by Apple to describe a display with pixel density sufficiently high that the individual pixels can’t be seen by eye at the normal viewing distance. The current iPhone and iPod touch models have retina displays with a resolution of 960 x 640 pixels on their relatively tiny 3.5-inch displays.

Tim first walks his readers through the mathematics of what resolution is required for a retina display for different size screens. For an iPad being viewed at a distance of 15 inches, the resolution needs to be nearly doubled. (The 15-inch Dell laptop I’m using today to write this post has a 1920 x 1200 display, and my eyes are about 24 inches from the display. By Tim’s calculations, this display verges on qualifying as a retina display.)

Tim continues by explaining why doubling the resolution of current displays is easiest to support for the graphical user interface. Based on this premise of doubling display resolution, Tim predicts that a Retina Display iPad will have a resolution of 2048 x 1536 pixels—a pixel density of 264 pixels per inch—at which density the individual pixels couldn’t be detected by a viewer 13.0 or more inches from the screen.

It’s only a matter of time and technology improvements. Can Apple achieve this for the next iPad?

[Updated 2011-04-26]

For more information, I recommend that you read The Resolution Gap at DisplayBlog.

I use NetNewsWire (paid user, only $15) to track more than 150 blogs about science and computers. I couldn’t possibly keep up with these blogs any other way, and if you’re a regular reader of this blog, you’ll have already figured out that I come up with many of my blog topics from reading other blogs.

Yesterday’s discovery was David McCandless’s Information Is Beautiful site. There is plenty to explore here. I especially like “Books Everyone Should Read: A Consensus Cloud,” created by David McCandless, Miriam Quick, and Matt Hancock for The Guardian (click the image to see the entire thing).

I learned about the workshop from Jan Aerts’s blog, Saaien Tist. Dr. Aerts provides a good summary of the workshop in his post, where he mentions that the videos from the workshop will soon appear. Unfortunately, this year’s videos haven’t appeared yet, although 26 videos from the 2010 workshop are available. This is a wonderful resource, and I need to find the time to watch these.

Dr. Aerts mentioned in his post that Tamara Munzner has already posted her slides from her keynote talk on her own website. Dr. Munzner has a well-organized web page with links to slides and other materials from her presentations going back to 1995. I spent some time last night viewing her slides from VizBi 2011, and even without the speaking notes, they were easy to understand. If you’re interested in this topic, then I highly recommend viewing them.

Dungeon Crawl Stone Soup is an open-source, single-player, role-playing roguelike game of exploration and treasure-hunting in dungeons filled with dangerous and unfriendly monsters in a quest to rescue the mystifyingly fabulous Orb of Zot.

In the mid-1980s, when I was in graduate school at Berkeley, I played Rogue quite a bit late at night while waiting for my electrophoresis gels to finish running. Rogue ran on a time-sharing university Unix mainframe. It was somewhat buggy, and I never managed to complete a game (the goal of which was to descend into the dungeon, retrieve the Amulet of Yendor, and return with it to the surface) because the game would crap out after a certain point and I wouldn’t be able to do anything other than control-C to quit.

I’ve found Dungeon Crawl to be more sophisticated in its use of graphics than Rogue (although Dale, a character in Questionable Content, asserts that only babies use the tileset instead of ASCII graphics). What surprised me is that I still remember how to use the keyboard to move around efficiently, and commands such as q (quaff a potion) are beginning to come back to me.

[Updated 27-Apr-2011]

There is a post at Mandible Games called “Roguelikes: The Misnamed Genre” and an accompanying discussion at Slashdot that might be of interest to Dungeon Crawl Stone Soup players.

Barrett’s post has provoked a storm of responses in the comments to his post and also at Slashdot. The responses are as entertaining but often more insightful than Barrett’s rant. (As usual at Slashdot, there are only a few diamonds in a sea of mud.)

It is illuminating to read Expensify’s description of the skills requirements on their “Who We Need: Engineers, Entrepreneurs, Skill-set Contortionists” web page. They want someone who is an expert at everything, who will be asked to do everything, and who will devote their entire life to their job. (And when the company goes overseas to focus on code-writing, you pay for the trip yourself.) This description doesn’t recognize that people have different abilities and skills. For example, the best programmer at a company may not have the people skills to provide good user support, and it’s unrealistic to think that such a person can be found.

The question is, given what Barrett has said publicly, do you want to work for such a person? I believe that Barrett, as CEO of Expensify, has damaged his company’s reputation and has made it more difficult to hire good people. This is a good example of when CEOs should keep their mouth shut.

Disclaimer: I don’t use .NET myself, but I work with creative and excellent programmers who do.

But today I read a review of GarageBand by Benjamin Jackson on his 90WPM blog:

My iPad is now a guitar, piano, synthesizer, drum kit, and track editor all in one. It’s like walking through Sam Ash with Steve Jobs’ AmEx. I can hook in a mic and whatever instruments I want. I could compose an album while sipping mojitos in a chaise lounge in Cozumel.

Benjamin provides a thorough review of the strengths and the weaknesses of GarageBand, and the result is that he has convinced me that I have to load it on my iPad immediately.

Thanks to John Gruber for pointing out this review on his Daring Fireball site.

The first edition has been an old friend that has provided me with weeks of interesting reading and study. The new edition is fatter; at first glance, much of the material has not changed, but I think I’ll just have to read it cover to cover like as did with the first edition to find what’s new and review what’s repeated from the first edition.

This book is clear but challenging; most of the linear algebra is beyond my skills, but I know that if I just worked hard enough at it, I could figure it out. One of the best features of this book is the use of color on every page. I also like how the authors return to some problems using different analytical methods to see how they give slightly different answers.

Dr. Wu’s post includes the most amazing use of PowerPoint I’ve seen, PowerPoint line-drawing art. You must see it.

I am not cheap, but I am frugal. For me, it is worth paying money for a top-quality product, but it is not worth paying money for more than I need. My considerations here are about getting the most for your money.

Eighteen Models

I keep hearing on various podcasts or reading on various blogs that there are too many models—eighteen—of the iPad. But the questions you need to ask are fairly simple.

1. Which carrier? The possible answers are None, Verizon, or AT&T.
2. Which color? The possible answers are White or Black.
3. How much memory? The possible answers are 16 GB, 32 GB, or 64 GB.

When you calculate all possible combinations for these three questions, you find there are 3 x 2 x 3 = 18 possibilities, hence the 18 models.

Carrier

Your choice of carrier depends first on whether you want to be online at any time. The 3G models cost $130 extra for the hardware plus at least $15 per month for a data plan, or at least $310 for the first year. You can rent more than 75 movies (at $4 per movie) or buy 31 movies (at $10 per movie) or buy 30 books (at $10 per book) for that kind of money.

I find I have access to wireless networks nearly everywhere I go, so I decided to purchase the Wifi-only model. I haven’t regretted that choice.

Color

I have no opinion on color. I own a black iPad because the first iPad came only in black. The white iPad looks good, too.

Memory

Your choice of memory depends on how much data, in the form of apps, books, music, movies, and photos, that you want to carry around with you. Unfortunately, you won’t have a good answer to that question until after you buy your iPad and use it for a few months, so I offer here the benefit of my experience.

I find Apple’s prices for memory hard to justify. For the Wifi-only models, the 16 GB model costs $500, the 32-GB model costs $600, and the 64-GB model costs $700 (I’m rounding up one dollar here). Why does adding 16 GB cost $100 ($6.25/GB) but adding 48 GB cost $200 ($4.17/GB)? If Apple’s prices were proportionate to the cost of memory, the 32-GB model would cost $67 more than the 16-GB model, making proportionate prices something like $500 (16 GB), $570 (32 GB), and $700 (64 GB). And this doesn’t factor in the fact that higher-capacity memory chips usually cost more per GB. Based on this analysis, I estimate that Apple is making something like $33 of pure profit on the 32-GB iPads by rounding the price up to the nearest $100.

By the way, let me warn you that if you go to Settings => General => About, you will find that the 16-GB iPad has a true capacity of 14.0 GB; presumably the remaining 2.0 GB of memory is used by the operating system.

I bought the 16-GB iPad, and it has been more than large enough so far. I currently have 318 songs (15 hours), 10 videos (6.5 hours of television show episodes), 6 Kindle books (30 hours at my reading speed), 285 photos, and 56 applications on my iPad, and I still have 3.3 GB of free space.

As a point of reference, a typical movie, such as one of the James Bond movies, has a size of roughly 1.5 GB. If you wanted to watch the first three James Bond movies on a non-stop flight to the West Coast, you need less than 5 GB of space. A Kindle book is tiny in comparison; an 800-page book such as Our Mutual Friend has a size of about 2 MB. You can store thousands of books on an iPad.

I have more than 50 hours of entertainment stored on my 16-GB iPad, not counting time I might spend with applications and the browser. My problem is not how much data I can carry but where I can find the time to consume the data.

The larger-capacity models make it easier to carry your data without having to shuffle it back and forth between your iPad and your computer, but that benefit wasn’t worth it to me. I can spend the money I saved on more music, books, and video.

Summary

I recommend the 16-GB Wifi-only iPad, which costs $500. You can choose the color.

[Updated 18-Apr-2011]

If you already own the original iPad, should you buy the iPad 2? I don’t think so, but Nick Bilton at the Bits blog on The New York Times website believes it’s worth it.

I use the Kindle app on both devices. However, after reading from my iPod touch, which truly is so sharp that my eyes cannot distinguish the individual pixels, I find the display on the iPad to be relatively coarse or grainy.

It’s difficult to show the difference between these displays, but here’s an attempt. On each device, I opened the Kindle app, set the font size to the minimum, and took a screenshot of the same paragraph (from Our Mutual Friend, by Charles Dickens). I transferred the images to my MacBook Pro, expanded the images to roughly the same size, and captured them using the Grab application.

Comparison of the two images reveals that text on the iPod touch is much sharper, with more pixels used to draw each character. Text on the iPad is coarsely drawn, with easily seen antialiasing required to make the characters look better. (Antialiasing is also used on the iPod touch, but it is much more subtle since it is not needed as much.)

Kindle App Smallest Text on iPod touch

Kindle App Smallest Text on iPad

Because my eyes tire easily if I use the smallest font in the Kindle app on my iPad, I usually set the font to the next size up. This means there are fewer words per page, and I have to turn the pages more frequently. Of course, the iPod touch is so tiny that it can’t display very many words per page, so it requires a lot of page turning.

Before the new iPad was released, there were many rumors that the new model would have a higher-resolution display. If Apple were able to double the resolution of the iPad display to 2048 x 1536, text and images on the iPad would be much sharper. I imagine that once display technology has advanced to the point that such displays can be manufactured, Apple and other tablet vendors will switch to high-resolution displays. I look forward to those days.

I have not been able to get a close look at the $139 WiFi-only Kindle sold by amazon.com. The Kindle has 600 x 800 pixel resolution at 167 ppi, 16-level gray scale, which is sharper than the iPad. I chose the iPad, however, as a general media consumption device, since I can also use it to watch television shows or movies and to view photos.

The Apple Store was closed, with black blinds drawn down over the doors and windows. There were about 100 people standing in line, waiting to get in.

The iPad 2 sounds like a fine piece of hardware, but I already have the first model, and the new model isn’t improved enough for me to want one. When Apple improves the resolution of the screen to 300 dpi or better, then I’ll buy another one.

[Updated at 7:05 pm]

The excitement is over (I suppose) on the East Coast. MacRumors has photos of lines at other stores. In the meantime, if you want to order an iPad 2 through the Apple online store, the delivery time is two to three weeks.

[Updated 12-Mar-2011]

Adam Satariano and Marc Perrier write on Bloomberg that many of the people standing in lines at the Apple Store to buy the new iPad 2 planned to resell them for profit in other countries.

[Updated 13-Mar-2011]

Some web sites are now reporting that Apple has sold out of iPads at most stores, and many people have confirmed that many of the iPads sold on Friday and Saturday are destined for the grey market.

I am a regular reader of chromatic’s blog, Modern Perl Books.

Modern Perl programming, circa 2011, relies on the collected wisdom of the entire Perl ecosystem. It’s time to write elegant, reliable, maintainable, well-tested, and predictable code.

In chromatic’s book, Modern Perl, he encourages his readers to write modern Perl.

[M]ost Perl 5 programs in the world take far too little advantage of the language. You can write Perl 5 programs as if they were Perl 4 programs (or Perl 3 or 2 or 1), but programs written to take advantage of everything amazing the worldwide Perl 5 community has invented, polished, and discovered are shorter, faster, more powerful, and easier to maintain than their alternatives.

Modern Perl is a loose description of how experienced and effective Perl 5 programmers work. They use language idioms. They take advantage of the CPAN. They’re recognizably Perlish, and they show good taste and craftsmanship and a full understanding of Perl.

You can learn this too.

I plan to work my way through Modern Perl, even to the point of learning how to use Moose for object-oriented programming. Watch this space to see how well I progress.

Once I had configured iTunes on my MacBook Pro to enable sharing, I discovered that I had to go to Settings -> Music on my iPod touch and enter my Apple ID and password to enable sharing. After these configuration steps, I was able to access my entire iTunes library, including movies and television shows (but not audiobooks from audible.com), from my iOS devices.

More information about using Home Sharing is available from ilounge.com.

Hey, I just realized that I’ve had this blog for more than 8 years, but never put out a best-of list. I’ve chosen these based mostly on my blog stats.

I was pleased that Bosco included a post from nearly four years about why he thinks Python is good for the scientist who programs. In brief, his reasons are:

• “Python has built-in modern data structures.” (Unlike, ahem, Perl.)
• “Readability counts.” (Python is compact, expressive, and enforces good formatting of code.)
• “Scriptability.” (Python can replace the complexity of shell scripts, make files, and compiled programs.)
• “Python is ecumenical.” (You can write object-oriented or procedural code, depending on your needs).
• “Interpretation is back in style.” (Python runs as fast as much compiled code without having to go through the compiling cycle.)
• If you “really need the speed,” you can write a plug-in module in a fast language such as C and execute the module from Python.
• “Python has powerful math libraries” (numpy, matplotlib, and other scentific libraries).

Read Bosco’s entire post about Python—you won’t be sorry. The other best-of posts are also excellent.

P.S. I do all my work in Perl, and I suffer from Python envy. If I were starting over in bioinformatics programming, I would start with Python.

I disagree immediately with Veteran Unix admin trait No. 1: We don’t use sudo. One of the safest things you can do for your Unix computer (including Linux and Mac OS X) is inactivate the root password. My trick is to launch a bash shell using the sudo command, that is, sudo -u root bash.

I agree completely with Veteran Unix admin trait No. 4: We’re inherently lazy, although I think the title is too vague. The point is that anything more complex than a single command should be written as a script. This gives you more control over what you are doing because you can edit a script before executing it, whereas once you have executed a command, it’s too late to recall it if you made an error in the command. A point made well in the article is that you can save scripts, because they will come in handy again when you encounter a similar or identical problem.

The last trait, Veteran Unix admin trait No. 9: Rebooting is almost never an option, caught me by surprise and taught me something I didn’t know. Paul Venezia followed up with another post, “When in doubt, reboot? Not Unix boxes,” and that post is well worth reading.

I usually connect my laptop to an external monitor and use both screens. At home, the external monitor is to the left of my laptop screen, but at work it is to the right. XP usually figures this out, but sometimes it gets confused about where the external monitor is and what its resolution is. XP gets even more confused when I plug the laptop into a projector or large display screen. Fortunately, I can use the desktop settings to fix this.

But a problem I couldn’t solve until today is this: I park a window (such as the Cygwin terminal) on the external monitor. When I disconnect my laptop from the external monitor, XP doesn’t figure out that I can’t see that window, and it doesn’t automatically move it back onto my visible desktop. XP lets me minimize and maximize the window, but I can’t move it to my visible desktop.

That is, until today, when I had the good sense to bing for a solution (“bing” is a new word I just invented that is like “google” only using Microsoft’s bing search engine). The trick is to right-click the window’s icon on the task bar, select “Move,” and press one of the arrow keys. For some reason, this magic combination moves the window back to the visible desktop.

I learned of this from John Gruber’s Daring Fireball. As Gruber says, it’s so true.

Yesterday I needed some baseball, and I couldn’t wait. On iTunes, I found Baseball’s Best, the original television broadcasts of 154 of the best games for only $2 apiece. Last night, I watched “1989 ALCS, Game 4: A’s at Blue Jays.” It was great to watch my favorite Oakland A’s players again, although unfortunately it was Bob Welch who pitched that game, not Dave Stewart.

From John Gruber’s Daring Fireball site, I learned about a new iPad app called Pennant. This app, currently priced at $5, provides summaries of every baseball game from 1952 through 2010. The presentations are unusual and sometimes not quite as informative as I would like. I expect the app will improve with later versions.

I purchased the At Bat 2010 iPhone app last season, and I’m eagerly waiting for At Bat 2011 to be released. There has been no word yet on when it’s coming out.

[Updated 28 February 2011]

At Bat 2011 was released on Friday, February 25, in time for the first games of spring training. Radio and television broadcasts and video highlights are now available.