Alyssa Goodman's "Desk"

python: The Programming Language for 2011—?

Once upon a time, I really could program.  Now, I’m lucky to have many students and postdocs who both use up all the time I could spend learning new computer languages well AND learn those languages well “for me.”  

As I write this in 2011, it is clear to me that python is currently the language of choice amongst the younger scientific research community.  In my own field of Astrophysics, great open-source packages like APLpy (the Astronomical Plotting Library in Python) are seeing widespread participation/adoption.  More generic open-source libraries like matplotlib are of use far beyond Astrophysics (as a 2D plotting library), and 3D plotting/Viz routines are in the works (ask me later!!).

• Software site link: http://www.python.org/
• Price: Free (open-source).
• Wikipedia: http://en.wikipedia.org/wiki/Python_(programming_language)

Adobe Acrobat: PDFs can do more than you think…

There are groups of the “avant-garde” in the scholarly communication world today who think of PDF as backward and limiting.  For now, though PDF is our “standard” document format—and it is NOT yet used to its fullest potential.  So many features built-in to PDF are not commonly used…but I’ll highlight just my favorite here.  Did you know that 3D models can be embedded as interactive figures inside PDF documents?  Check out our example of this here, or a movie about it in this video post. Meanwhile, I say keep trying to find more nuance in what you can do with PDF, keep your PDFs in a Papers-like App for your Scholarly LIbrary, and hope that Adobe supports easy transitions to whatever does come “beyond-the-PDF.”

• Software site link: http://www.adobe.com/products/acrobat.html
• Price: Reader is free (and yes, it does read 3D PDF), “full version” not free—academic discounts available.
• Wikipedia (on PDF): http://en.wikipedia.org/wiki/Portable_Document_Format
• Wikipedia (on Acrobat): http://en.wikipedia.org/wiki/Adobe_acrobat

Keynote: Presentation Software for the Aesthetically-Inclined

When Keynote first came out in 2003, I was a PowerPoint guru.  Being a bit of a Mac person, though, I was willing and excited to try Keynote in its early days…BUT I was disappointed with its extremely lacking feature set in comparison to PowerPoint.  Today, though, my allegiances have changed completely!  I am a Keynote guru now—I fully admit to spending way too much time on my presentations to make them “just right,” but the options now offered by Keynote to perfectionist/aesthetically-obsessed people like me are irresistible.   The iPad version is pretty cool too, but it’s still a bit limited for my ~300MB/presentation style!

Some favorite features: 1) Moving images are handled better in Keynote than any other presentation software I’ve ever seen… you can overlay a movie on a still image & make it transparent!  That’s very important to those of us who compare “3D” images as slices with 2D images as backgrounds.  You can also control movies frame-by-frame with a slider within a presentation in order to make your point. 2) iWork.com.  This is a little-known service of Apple that allows users of the iWork suite of applications to share their work at a web site called iWork.com.  Keynote presentations uploaded to iWork.com can be not only shared/commented upon with others, they can also be viewed—with ALL the animations working(!)—in a full-screen browser mode to look exactly like the original presentation.  [Here is a sample ..make sure to click the “play” button.] The BAD part is that storage space on iWork.com is currently not expandable, and is very limited.  Perhaps this “beta” service will finally expand with the advent of iCloud? 3) Import/Export to PowerPoint is very good, and improving all the time—so you can collaborate with PPT users, cross-platform. 4) Image-editing (e.g. instant alpha for background removal in images; transparency control; masking with shapes) is so good in Keynote that I frequently use it for manipulating images beyond those to appear in presentations.  It’s simpler to use than Photoshop and Illustrator, and much cheaper.

• Software site link: http://www.apple.com/iwork/keynote/
• Price: Not free, but both Mac OS and iPad versions are inexpensive.
• Wikipedia: http://en.wikipedia.org/wiki/Keynote_(presentation_software)

Basecamp (is easier for straightforward project management than a Wiki)

Many of us use wikis, or Google(-like) Docs/Sites, to collaborate with each other, and those are great in many cases.  BUT, when what you want is to robustly manage the activities of group of people who collaborate both with each other and with other groups of people, in a secure and simple way, Basecamp is hard to beat.  The hard part is the cost.  This is not a free service: it will cost someone hundreds of dollars per year to use. The trick is to get your institution (or group leader) to decide this is worth it—and then use it.  

Notes on features: 1) Basecamp allows for all communication to flow through it, even if responses are only through email—as long as the original message of a thread was started on the project site (thus, people won’t complain as much about having to go to a web site to send a message).  2) Files can be directly uploaded, and/or attached to messages. 3) Excellent calendaring/to-do/reminder systems are built-in and easily integrated with other apps. 4) Collaborative document editing is possible through “Writeboards,” but these are NOT as powerful as a Google Doc, so beware. 5) Permissions can be easily managed across projects, and administrator privileges can be distributed.

URL: http://basecamphq.com/