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.”
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.
When I first saw Boxee in 2010, and installed in on a Mac Mini connected to a projector in my den to manage home entertainment, it blew my mind that it was free software. I’ll explain what I think Boxee has to do with research in just a minute, but here’s what it is in a nutshell, as quoted from Question 8 of the Boxee FAQ:
“8. What can I watch on my Boxee? If it’s available on the Internet, then you can probably watch it on your Boxee - there are more than 40,000 TV show episodes and movies currently available through Boxee. Plus, you can play personal stuff from your network or hard-drive, and use the Boxee Browser to watch video from your favorite websites.”
Now imagine that I re-write that sentence, changing very few words, to read:
“8. What can I do with Resarchee? If it’s available on the Internet, then you can probably get it on your Researchee- there are more than 1,000,000,000 papers and data sets currently available through Researchee. Plus, you can use personal stuff from your network or hard-drive, and use the Researchee Browser to information from your favorite websites.”
I think that’s how research will look with the tools of the future. WorldWide Telescope and the Seamless Astronomy/Virtual Observatory efforts are getting us ever-closer to that future in Astronomy. Try Boxee and then you’ll see what Academia’s Future COULD look like.
Skype: A+ for voice; B for interface; C+ for multi-user screen share
It’s hardly necessary to explain the utility of Skype to anyone these days, but I list it here in order to qualify what it is/isn’t good for. Clearly, it’s fantastic (A+) for “free-ish” voice communication on a multitude of devices, and ~everyone knows that. Its interface LOOKS really nice, but even the tech-savviest of us get lost in it all the time (B). The worst part about the interface is that options and icons seem to move around from one version/OS to the next, so just be patient & keep looking for the button you want—it’s worth it. The present version of Skype offers group video calling, if at least one participant has a Skype Premium account. This sharing does work, but only when the Premium account is paid-up (hard to tell when it’s not), and when you can find all the right buttons/menus to make it work. I have found that participants’ patience often runs thin in trying to use this group app, so for now I have to give it a (barely-passing) “C+.” If you can do with just 1:many screen sharing, go try yuuguu.
-Too many places to be at once? -Too many collaborators around the country or the world? -Too many meetings to be at? -Too much carbon in the atmosphere? -Too many collaborators complaining they “couldn’t get screen sharing to work right last time they tried…”?
Screen-sharing and web-conferencing sound like great solutions to so many collaboration problems, but very often Skype, iChat, and WebEx are still “too complicated” or “not cross-platform enough” for “everyone.” I have found yuuguu to be a fantastic solution to that problem! Often, only 1 person needs to share his or her screen in a meeting. When that’s true, the best solution is for the “sharer” to have the lightweight (free) yuuguu application installed on his or her computer, and for (up to 30) “sharees” to just go to a URL generated by the yuuguu app to “see” the sharer’s screen.
Yuuguu has audio-conferencing built-in as well, but it’s real power is in generating a simple URL sharees visit in a browser with zero installation.
Adobe Illustrator is a very powerful inherently object-based (rather than pixel-based) image-editing program. Illustrator’s companion, Adobe Photoshop, is better for dealing with pixel-based files where one wants to manipulate the look of an image, rather than computer-generated objects within an image.
Many scientists think Illustrator isn’t for them, and for many, that’s correct. To be “good” at Illustrator takes concerted effort and training, and some innate aesthetic sense as well (and quite a bit of money, usually). However, Illustrator has the critical ability to open and manipulate Adobe PDF files directly. To many scientists, this (at least) should be a critical feature, as manipulating PDF output created by other programs lets users optimize graphics for the clearest presentation. The full version of Adobe Acrobat will also let users open PDF files and edit them, but its graphical capabilities are very, very, limited in comparison with Illustrator.
Adobe Photoshop is a very powerful inherently pixel-based (rather than object-based) image-editing program. Photoshop’s companion, Adobe Illustrator, is better for dealing with object-based files that have curves, shapes, or text in them one wants to edit as “objects.”
Many scientists think Photoshop isn’t for them, and for many, that’s correct. To be “good” at Photoshop takes concerted effort and training, and some innate aesthetic sense as well (and quite a bit of money, usually). However, Photoshop has the flexibility to open more image formats than most image-editing software, and even a novice can manipulate images within it very usefully. In addition, the “FITS liberator” program makes Photoshop especially useful to astronomers, as this opens their standard “FITS” format files in Photoshop, even offering integration with “AVM” tags for adding/manipulating astronomical and outreach metadata attached to images.
Seamless Astronomy: Keynote at Sage Bionetworks Congress (April 2011)
The embedded video here is just a teaser—the full 29 minutes (with intro + Q&A) is online at this FORA.tv site. This talk is a good summary of why and how astronomical research is facilitated by the “seamless” integration of research data, literature, and software. More information, including an online copy of the slides used here, is online at the Seamless Astronomy website.
A lot of what you read and hear about the “cloud,” and information stored there, is hype. But, Dropbox is real, and it’s unbelievably easy. ANY document that you might want to share with others, and/or collaborate on with others can be stored on Dropbox as if it was on your own computer (Mac, PC, Linux and mobile). I have come to rely on Dropbox to store any file I’m actively working on with others. Try it if you have not: its cross-platform, cross-device compatibility is pretty close to a miracle.
There are 
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 
It’s hardly necessary to explain the utility of Skype to anyone these days, but I list it here in order to qualify what it is/isn’t good for. Clearly, it’s fantastic (A+) for “free-ish” voice communication on a multitude of devices, and ~everyone knows that. Its interface LOOKS really nice, but even the tech-savviest of us get lost in it all the time (B). The worst part about the interface is that options and icons seem to move around from one version/OS to the next, so just be patient & keep looking for the button you want—it’s worth it. The present version of Skype offers 
-Too many places to be at once?
A lot of what you read and hear about the “cloud,” and information stored there, is hype. But, Dropbox is real, and it’s unbelievably easy. ANY document that you might want to share with others, and/or collaborate on with others can be stored on Dropbox as if it was on your own computer (Mac, PC, Linux and mobile). I have come to rely on Dropbox to store any file I’m actively working on with others. Try it if you have not: its cross-platform, cross-device compatibility is pretty close to a miracle.