The Futile Cycle

This will be a small rant.

Why don’t journals put abstracts into the RSS feeds of their table of contents? The abstracts are open to the public anyway, and it would make their feeds much more useful. Because Nature, PNAS, and other journals don’t include their full abstracts, I’m regularly subjected to the overflow of windows:

I use LaTeX a lot. As in, for almost everything where I have to produce a written document, whether it be writing an essay or paper, taking notes, or doing my problem sets. I try to minimize the amount of time I touch Microsoft Word, because it hurts whenever I do. Getting things done in Word is almost painful, as the interface is awkward and slow (especially since I have to run Word in Rosetta, which is essentially emulation). I also really like LaTeX because the documents it produces are very, very beautiful and much easier to read.

The one time I pick up Microsoft Word, however, is when I have to edit and collaborate on documents, because there’s really nothing better than the “Track Changes” feature that Microsoft has. Adobe’s collaborative editing features for PDFs are really shamefully bad, and I don’t know anyone who uses them.

That may change now, though. via GeomBlog, I found latexdiff, a program that’ll output a diff file that will mark changes. It apparently also supports basic accept and reject changes, as well, through the editing of the diff file. The example given seems to be absolutely perfect!

For those who are interested, Papers has reached version 1.0. I’ve written before about this Pubmed-integrated literature organizer and viewer.

In addition to a whole slew of bug fixes, my favorite new feature in this version is that Papers has gained built-in integration with proxy servers and authentication pages, which most of us need to use in order to access institutional subscriptions to journals. I, for example, have to append “ezp1.harvard.edu” to all website domain names (so, something like www.sciencemag.org.ezp1.harvard.edu). Up until recently, I’d been using some Perl scripts and a patchwork of programs to let me switch over to the institutional subscription with keyboard shortcuts whenever I needed (yes, it’s only 16 characters, but it was maddening); now Papers will do it for me!

Papers won’t be taking over my entire workflow (Pubmed still doesn’t update as frequently as, say, my email news alerts and RSS feeds), but it’s definitely taken over every aspect of actually reading papers.

UPDATE: Ok, so Papers’ authentication and proxy-server support is actually broken right now (at least, it doesn’t work for me). Not so great, especially for a supposedly 1.0 release, but I still appreciate the other bug fixes.

UPDATE 2: With the new bugfixes, Papers now works with the Harvard authentication server (at least). I can’t verify it for other servers, but it works swell for me!

I find it really hilarious that an outage of the Blackberry email network for a dozen hours or so at night warrants widespread coverage in the media.

I understand that Blackberries are really addictive; I myself can get addicted to information sometimes (what with my 100+ news feeds that I follow), but this is a little ridiculous. Most of it didn’t even happen during normal North American business hours. I can step away from the computer (though it does take some coaxing, occasionally). Can’t they?

There’s yet another PDF reader for Mac OS X out called Skim. This is another one based on the Webkit PDF reading system built into OS X that Papers, Safari, Yojimbo, and tons of other programs use to view PDFs. The difference here is that it’s geared towards reading scientific papers, and it’s written by the creators of BibDesk.

There’s not much of anything remarkable in Skim. It opens PDFs, has some notation interface (slightly better than Preview, which comes with OS X, and comparable to Adobe Acrobat, though that’s not saying much), and it can view PDFs in full screen, which is nice. The search feature isn’t much better than Preview, and the reading bar I find to be sorta useless. Bookmarking would be handy for those long review papers (or any paper from Cell, with 9+ pages).

There is, however, one really, really great feature that I find to be so amazing, and yet so so simple. By holding Cmd and click-dragging a box over a specific figure, a new window will open with that figure, so that you can keep scrolling the PDF and still refer back to that figure. After seeing it, I can’t believe that no one did it before. I mean, it makes PDF reading so much easier, almost (but not quite) as easy as reading on dead trees.

It’s not implemented particularly well, but Skim is still beta (and version 0.2, at that). It’s a great idea, though, and if they tweak the user interface defaults just a bit (like the default magnification on the figure popup window), it could become a really great feature. For free, though, it’s pretty sweet.

I’m slowly making my way through my journal Table of Content RSS feeds. I suppose I should make this weekly habit, so that I can keep up without being swamped. I’m all caught up in PLoS Computational Biology, PLoS Biology, Nature, Cell, and Science, for example, but I still have PNAS and Molecular Systems Biology to get through, not to mention the quantitative biology section of arXiv. Mostly, I’m just reading abstracts. Every once in a while, I find a paper I find interesting enough to skim, and sometimes they’re so interesting (and short enough!) that I read them. But I haven’t read a full paper in a long, long time.

I’ve been trying out different workflows to see what sticks for reading the literature, and actually I’ve found a great program, Papers, for reading and keeping all my PDFs organized. I used to use a workflow that centered around BibDesk, downloading PDFs, importing the citation into BibDesk and linking it to the PDF, and so on. It wasn’t the worst thing in the world; actually, the best part was being able to tag papers and group them into various subjects. The metadata handling with BibDesk is pretty good.

Now, though, I think I’m slowly converting to Papers (still in Beta), which is integrated with Pubmed to allow one to download citations and organize PDFs. Papers resembles iTunes and NetNewsWire, in a way, which I guess is a complement. It’s still quite buggy and very beta, though; it’s sometimes lost a few of my PDFs, crashed a couple of times, froze a few times, and so on. Overall, the workflow is much simpler here than it was with BibDesk. There’s less “stuff” to deal with, subjectively, in terms of the user interface. It’s definitely a lot less painful to organize my PDFs now. If the next few releases increase the stability significantly and iron out some of the weirdness with losing PDFs (and maybe some user interface cleanup), I’d be quite willing to shell out money for it.

To celebrate a friend getting a new Macbook, I’ve decided to post some links to good switching hints (i.e. how to get used to the new simplicity) and what I install on my new Macs.

First, a link to a guide on switching from PCs to Macs:
The Lifehacker Guide. Covers things like what the main keyboard shortcuts are, what hiding, minimizing, and quitting do, and how to install programs.

Also, a good page on most of the Mac OS X keyboard shortcuts.

EDIT: More keyboard shortcuts that Apple doesn’t list

The one useful thing most people don’t often learn is that when switching applications (Cmd-Tab), you can hold down the command button and let go of Tab. This keeps the switching bezel open, and you can then do things like hit ` (above the left Tab) to go backwards (easier than hitting Shift-Tab), Q to quit the selected application, or H to hide the selected application. Also, Cmd-` switches between the windows of an application, though I find Expose to be more useful there.

And next, all the freeware I install:

Quicksilver, for ultimate keyboard access to everything.

Windows Remote Desktop Client, for remote access to random PCs.

Perian, a set of almost all codes for Quicktime, so that you can play XviD files, random other AVI compression formats, etc.

Windows Media Components for QuickTime (a.k.a. Flip4Mac), which allows you to watch Windows Media files in QuickTime.

VLC, which is actually all you need, but it’s nice to have everything work with QuickTime, too, as the interface is a bit nicer.

Adium, a good all-in-one IM client.

TextWrangler, one of the best free text editors in the world. It supports regular expressions, which is rather key, but also good things like zapping all non-ASCII characters, straightening or curly-fying quotes, etc.

Cyberduck, a free, good FTP/SFTP/SCP program. That’s all there really is.

TeXShop and the TeX Live package, which installs all the goodies, like LaTeXiT (mini PDF clips of equations that you can drag-drop to Keynote or Powerpoint or wherever), and BiBDesk (bibliographic references manager for LaTeX).

Transmission, a really light BitTorrent client that’s simple enough to use and isn’t the massive memory-hog/behemoth that Azureus is.

Stuffit Expander, which opens archived files. Most of the built-in stuff works just fine (opening zip files, etc.), but sometimes Mac stuff, especially older stuff, is in SIT compression, which requires StuffIt Expander.

X11, an X-Window system implementation. This is for running UNIX/Linux GUI programs. For some reason, it doesn’t come installed by default, but it’s on the Apple install/restore disk. Try something like “Optional Software” or something. This is necessary to use things like MATLAB or Fink. Install this before Fink.

The customizations I do:

Turn on two-finger scroll and two-finger click: This is the laptop equivalent of the scroll wheel and right click (e.g. Ctrl-click). Do this in the Keyboard & Mouse preferences panel.

Customize my Dock: I personally find the magnification pretty, but annoying. So I turn it off. I don’t like hiding it. Your mileage may vary. I also don’t like random links in my dock. In fact, I like it as small as possible.

Show all file extensions: This is in the Finder preferences, under the Advanced tab. Extensions show me what files are, even if the icons get screwed up sometimes.

Spring-Load Folders: OS X is great for drag-drop support, and part of that is via spring-loaded folders, which is that if you drag an item over a folder, it’ll pop open the window so you can drill down to where you want to drop the file. Enable it (if it isn’t on by default) in the General tab of the Finder preferences.

Make desktop icons huge: I drag-drop a lot of things, like images from web pages, links, files, text clips, and so on, so having huge icons on the desktop helps. Also, it encourages me not to leave too much clutter on my desktop. Thus, when I was on the desktop, with Finder as the active application (see the bolded menu item at the top left), I selected View > Show View Options, and set my icons to 88 x 88.

Turn of Caps-Lock: Does anyone actually use this key? I really get annoyed by accidentally hitting it, so I turn it off. Go to Keyboard & Mouse, click on the Keyboard Tab, click the “Modifier Keys…” button and change the mapping for Caps-Lock.

Turn off “illuminate keyboard in dim ambient light”: Yes, it looks cool, but I know my way around the keyboard, so I don’t need this feature; I’d rather have the extra battery life.

Turn Bluetooth off: I don’t use Bluetooth, so I’d rather save the battery life.

Set Expose corner mouse shortcuts: I mouse with my right hand, which means that when I’m dragging stuff, Expose keyboard shortcuts are a little inaccessible, so the mouse shortcuts help a lot, especially the Desktop shortcut.

One reason I stick to Macintosh is that I rarely have to lose hours of my time online trying to figure out how to get hardware to work. I plug in, try things by following intuition, and then it almost always works. I don’t know any other company that understands this.

Take Logitech. It’s a strong brand name in the keyboard/mouse peripherals market, and yet its software sucks. Completely. I bought a wireless keyboard and mouse to use with both my MacBook and my PowerBook, since my PowerBook’s monitor is broken, making it a de-facto desktop computer by being tethered to an external monitor. Logitech touts one of the features of this set as having an easy-to-reach USB wireless receiver, for plug-’n'-play usability. Unfortunately, when I unplug the wireless receiver from one computer and plug it in again (either to the other computer or the same computer) Logitech’s software fails to recognize their own products. Thus, all the extra buttons on the keyboard don’t do anything, and ocassionally, the keyboard reverts to the “Windows” layout, where the Option and Command keys switch places.

I haven’t found a fix, other than uninstalling and reinstalling Logitech’s software each time I unplug and plug in the wireless receiver. This is not progress.

I wish more companies did their engineering like Apple, because although Steve Jobs’ minions aren’t perfect, they pay attention to details to make things work as seamlessly as possible. Most companies do not. Logitech, your brand represents shoddy design.

Since one of my friends sent me an email about this Nature newsletter, I thought I’d get my opinion out about Open Access Publishing.

Firstly, I like the idea of it. Part of the optimism of science is about the free flow of information, for the betterment of all. Open access publishing, in a sense, utilizes the great infrastructure of the internet to provide a free peer-reviewed (i.e. non Wikipedia-style) repository of the latest and greatest research coming from academic labs. Since much of the research is funded by the government and taxpayer-money, it would be nice (though not a moral obligation) to open the publishing to the public. Open access also allows for more collaboration, a wider dispersal of knowledge, and a lower barrier of entry for smaller research units (like private researchers, small colleges, and other individuals). In all sorts of ways, open access publishing might be a good thing.

I wouldn’t, however, want to require that all published materials funded by the government get opened to the public. Just because something is paid for by taxpayers doesn’t mean that it has to be opened to be public. The point of spending taxpayer money is to fund things that would have a benefit to the public, something that under normal market situations wouldn’t occur. Thus, things like building highways, the police and fire-department, funding hospitals, funding innovation via patents, and funding basic-science research via grants. None of these have any guarantees that the public can use them directly, since all that is a moral necessity is that the public somehow benefits from their continued funding and existence. Thus, toll highways allow for better trade and transportation, even though some people might not be able to afford to use them. The public, by default, can’t just use patented products, even though they (technically) pay for it by giving the owners monopolies.

In addition, the main point I want to talk about is that I don’t know how sustainable Open Access Publishing is. Publishers have continuing costs every year, from server costs to print costs, and not all of that can adequately be covered by the publishing fees that are charged to every author. These one-time fees eventually run out for each article, so the best way to cover their costs would probably be through advertisements, but online advertising is a tricky and fickle business, and I don’t know how I’d feel about the possibility of a journal going belly-up based on the rapidly fluctuating online market. This isn’t a precise analysis of any finances, and this is all pure speculation, but it’s just something I’m worried about (since I do happen to like the model very much). I’d like it to succeed, but we’ll have to wait and see if they stick around after 10 to 20 years.

What I don’t like, however, is that the old model of publishing is attacking the new, as described in the Nature article. I really dislike the ACS, as their journal qualities are declining as of late, with too much bloat and not enough content, and this is just the final straw. I would never subscribe to an ACS journal, as they just aren’t very interesting. I don’t like Elsevier, either, because their websites suck, they facilitate arms trading, and now they’re involved in this mud-slinging.

The two models should compete on the open playing field. If Open Access is unsustainable, it’ll collapse, eventually, and go back to the traditional publishing method. If the Open Access umbrella succeeds, then too bad, publishers, go on to your next job. I don’t have any pity for those who can’t learn new skills or transition; that’s why you get paid less, because you’re less valuable to others. If you’re losing subscribers because of Open Access, then give people more value for their subscriptions. Bundle online access, utilize your huge archives. Maybe make your journals that much better edited, or more carefully selected. Write more interesting highlight articles. Solicit more review articles. If you’re losing money to the free, what it means is that your journal isn’t worth anything more than free, and that means you’re doing a terrible job.