Annotatr

A new take on commenting papers.

citeulike+disqus mashup. Find abstracts and comment on them.

I can’t see it going very far right now, but it’s a good start. It’s scanning the citeulike database to get the abstracts and is using the Disqus commenting engine. I am not sure how a decentralized system like this could be convenient for the users. The main problem I see with it is having the comments separated from the paper. They also need to reach a critical mass of users to make it worthwhile. What I would like to see is using Disqus (or something equivalent) directly with the publishers, or with the major databases (Scopus, Mendeley, etc…).

iPad for academics, a personal feedback

I got one almost as soon as it was out. I knew this was the device I have looked for, for a long time and for several reasons. I spend a good chunk of my day reading, and you’re more comfortable reading on the sofa that in your office chair. I haven’t had the slightest regret since I purchased it. It changed a lot of my workflow, for the better. I went a long way toward a paperless office and workflow.

A few quick thoughts on the device. The form factor is excellent. Smaller would be uncomfortable, in particular for reading papers. A larger screen would make reading papers more comfortable, obviously. The weight is ok. The Apple case is poor, but you need a case. Battery life is amazing, I can use it a couple of days in a row without recharging it. I went for the 16Gb Wifi (there is always wifi at hotels and conferences), since I am only storing papers and misc docs on the iPad. Almost no music or pictures, so 16Gb are more than enough (my whole papers library is around 1Gb). Reading in daylight is ok, contrary to what others said, just increase the brightness of the screen.

Here is a rundown of the apps I am using regularly so far, or that I tried. A fairly exhaustive list of app for scientist can be found here.

Reading

  • Reeder, the most beautiful and most convenient RSS reader, as far as I can tell. It syncs with Google Reader perfectly. $4,99
  • Instapaper. For curated reading. I sometime even send full papers there. The comfort of reading is amazing. I never read long text on websites anymore. $4,99
  • Kindle and IBooks. For books. Not for PDF (for me), see below. Free.
  • Pulse. Excellent for browsing a bunch of website for which I did not subscribe to the RSS feed. Free.
  • Safari. I spend at least half of my iPad usage time in Safari. Browsing the web with swiped and pinches is just incredible awesome and comfortable. You are living in the future.

Papers and PDF reading

  • Papers, of course. I am using the desktop version too. The iPad version is good for reading, in particular since annotation tools were introduced. I haven’t printed a paper for the past six months, I think. Not good convenient for bibliographic searches on the fly, though. $14,99
  • Mendeley. I am using Mendeley more and more, in particular since I have to use a PC. I don’t use too much the iPad app, though. I prefer Papers. Free.

Notes taking

  • Simplenote. Almost perfect, really, in particular since tags were added. Perfect for taking notes during meetings, conference, or ideas on the fly. Free.
  • Dropbox. Of course. How could you live without Dropbox, today ? Free of course. Not using it yet ? Do me a favor and use this link to register, and both of us will get an extra 250Mb for free.

Publishers and journals

  • PLoS reader. Pretty good. Not many of papers of interest for me inPLoS, though. Free.
  • ACS Mobile. Not very good actually. Nothing more than an  RSS feed of the various ACS journals. Avoid it if you are using RSS already. $4,99, which is a shame considering it’s nothing more than a toc feed.
  • Nature. Quite good, I like it so far. Free … except for the actual content, of course !
  • PubMed Tap. Quite good, but I don’t get many papers from PubMed. Free for the lite version.

The platform is still young, and I miss a couple of apps, such as Scopus (a dedicated iPad app). The iPhone app is ok, though I does not sync to the Scopus profile, too bad. I am using it through the website, which is very usable on the iPad. I’d love to see a Sketchup app, too.

A couple of apps I am not using, related to writing. This includes Papers, for instance. I don’t have a bluetooth keyboard, since I want to travel light. And extensive writing (hours long) without a keyboard is not comfortable. There are a couple of editors with or without syntax highlighting, such as Textastic, or TexTouch (with remote compiling), which would be useful when I’m writing TeX docs.

What I like above all ? Not having to carry my portable transportable laptop anymore. I only take my iPad when I’m traveling for a couple of days or go to conferences. Incredibly comfortable.

Reading levels in Google search

Fascinating new option from Google for the search results. You can filter the search results by reading levels. They did this by analysing pages from Google Scholar and similar pages and comparing the statistical output to the other sites in Google’s index. Access this in Advanced Search>Reading Levels. A very helpful addition for academic research, help you filter a lot of the crap when doing some basic search on a new topic.

You can also get some funny information’s by limiting the search to specific site. A few examples below.

 

[Source: Official Google Blog]

RSS, (the most important tool) for academics

If you know what RSS means, you probably don’t need to read the rest of this post. If you don’t, well, keep reading, as this is probably the biggest time saver of my day-to-day work. If you’re like me, I mean, doing any kind of research, and trying to keep up with the papers in your field, you probably spend a certain amount of time looking for papers from various journals. And there is also a fairly high probability that  you are reading papers from several journals. So how can you deal with that more efficiently ? There are a couple of ways to keep updated on new papers:

  • have a student doing the work for you (lucky you).
  • go to the library and check out the hardcopy. Less and less likely as most of the subscriptions are now electronic.
  • subscribe to the table of contents email alert for each journal.
  • check out the journal’s website whenever you want to look for recently published papers. If you are reading anywhere from 10 to 30 journals, this can take a considerable amount of time.
  • use a dedicated mobile app on your phone or IPad, like this one or that one.
  • use RSS to be up to date with no effort, which I am going to explain right now.

So what does RSS stand for ? Really Simple Syndication. In a nutshell, you can see it as a tool for keeping you informed when the content of a website is modified. Like, let’s say, when a new paper is published in a journal… The basic idea is that pretty much each journal is now offering an RSS feed for its publications. If you are collecting all these feeds in one single place, you don’t have to check out every website everyday looking for what’s new, every single new paper notification will be delivered to you. All you have to do is:

  • subscribe to a RSS service, the inbox for your feeds. There are plenty of them out there. Alternatively, you can use dedicated softwares or even use your email client. My favorite one is Google Reader, by far the most convenient, but your mileage may vary.
  • check out the website of your journal, and look for the RSS feed. It’s usually a small orange icon, like the one of the bottom right here. Like here:
  • click on the feed icon to add it to your RSS client, or copy/paste the feed address in your RSS client.
  • that’s it ! Now when you fire up you RSS client, you will see a list of all your subscriptions, and every time that a new paper is published, it will show up automatically in your feed. I have something like 25 or 30 feeds, and all I have to do is to spend 5-10 min every morning looking for papers of interest for me. Whenever you click on a paper, you’ll be redirected to the journal website where you can grab a pdf for instance.

In pretty much any RSS client, you can “star” an item which you are interested in. When I’m checking the new items every other day, I usually scan rapidly through the list of new papers, star the one which sound interesting from their title, and then review all the starred papers when I am done.

Overall, RSS are probably the biggest time saver for me, and a terrific way of keeping updated with new papers as they are published. RSS is everything but dead for academics. There are plenty of other tricks with RSS for academics, but I’ll save that for another day.