Tag: bibtex

Reviewing Paperpile 0.5 beta

paperpile logo

Paperpile is a nice software which hit the 0.5 beta version some days ago. It’s been a while that I’m using it and being in the full swing of writing my Thesis, I tend to use it on daily basis, so I decided to review it a bit.

First of all Paperpile is a reference manager, which help to manage, organize, cite and share the collection of scientific papers that you have on your computer. If you do science you know exactly what I’m talking about. If you don’t, imagine you have at least 200 different articles lying on your hard drive, which analyse different but related subjects. When writing a new research article, it’s necessary to cite all the relevant previous work to put you new work in contest. It’s the incremental delta of new information which science uses to evolve (when there is not a quantum leap).

Retrieving, organizing and citing those piece of work is necessary and can be a daunting task, but a good reference manager can help to make your life easier. There are several softwares out there, and I had different experiences, however it seems Paperpile is overcoming anything else and I’m using it productively, making me even to read more papers!

So let’s jump into it.

Paperpile general

General view of Paperpile

This is the general window of paperpile. On the Top left you can see the label la gmail. More than one label can be added to a paper and different background/foreground colour can be used to personalize it. To add an existing label to a paper just pick and drag it over it. Super easy.

On the Mid right you can add the RSS from journals, which can help you to be updated with the latest articles published. I used to have this RSS in my google reader, however having it directly in paperpile makes super easy to import new papers and collect the pdf.

Bottom right there is a collection of different tool, from being able to search Pubmed to import a directory full of PDF.

Central window is where the meat is. All the paper, ordered by addiction Date (you can change to what you prefer) and the most important feature: the search box. Paperpile implements a search as you type system, so as soon you start to type it it start to search in author title and also abstract.

One very interesting bit is that the search box actually find the article I’m usually looking for, and it’s pretty precise. It really saves me a lot of time. This is a clear edge over Mendeley for example, where the search was a disaster. At least in the version I’ve used so far.

The central window also give you the possibility to add notes to a paper.

On top left there are very useful actions which paperpile can perform for you. Paperpile makes easy to retrieve the article on to the publisher site, either giving you a link to visit the webpage or can automatically fetch the paper for you. Sweet!

Another very useful features, which I used so far at least 3 times, is the automatically generated email, which fire up an already ready to send email to your colleagues with the citation reference.

One last thing that I would like to put under the light is the LaTeX integration. With an easy Ctrl-K the label will be copied in your clipboard ready to be pasted in your LaTeX file. If you need the more standard citation, Ctrl-C will do.

To set up the automatically synch for your bibtex database just click on All Papers, on the top-left and turn it on, choosing the location for the file. After that every new paper you’ll add to your collection is automatically exported in BibTeX and you don’t have to care about it at all 🙂

Paperpile BiBTeX setting

Go and Check it out.

Bibtex, some tips

I’m writing a report and I had to cite an article from a book. It’s one of this book which every article can also be used as a standalone paper. The problem is that if you use an article record, you will miss the book and if you use the book record, you will miss the article.

How to solve it? Google it! (somebody has already solved it and post it somewhere)

And it is. The solution is to use @incollection:

author = {John Doe},
title = {Dynamic Ambient Paradigms},
booktitle = {Paradigm Gems 2},
pages = {223--233},
publisher = {Addison Wesley},
year = 2005,
editor = {Averell Doe}

More BiBTeX tips (where I found this solution) on this page.

SincUThink — Interview with the developer

SyncUThink unofficial logo

So SyncUThink is a tool to synchronize all the papers that you have on CiteUlike with the one that you have on your computer.

The developer is one of my friend and I manage to get an interview for this blog. So enjoy.

Mattions: Hi Greg, Why you don’t introduce yourself to our readers?
Greg: Hi, my name is Greg Jordan, and I’m a new Ph.D. student at the European Bioinformatics Institute in Hinxton, Cambridge. I’ll be working in the area of biological sequence analysis, though I’ve just started, so who knows where I’ll end up.

Mattions: So, why did you start to write SyncUThink?
Greg: I’ve always been a bit frustrated by the process of finding, organizing, and exporting citations when writing papers while at University. So when a friend recently showed me CiteULike, I sure liked!

But I also like to save paper and read things on my computer. So, this tool simply automates what I got tired of doing: finding PDFs for articles stored in my CiteULike library. I’m also a bit of a nut for user interfaces, so I used this program as a test to see how quickly I could “whip something together” as a Java applet.

Mattions: That’s pretty clever and useful to keep everything on sync. So how long did it take to get out the v 0.1?
Greg: I started on Monday afternoon, and by Wednesday I had something working fairly well.

Mattions: Wow, that’s really fast :). Do you want to develop it further?
Greg: Not really. I created the program because I wanted something to automate a very specific and simple task that found myself doing lots of recently (finding and downloading PDFs for reading journal articles), and if I spend too much time trying to satisfy everybody’s very last suggestion or wish for the program, it will nullify the time I tried to save by writing the thing in the first place!

However, I would love to see someone take the original code and develop it further, perhaps making it compatible with a more open reference manager platform such as Connotea.

Mattions: Do you choose any type of license or are you not interested on it?
Greg: Yes, I’m licensing it under the GNU GPLv2.

Mattions: Is the code available or do you think to make it available some day?
Greg: I find Google Code really easy to work with, so it’s available at http://syncuthink.googlecode.com/ .

Mattions: Ok, Greg thanks for the interview and for your time.
Greg: No problem, thanks for the chance to chat about the program. Hopefully some people will find it useful!