Manage references from the comfort of your browser with Paperpile

Screen Shot 2014-02-16 at 8.18.46 PMPaperpile is a web-based reference manager that works with Chrome and Google Apps to help you find, organize, read, and write papers online. Another reference manager you might say? Well, yes. But for having tried it myself, I must say Paperpile is a solid contender. Let’s have a closer look.

Paperpile comes in the form of a Chrome App. This means that it is dependent on Google’s Chrome browser to function. It also heavily relies on Google Apps such as Google Docs and Google Drive. But as you will see below, this dependence is also its strength (if you can resolve to adopt Google’s services).

Start a collection of references – Like other reference managers, you start your collection by importing references from other reference managers, by uploading your pdf collection (that will be analyzed and added to the collection) or by browsing the web for papers. Paperpile is particularly well integrated in a number of scholar search engines such as Pubmed and Google Scholar. With one click, references can be added to your collection and the pdf downloaded. For those of you with limited access to pay-for-access journals, a neat function allows you to search for the pdf of the paper through Google search. An increasing number of pdfs are indeed available through repositories or personal websites. Newly added papers are automatically tagged as new, which makes it easy to come back to them after a long literature search.

Paperpile integration in Google scholar. Notice the Paperpile button on the right of the reference

Paperpile integration in Google scholar. Notice the Paperpile button on the right of the reference

Store your papers – Paperpile uses Google Drive to store all your pdfs, which makes them available to you wherever you are, including on mobile devices.  You won’t have to worry about running out of storage space with the 15Gb (30Gb on Google Apps for education) of free space Google Drive provides. Paperpile automatically renames uploaded or downloaded pdfs and organizes them in folders on the Drive. My paper collection was a bit messy but Paperpile helped put some order into it. It recognized a large majority of the pdfs I had, standardized the file names and arranged them in folders (thanks Paperpile :-D!).

pdfs can be accessed on mobile devices through Google Drive.

pdfs can be accessed on mobile devices through Google Drive.

Use your references – Once you are ready to write, you can use Paperpile with Google Docs to search your paper collection, include citations and generate a bibliography. Google Docs has a lot going for it: it has many of the basic functionalities other word processors have, is constantly evolving and is a great solution for collaborative writing. Google Docs can also be accessed and edited offline (but Paperpile will not work without internet connection). Still, at the end of the day, many prefer working with Word, and biology journals typically only accept Word papers. On this, Gregory Jordan, co-founder of Paperpile, said that integration into other word processors such as Word or Latex authoring tools is next on their to-do list. So wait and see!

Add references to you Google Doc manuscript.

Add references to you Google Doc manuscript.

Navigation in Paperpile – Navigation within paperpile is pleasant and the search function is very responsive. Articles can be given multiple labels that help organize papers by research field or project. Preset filters allow easy access to papers, book chapters or review articles of your collection. A ton of other small functionalities give Paperpile an overall mature and user-friendly feel.

You can give it a try for free for 30 days, then you are charged $2.99/month to use it. Paperpile is an initiative from a couple of researchers, Stefan Washietl, Gregory Jordan and Andreas Gruber that saw there was space to create a web-based reference manager that rivals the best desktop versions. And it seems they are very close to prove us right.

Labfolder released mobile app

labfolder_logo_02_no_tagline_2083x500Labfolder is a cloud based digital lab notebook where users can write, draw and put together reports of their latest experiments (see blog post). They recently announced the released a mobile version of the service..

Users can now directly access their data on the go. They can also record their experiment in the lab using their mobile device, annotate them and store them in the cloud. The app is available for Android and AppStore.

Zappylab launches Protocols

Screen Shot 2014-02-18 at 11.14.43 PMA centralized location where all protocols could be described in detail and shared with the world. That is what Protocols from Zappylab (also creators of the PubChase literature search tool) is set to be. This could be an solution that researchers have been waiting for when faced with the often incomplete or incorrect protocols published in our favorite journals.

The website has gone live a few days ago, offering a simple interface to enter protocols. But Protocols is in Betra and more is to come. The launch is accompanied by a Kickstrater campaign to help get it started. Have a look!

Journal Guide helps you find, compare and rate journals

Screen Shot 2014-02-03 at 1.03.11 PMSo, after years at the bench, months fighting with your co-authors about the wording of the second phrase of the 5th paragraph, you are ready to publish! The question is, where should we publish the paper? With over 25,000 journals to choose from, the possibilities are plentiful and can be overwhelming. And for your paper to have impact, you must find your audience and thus find the journal that your audience reads…

Journal Guide is a platform that helps authors navigate through this profusion of scientific journals. It asks for your paper’s title and abstract, then extracts the important keyword and identifies a series of journals that seem to be a good fit.

Screen Shot 2014-02-03 at 12.59.32 PM

Example of search result in Journal Guide

The results are displayed in a table (see image above) with the search score, journal name, publisher and impact factor. For each journal, Journal Guide also identifies published articles that are related to your title and abstract. If others in your field have chosen a particular journal, you might want to consider it as well. Once you have chosen a couple of journals that seem appropriate, Journal Guide offers a tool to compare their characteristics side by side (see screen capture below).

Screen Shot 2014-02-03 at 1.00.12 PM

Comparison of three different journals

At any time during your search, clicking on the name of the journal will display another layer of information. There, one can learn about the journal’s aims and scope, costs and open access policies. But even more interesting is the ability of users to provide anonymous feedbacks about their personal experience with the journal. Information such as the speed of publication can be particularly useful.

Another online service provided by Edanz also helps authors decide on a journal by analyzing title and abstract. Journal Guide pushes the concept further by offering user accounts, side by side journal comparisons and journal rating. Although still in new and in beta version, Journal Guide has the potential to help create a more healthy competition between journals by making it easier to compare them and can already help young researchers better promote their research by choosing the right journal.

Out of curiosity, I have tested a few of my publications. Entering the title and abstract and looking down the list to see how the journal that I have selected are ranked by Journal Guide.  Some of my articles came up with the journal I published in as first choice. Others did not even show the journal they are published in. Perhaps this is a sign that the choice of journal can be quite irrational some times. Journal Guide could help us make more objective decision.

Journal Guide is a division of Research Square, a for profit organization also creators of AJE and Rubriq.