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As an experimental biochemist embedded in a largely computational research group I was lucky enough to be exposed to some clever software tools that simplify everyday tasks such as primer design, DNA sequencing, homology modelling, and viewing protein structures. However, I noticed my peers were still performing many tedious tasks by hand, or using some really terrible software. The best example of this was reference management, although there are programs to collate and present your references, some can be troublesome. However, there is a better way for writing your PhD thesis. Mendeley is a free reference management tool that integrates seamlessly with MS Word, and Open Office. The developers of Mendeley have an excellent website with easy to follow tutorials on the main features, see http://www.mendeley.com/videos-tutorials/, but nothing beats the experiences of someone who uses it on a daily basis.
Essentially, Mendeley is iTunes for your research papers. It allows for easy uploading, storage, and retrieval of your papers from multiple computers, in multiple formats. In addition, it automatically generates a copy of all your documents on a cloud, thanks to the free 500Mb of storage space they provide for every user. After using this software for over two years the main features I think people will be interested in are as follows:
Creating your library is straightforward. I found the best way was to simply select the Watch Folder option from the add files menu in the main toolbar, and browse to the folder which contains your documents of interest. They can be pdf or word documents. Mendeley will now proceed to add each document to the library, scanning each for useful details such the title, the authors, the journal it was published in. In addition, any documents subsequently added to the folder will now automatically be visible in Mendeley. The documents do not need to be labelled logically for Mendeley to populate the metadata for each article. This is akin to letting iTunes fetch the details of a particular track for you, so that you have the correct album art, singer, album name etc. However, Mendeley does not always get this right, so some manual manipulation many be required to clean up the data. I consider this a small price to pay considering the benefits granted by the rest of the functions. Once your documents are imported, I suggest using the synchronization functionality: this uploads everything to the cloud storage they provide, allowing you to access it from any computer with an internet connection.
Once you have imported your documents the first thing you'll notice is that double clicking on any one of the articles brings you to a full version of the document. This is fully searchable via the toolbar on the top right. It might not seem like a major feature, but when you're trying to remember where you came across the evidence for that statement in your thesis it's an extremely valuable and time saving feature. In addition, your whole library is searchable, so you can search for authors names, or journal name, or just individual terms you are interested in. It's happened to me before that I couldn't remember the author, but I could remember a particular term used with the article, a few keystrokes quickly narrows down the list of possible suspects. It's worth noting, the more effort you put into having the correct details for each article the better the results of any search will be. If you're slightly OCD like me, you'll actually get enjoyment out of making sure everything is correct and welcome the distraction from writing your thesis.
How much you use this feature depends on how collaborative your research group is, and how many other people you can convince to use Mendeley. Essentially it allows you to select any number of journal articles from your library and send them to any other Mendeley user that you have invited to join Mendeley. It's actually much quicker than email, and the document is automatically integrated to your existing library, including any notes, and annotation made by the previous owner. The recipient does not have to have a subscription to the online publisher of that article, so it's an excellent way to share papers among less privileged colleagues.
This is perhaps one of my favorite features. Frequently, I will be reading an article which cites some other articles I’d like to read. Tracking down references can be extremely time-consuming depending on the way the references are cited. However, by far the easiest way is to go to the URL of the article you are currently reading, and hope that there are hyperlinks to the articles referenced in that paper. This still means entering the details of the current paper in Google Scholar, or PubMed, and getting to the right location. Mendeley bypasses all of that by providing the URL of the source article you are reading. You simply click on the link and you are on the correct webpage for that article, from there you can go straight to the reference section of the look for hyperlinks. It's a very fast and effective way to navigate from source to source with no typing involved.
A relatively minor, but useful feature of Mendeley is that individual documents can be have sticky notes attached to them, essentially a collapsible text box which you can place anywhere. Generally useful for making quick notes of questions or thoughts as you read the paper. It's also possible to make more detailed notes in the toolbar on the right hand side, this is a better option in my opinion, since these notes are searchable, so you can actually pick out a paper based on the contents of the notes you made as you were reading it.