Research tips
Every researcher collects large numbers of papers, references, and notes, and it is important to have a good system to keep them all organized. For many years I had several thousand papers all numbered and stored in filing cabinets, with a JabRef database providing an index to them.
These days, it’s much easier to have everything stored electronically, and so I have accumulated many pdfs (about 1300 so far) of published articles. But the problem of being able to find something fast is still important.
Mendeley is a free software tool for managing your reference database. It actually solves many problems simultaneously and is likely to become an important part of how I work.
Managing pdfs
A key component of Mendeley is the desktop software, available for Windows, Mac OS X and Linux. Install it and it will automatically collate, organize and manage your pdfs. Just dump all the pdfs of published articles and working papers into a single directory and tell Mendeley where it is located. Then it will automatically extract authors, titles, publication details, and set up your database. Immediately you will be able to search for papers by author, journal, title, etc. I’ve delayed moving to Mendley for a year or so until this feature was working properly, but it looks like it now extracts the information with only occasional errors.
One of the nicest parts of the desktop software is you can read the pdfs within Mendeley (you don’t need to fire up Adobe Reader), and it allows annotations, highlights, notes, etc. So instead of scrawling all over a paper version, you can add your notes directly to the pdf from within Mendeley. Searching within Mendeley also searches within the pdfs, so even if the words you are looking for are not in the title, you can still find the paper.
Managing citations
Mendeley also takes care of bibliography generation. If you use LaTeX, you can have Mendeley automatically maintain a BibTeX file which can then be called from with LaTeX. So as long as the details are correct on Mendeley, they will be correct in your bibliography. (I am yet to actually use this feature, but in theory it should work seamlessly.)
If you’re still stuck with the awful MS-Word, Mendeley will allow referencing there too, via a Word plug-in. So throw away End-note, this is so much better.
Web-based references
Another feature of Mendeley is that it has a web interface which is synced with your desktop database. So you can access your references on any computer connected to the internet. You can also sync all those pdfs online, but if you need more than 500Mb, you have to pay for an account. Personally, I use Dropbox which backs everything up for me, so I’m not paying to do it again. The only disadvantage of using Dropbox is that I can’t access my pdfs from within Mendeley’s web interface.
My two computers each run Mendeley and are kept in sync automatically via the online database. However, I don’t think my annotations are synced because I am not backing up the pdfs via Mendeley.
If you’re are browsing a website such as ScienceDirect, JStor or Google Scholar, and find a reference you want to add to your database, there is a neat bookmarklet which automates the process.
Sharing references
It is possible to set up collaborative groups to share papers. I’m yet to try this, but it could be useful for my own research team. It is also possible to network with other researchers, although it is not yet clear to me what the point of this is.
There’s a lot more to learn about Mendeley, but I’m excited about what I’ve seen so far. I’ve imported my BibTeX file into Mendeley, and all my pdfs. My Mendeley database now contains about 5500 papers, books and other references.
©
Every researcher collects large numbers of papers, references, and notes, and it is important to have a good system to keep them all organized. For many years I had several thousand papers all numbered and stored in filing cabinets, with a JabRef database providing an index to them.
These days, it’s much easier to have everything stored electronically, and so I have accumulated many pdfs (about 1300 so far) of published articles. But the problem of being able to find something fast is still important.
Mendeley is a free software tool for managing your reference database. It actually solves many problems simultaneously and is likely to become an important part of how I work.
Managing pdfs
A key component of Mendeley is the desktop software, available for Windows, Mac OS X and Linux. Install it and it will automatically collate, organize and manage your pdfs. Just dump all the pdfs of published articles and working papers into a single directory and tell Mendeley where it is located. Then it will automatically extract authors, titles, publication details, and set up your database. Immediately you will be able to search for papers by author, journal, title, etc. I’ve delayed moving to Mendley for a year or so until this feature was working properly, but it looks like it now extracts the information with only occasional errors.
One of the nicest parts of the desktop software is you can read the pdfs within Mendeley (you don’t need to fire up Adobe Reader), and it allows annotations, highlights, notes, etc. So instead of scrawling all over a paper version, you can add your notes directly to the pdf from within Mendeley. Searching within Mendeley also searches within the pdfs, so even if the words you are looking for are not in the title, you can still find the paper.
Managing citations
Mendeley also takes care of bibliography generation. If you use LaTeX, you can have Mendeley automatically maintain a BibTeX file which can then be called from with LaTeX. So as long as the details are correct on Mendeley, they will be correct in your bibliography. (I am yet to actually use this feature, but in theory it should work seamlessly.)
If you’re still stuck with the awful MS-Word, Mendeley will allow referencing there too, via a Word plug-in. So throw away End-note, this is so much better.
Web-based references
Another feature of Mendeley is that it has a web interface which is synced with your desktop database. So you can access your references on any computer connected to the internet. You can also sync all those pdfs online, but if you need more than 500Mb, you have to pay for an account. Personally, I use Dropbox which backs everything up for me, so I’m not paying to do it again. The only disadvantage of using Dropbox is that I can’t access my pdfs from within Mendeley’s web interface.
My two computers each run Mendeley and are kept in sync automatically via the online database. However, I don’t think my annotations are synced because I am not backing up the pdfs via Mendeley.
If you’re are browsing a website such as ScienceDirect, JStor or Google Scholar, and find a reference you want to add to your database, there is a neat bookmarklet which automates the process.
Sharing references
It is possible to set up collaborative groups to share papers. I’m yet to try this, but it could be useful for my own research team. It is also possible to network with other researchers, although it is not yet clear to me what the point of this is.
There’s a lot more to learn about Mendeley, but I’m excited about what I’ve seen so far. I’ve imported my BibTeX file into Mendeley, and all my pdfs. My Mendeley database now contains about 5500 papers, books and other references.
©
