Mendeley!

Heh, i've been posting quite some bit recently, many of them with more photos than words. Well, I'm certainly glad that i managed to keep with my 'at least one post a week' promise… though it doesn’t exactly help with my writing skills since i've not been doing much of a proper writing recently. One thing for sure, is that MarsEdit really helps a lot in encouraging me to post. I can see at a glance which blog i've been neglecting etc… being able to see when my previous posts was motivates me to post things. And i don't have to go through the trouble of opening up my different blogsites. And ah, the ease of posting photos…. its much easier to post just a short entry with some text and loads of pictures. In a way its cheating, since it defeats the purpose of me wanting to practice my writing and typing skills… but it's not always that i have the time and mood to type long entires… nor the material/topic to talk about… so i guess all's good.

FYP is getting pretty hectic. We are, indeed running rather behind time… however, since i've decided to take time off to blog, (spent quite some time on blog entires in my other blog already)… I might as well spend some time to talk about this wonderful program i've found…

So, some time back, i was thinking to myself that i HAVE to start organizing and filing my small but steadily increasing collection of research papers before things get way too messy. The big problem with research papers for me is that, organizing them is such an awful chore… worst still, i don't even know how to organize them. 1st: the naming problem. When you fetch the pdf from the database, they either call the pdf by 1) some weird jumble of letters and numbers 2) some generic thing like 'science' or 'fulltext' 3) sometimes if they are nice, they'll call it something relevant, like the author or something… Most of the time though, i have to rename the file, and it always leaves up struggling to find a way to name my files WHILE allowing me to know what the article is about. Some ppl go by the arthur names and year, but that really doesn’t help me understand what the article is about… since I'm not familiar with the researchers in the field and all… Paper title? Most of the time the titles are very lengthy…!

After wasting loads of time searching and trying various apps (i was even seriously contemplating using iTunes to organize my files!), I finally found Mendeley. Actually, quite a lot of reviews have mentioned it, but i was reluctant to take it up at the beginning because it can sync the documents online… which ironically is a feature i found very useful later on.

Mendeley is an app like no other… None of the other programs i saw or tried even comes close… There's endnote, there's many other pdf file managers, there's Papers - this expensive 80 dollar app that sounds really great in functionality… but ah, the price tag...

What can Mendeley do and just why do i like it so much? Let me try and explain one by one.

First of all, its FREE. Yes… FREE! Well the free account includes 1GB of online storage, 500mb for your personal use and 500mb for sharing (more on that later). Well its not a lot, but than research papers usually don't take up THAT much space per paper… and if you have too many papers, that means u just can't sync them all online, you can still use it normally on your desktop, no problem. You can also pay for more storage space of course.

2) It runs on mac. And windows. And iPhone/iPad. Cool! That means that you can sync your collection of papers over your various computers, and i can even read the papers on my phone if i want to. Doesn’t let you do much else on the mobile apps but… i don't really need to do much else.

3) It manages the pdfs really really well. There's a lot of factors that make me feel that way… like:

Watch Folder - You can select folders that you want Mendeley to watch. That means that any pdfs you dump into that folder will be automatically added into Mendeley. Convenient much? Now i can simply save the pdf in my folder labelled 'papers' (oh how informative) and be done with it.

It scans the pdf for data - Mendeley doesn’t just rely on the pdf's metadata, it also SCANS the pdf file and will try to pick up details such as the DOI, title etc etc… It will also automatically check out their own database as well as google scholar to try and find any missing details… if in doubt, the program will ask you to check the data - you may have to put in the title manually (well, just copy and paste from the pdf) and ask it to do a web search… well if all else fails… there's always the manual input option.

It is a pdf reader on its own - Now that all your pdfs are nicely organized, you know which file is which… its time to do the actually reading. Wonderful news: Mendeley has a built in pdf reader, and lets you do things like annotations, highlighting, writing notes etc… and with the tabbed browsing, i find it much neater than preview. I also don't have to switch between finder and preview to call up another pdf file - i get it all done in one app.

Folders, smart folders - The usual folders allows you to group your papers. There's also a favorite button for marking really good/useful papers.

4) It can also manage citations and bibliographies. It can plug in to msoft word, open office etc… even has a nifty little shortcut key for adding citations etc in MS word. Neat.

 

I've tried endnote too, even attended a short course on it… but it was precisely during the course that made me aware of Mendeley's advantage over Endnote. (The librarian did mention mendeley at the start too, makes me wonder why they don't offer courses on how to use mendeley instead… but than again, mendeley is really easy to use… wait, endnote is really easy to use too, i didn’t quite need that course actually :S)

While endnote works really great as a citation tool, it fails so much in terms of pdf handling capabilities when compared to mendeley.

Endnote cannot scan the pdf. So if the metadata of the pdf fails, the whole pdf entry fails and you have to manually edit it. Sure, endnote is able to search many online databases, but it cannot merge entries. So i'll still have to manually key in the data for the pdf file, or i have to manually attach my pdf file to the online entry. Either way, its troublesome.

Mendeley is working to have more sites include a button to import the citation directly to the program, and they also have a little bookmark that lets you do that… but for me, I'd want to read the paper rather than site directly… i want a copy of the paper… so i pretty much add my mendeley entries only using pdfs. Same goes to endnote… only that mass importing of all my pdfs doesn’t work very well since quite a number of the files don't have proper metadata. It doesn’t have a watch feature either so i'd have to manually add in the pdf files… and if the pdf doesn’t have metadata, I'd still have to copy the title over and do a web search. So it quickly became such that i had to search the web database every time i want to cite the new article i just read (while simply writing down and organizing my background information in MS word)… which is quite a chore.

Endnote doesn’t have a built in pdf browser. AND because of its limitations in handling pdf file based citation entry additions, I'd rather use the web search to get my citations quicker. That means that it's not managing my pdf files at all (even having to file the right pdf file to attach to the right citation entry would in itself, be a challenge!).

So while endnote is a good citation tool… I'm simply going to stick with mendeley for my citation needs. It seems to do the job just as well anyway, and coupled with the easy library management, i'd say that it does it even better.

Things like scanning of pdfs is something that all other free/cheap pdf managers does not have. Oh yes, the scanning of the pdfs means that you can search within pdfs. Like you recall something that you read somewhere and want to call out the pdf, but that something you remember isn't in the title or even the abstract… mendeley's search function will be able to find it for you.

 

Overall, the program looks really neat, and has all the features i need. Oh there's even addition features that i don't need at the moment, like groups and file sharing. Its like a social network on its own, allowing you to create groups and share papers with other researchers. It'll be useful if say your research group are all using mendeley for example. But right now its just me by my lonesome self so yeah...

If you're looking for something to organize your papers, I'd say Mendeley is your one and only choice.