I’ve been meaning to write about my academic work flow for a long time as it’s something that I’ve been trying to figure out. After talking with Susan and then looking at Graham Webster’s academic workflow, I offer you my process on how to deal with pdfs, citations, and academic books.

A big part of my process now involves the ipad! I got it for the same exact reasons as Lokman Tsui -it was really so that I could deal with the massive amounts of pdfs and books that I am unable to carry and don’t want to lug around This has been a life changer. No more printing of pdfs. No more carrying around books. No more shipping books back and forth between both coasts. No more hoping that there is enough ink in the printer.

If you didn’t already know - I’m a fan of Mendeley and I’ve written ad naseum about it - I’ve been trying to get all my colleagues in the research world to switch over. It’s not perfect, but it’s been the best thing out there that I could find for academic citation. It is totally behind on ipad and iphone apps dev - but I assume that the people up in London have out-sourced this to a good company and will be delivering an app soon? Mendeley’s current ipad and iphone is only useful to look up citations and notes; you can’t make changes to it or view papers attached to it.

So there are two different routes that I can take depending on the source of my material. I deal with either 1.) ACADEMIC PDFS from journals - which means that it already includes meta-data OR 2.) DOWNLOADED BOOKS from Amazon Kindle or downloading book sites. Below I explain what I do when I encounter these files.

When I find an ACADEMIC PDF to download from Google Scholar:
1.) starting on my laptop - I go to google scholar (represented by firefox icon) - I download the article into a downloads folder on my laptop
2.) and drag the file into Mendeley Desktop on my laptop. I explain here how to set up your Mendeley under Update June 2, 2010 so that your file is automatically renamed and copied into a folder for all your PDFs
3.) delete the file from my downloads folder (delete it because if you’ve followed up the directions from the link above Mendeley will have already created a new file with new name)
4.) it will sync with dropbox (you need to have dropbox set up - this is super easy! just sign up for it and leave all your files in your dropbox from now on. If you are an Apple idisk user, leave your dropbox folder inside your idisk folder as a double back up.)
5.) turn on ipad with wifi connection 

5a. - open dropbox on ipad and open file in iAnnotate.  Let’s open Philip Agre’s Real Time Politics: The Internet and the Political Process PICTURE ONE BELOW

5b- or sync ipad with itunes on mac and then drag the file into iAnnotate

5c - sometimes I want to read the file asap on my iphone so then I will sync it to goodreader but I try not to do this because you can’t highlight in goodreader. If you don’t need to highlight or draw on your pdfs or books, then goodreader is the best app to use on your ipad or iphone!

6.) you will then see your marked up iAnnotate file  PICTURE TWO below

I will sync it to my iannotate folder that sites on dropbox or you can prepare it for an itunes upload next time you plug your ipad into your mac. Hit the arrow UP button below to upload for itunes. You can also email the document to yourself.

7.) I then email myself the entire summary of my highlights - PICTURE 4 below. iAnnotate is great because it gives you the text of your highlights organized by the color of your highlight. I then open my email and copy the notes into my Mendeley document under “notes” in the meta-data field.

On my ipad,  I’ve already synced up two folders  (ALL PDFS and Downloaded books)   with my goodreader  or iAnnotate (using Aji Reader Service). I explain here (under UPDATE June 2, 2010)  why I have one PDF folder (ALL PDFs). I haven’t finished syncing all of my files yet but I know of two alternatives that may be more practical for people dealing with smaller PDF libraries. 1.)  do this through iAnnotate’s dropbox sync service or 2.) drop files directly into goodreader  or iAnnotate in itunes when syncing your ipad.

I keep all my downloaded books inside my DOWNLOADED books folder and below I explain how I deal with books.

******PDF READER UPDATE NOV. 10, 2010****

I just found out about PDF EXPERT. It’s UI is awesome - innotate’s UI sucks. PDF Expert is wayyyy faster! HEre’s a great recap of why PDF Expert is lovely. The only caveat is that right now PDF Expert does not export highlighted text as text to email. This is a big downer! But once this happens I’m moving completely over to PDF Expert. Iannotate’s buggy app, slow render time,  and horrible UI is not tolerable for much longer.

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When I find a BOOK PDF to download
1.) I download the book (or buy it on amazon kindle if you can’t find it online - you can download kindle for your iphone or ipad)
2.) unzip the file
3.) go to Google Books or Amazon and import it into Mendeley using the Mendeley bookmarklet. I explain this bookmarkletting process in my Mendeley love post.

4.) then I move it to my “downloaded book” folder that sits on my dropbox. Then follow steps 5 and on from above.

5.) In my Mendeley I’ve created a folder called “DOWNLOADED BOOKS.” I put all books in that folder that I’ve downloaded. And then tag the mendeley documebted “downloaded.” This is important because if you need to see if you own a digital copy of the book already, you will know because it will be in the folder. As a backup if the folder gets erased, you also have the tag to identity which books you own.

6.) I I’ve started a new folder called “PAPER BOOKS” to indicate these are books that  own in real life in non-digital format. This way I Can keep track of all the books that I have. Again, tag the book “own” or something like that.

7.) DO NOT put the book pdf into your Mendeley! This will take up way to much online storage space, slow your sync time, and recreate the file in your pdf root folder! Mendeley only automatically renames academic PDFs. Mendeley is really useful for small pdfs < than 50 pages.

***BOOK UPDATE*** Sept 15, 2010 - I just discovered Calibrae, an online book management system that is similar to what Mendeley does for PDFs.  Calibrae works on all PCs and MACS! I will post in the next few days if I find it useful.

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***BOOK UPDATE*** Sept 20, 2010  - ok update on Calibrae

it’s not robust enough to use as your e-book management app. However, it is an amazing file converter. It may work for those who just have a few books, but I have around 2000 ebooks so calibrae is just too slow. 

Positives of Calibrae:

• it automatically renames files, sorts authors into folders
• allows you to designate where the main calibrae file folder sits  = put it in your dropbox!
• you can also edit a file and enter the ISBN or author name and tell it to fetch the meta-data from the Google Books database.
• convert books beautifully and quickly to epub or other formats in batch. You can batch convert! and batch output into a folder!

• you can outbook your books as a spreadsheet
• mac/pc compatible!
• recognizes your apple ipad! The best part is that you can chose “SEND TO DEVICE” and it will send it to your itunes automatically as an epub file! But you have to convert the pdf to your epub file first!\
• supports almost ALL book formats - accept .azw wifes!\

negatives:

• no cloud computing - there is no web interface
• most books are not formatted for correct meta-data fields - so you actually have to spend a lot of time looking up the details of the books
• the user-interface isn’t always that intuitive - but it could be way worse!
• doesn’t generate a works cited list
• doesnt’ interface with Mendeley or Good Reads
• it is way too flow - freezes a lot

So I’ve figured a new workflow for reading ebooks.

I’ve downloaded the free apple ibooks app. I like that I can visually see my books. So I still do everything that I wrote above. But if I know that I want to read it one day or soon, I will import it into Calibrae so that I can read it on ibooks. I just love the UI on the ibooks - more than goodreader! Then I make sure all the data is correct (fetch if you need to). Then convert your files into epub - you can also do a batch convert! And then sent them over in batch to itunes or ipad!

Tip: if you are an idisk user, keep your dropbox in your idisk so that you are backing up to two different places!

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Where I write:

There are 3 different ways I start off a document: google docs, scrivener, or evernote.

1a.) Many docs are started in google docs. This gives me a peace of mind that my document is being saved as I write. Word has crashed on me TOO MANY TIMES for me to do heavy writing in word. I wish that google docs was editable on the ipad - it’s not. This must change soon. You can create links within google docs and when you copy and paste it over to tumblr the links are recognized.

1b.) I am now a Srivener convert. I start large documents in Scrivener - documents that have chapters, multiple sections, or sections.

1c.) I am also an evernote convert. I tried this back in 2008 and gave up on it. But now in 2010 it is awesome!!! I have a running list of features that I would like to see and bugs, but it’s still very usable!

2.) then I move over to Microsoft Word when I’m in a state where I need to do formatting or to tumblr when I am ready to post my blog.

That’s it on the academic work flow stuff. What’s your workflow?

I’m kinda obessesed (no thanks to David Sasaski!)  with writing about my information work flow. So here’s a post on how I manage information overall and how I flash-blog.

***** UPDATE Nov. 11, 2010****

A new drawing that reflects my new workflow - incorporates Scrivener & Evernote. Also includes updates on my fave ipad apps - popplet, noteaker HD, sketchbook pro, and air brush. And I have a box of my must-have bookmarklets that make this entire cloud process seamless - mendeley, instapaper, amazon wishlist, notes in google, google reader subscribe, evernote clipper, facebook share, tumblr share

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