Reference Workflow

22 01 2023

This past May I graduated with my PhD. I initially typed that sentence as “I finished…”. But, truly, like a wedding is the formal start of a marriage, the conferment of the PhD degree is just the formal start of a writing career. In the months since I walked across the stage I’ve been trekking through the bog of drafts, revised drafts, and revisions of revised drafts in the pursuit of the research Holy Grail… the peer reviewed paper in an impactful journal.

For me, the most challenging aspect of completing my dissertation, and revising it into publications, has been keeping track of my source material. Over the past five years I’ve tried, discarded, and modified countless ways of tracking the dozens then hundreds, maybe thousands, of references that inform my writing. It turns out, the reading is the easy part. Finding that idea kernel a month later in mounds of paper can take a frustrating amount of time. Enough time that a tracking system became essential. I needed a system that was flexible yet powerful – that would get me to the key ideas easily. I tried color coding, accordion folders, foot high paper piles… until I burned through reams of paper and boxes of laser toner. But, as the piles grew, and the more I organized, the harder it became to find the ideas I was seeking.

I like reading on paper. I like highlighting. I like making notes in the margin. I adore index cards. But, I was drowning in paper. I had to change.

I’ve long read novels on a Kindle. However, I resisted electronic reading for “serious” work. I couldn’t see how it would work for me. But, I had an iPad mini. And, I saw how my students were using the app GoodNotes for annotating class materials. So, I gave it a try. What a game changer!! Going electronic meant giving up my trusty paper, but pdf scans still look like paper. I thought it would mean giving up my fun highlighters and pens. No – Good Notes has fun highlighters and pens.

Okay, so I was making good progress plugging along with my electronic reading – but as I mentioned above, the reading is the easy part. I still had to figure out how to index the key insights for easy retrieval. I had to let go of my trusty index cards, and move to trust a citation manager. I tried a few and found Zotero had the most reliable sync. It allows notes and tags – but they do require some maintenance to be maximally useful. Initially my Zotero was kind of a mess. The resources were entered by the system through a Google Chrome extension button, but I didn’t maintain it beyond that. It was useful for making reference lists, absolutely, but it didn’t help me track my ideas.

My organizational break through came through an ordinary tool that turned out to have extraordinary usefulness – Google Drive. When I realized that Good Notes and Google Drive can talk, I had found the workflow key. I could let go of trying to keep all the reference plates spinning in my head, and trust the system. And, it also gave me a way to pair my reading habit with my Zotero organization, building a stronger system.

The system:

Workflow diagram
  • First, I download the article. I typically search through Google Scholar, because it’s linked to my school library account. EBSCO and other search engines are also options, depending on what paywalls I need to go through.
    • I name files of downloaded articles very specifically so I can quickly identify duplicates: topic, last name of first author, year of publication, title
  • Next, I load the pdf into Google Drive.
  • When I sit down to read, I pull articles from Google Drive into my iPad GoodNotes app.
  • As I read in GoodNotes, I highlight and annotate the articles electronically – directly on the pdf pages.
    • I also highlight any supporting references cited by the authors that may provide further insight
  • I then upload the annotated pdf back into Google Drive.
  • Next, I use folders to keep order in my Google Drive.
    • I upload each article into the topic folder it matches. I’ve found it’s best to do this soon after reading, or I get bogged down
    • Within the topic folder I have three subfolders.
    • 1. One for the unannotated original article copy
    • 2. One for the annotated copies of articles I’ve read but won’t be citing in my manuscript
    • 3. One for the annotated copies that I am likely to cite in the manuscript
  • For the articles I plan to use, I add their citation into Zotero
    • In Zotero you can go wild with folders and tags, but that’s a topic for another day
    • I add my notes from my reading into the notes tab in Zotero – this is key because it makes them searchable (side note of a benefit to GoodNotes – handwritten annotations in GoodNotes are searchable within that app).
  • Finally, I go through the references of the article and search, typically in Google Scholar, for any I want to read. I download them or request them through Interlibrary Loan right then, before I forget
    • Those pdf downloads then get loaded into Google Drive, and await the process starting again

A workable workflow combines flexibility with enough ease of use that I’ll stick with it. My goal is to read one article a day, at least five days a week. I’ve stuck with this now since October. Searching my notes in Zotero allows me to identify insights quickly, making my writing time much more streamlined.

What works for me is not going to seamlessly work for others. But, I share this to provide insight into elements of a system that may also help others tame their piles of paper.


Fifteen apps for productive online teaching and learning #onlineed #OER

17 10 2015

Photo Oct 09, 7 26 05 PMLast week, I wrote in support of mobile devices in the classroom.  This week, I’ll explore some apps I use in my own teaching and learning process.  As I redesign my curriculum to emphasize depth of knowledge and decrease reliance on commercial textbooks, I rely heavily on apps that sync across all popular platforms.  Throughout the day, I move continuously between my PC, phone, iPad, and Mac so any app I use must either sync reliably across those devices or must offer cloud access.

Productivity and Organization:

  1. OneNote: My blog posts are composed in OneNote. The unit outlines for my writing projects, including my OER textbooks, are in OneNote. My grading rubrics and keys are in OneNote.  My semester grading checklist, curriculum revision lists, and committee meeting notes are all there.  My academic department started using it this year as a collaboration space.  I was a late comer to the OneNote party – I’ve been using it less than a year – but within a few days of starting it took over as my primary ongoing work tool.
  1. Wunderlist: To-do apps are my weakness – I have no idea how many I have tried – dozens for sure. When I got my first iPod touch back in the day, I tried app after app – eventually landing on Wunderlist.  Whereas I use OneNote for ongoing and long-form projects, Wunderlist is my daily task app.  With repeatable tasks, Wunderlist is what I use to remind me that my textbook order is due each October and that I need to email my students next Thursday to encourage them to start their project.  My grocery list, travel packing list, and Kindle pre-order release date favorite author list are all in Wunderlist.  The benefit to Wunderlist over OneNote is timeliness.  Wunderlist pops the task out to me, OneNote makes me remember to go to the task.  In theory, you can set due dates and reminders for OneNote, but my version doesn’t have the “Task” tab in the menu bar and I haven’t been able to figure out how to add it.
  1. Dropbox: When I was in grad school, in the 90’s, I saved my research data Excel files to floppy disks and snail mailed a backup to my mom.  I also gave a backup to a neighbor.  Later, when I needed to move files between my home and work computers, I used thumb drives.  Now, I use Dropbox – files, pictures, screen shots all go to Dropbox.  My camera roll uploads automatically from my phone to Dropbox. It’s is accessible from all of my devices – including my phone – so sending a file or example photo to a student is easy, even away from my desk.
  1. Sunrise Calendar: Like to-do lists, I’ve lost track of how many calendar apps I have tried. Sunrise is the first one I have found that fully and reliably integrates my work calendar, personal calendars, and Wunderlist tasks in one place.  Sunrise is available as a Chrome extension and as a mobile app.
  1. Pocket: I have a love/hate relationship with bookmark apps/sites. I use Pocket as my “read later” repository.  Unfortunately, it seems I rarely have time to actually “read later” so it’s become a sort of link graveyard.  But, I still send links to it regularly, most frequently from Twitter.  Pocket allows tagging and sorting, but I don’t use it to store active resources.  Items I have actually read and want to save for later are stored in Diigo.  Links I use daily are stored on my homepage.
  1. Relax: My kids are in their 20’s and are at that in-between almost-launched stage. Since I work from home, a good pair of headphones and a relaxing noise reduction program is essential to my ability to focus productively.  On my phone and iPad I use the Relax app.  On my PC, I use YouTube playlists of either focus music or nature sounds.

Content Creation: 

  1. Paper by 53: I write OER textbooks and develop OER activities. Engaging content requires illustrations.  Although open photo resources are available through Creative Commons licensing, I’ve found that I enjoy drawing my own diagrams and cartoon pictures.  I am no great artist, but I’ve been scratching out teaching images since back in the days of chalk on the green board.  One of my fondest memories is of my first whiteboard and the amazing four colors of Expo markers with which I could suddenly draw.  As a science teacher, diagrams and images have always been the bulk of my lectures. The Paper app provides an easy way to include my sketches in my OER content.  Creating the illustrations saves me the time consuming step of explaining what I want to an illustrator, paying said illustrator, and/or spending hours searching through open source images for what I need.
  1. MindMeister: When I outline content, I use OneNote. When I move the outline to text, I use Scrivener.  But, before I get to the outline or writing stage I first need to brainstorm idea links and relationships.  I’ve found that brainstorming is most effective when I use a free-flowing mind map.  MindMeister is a bare bones mind mapping tool that is accessible from both a browser and an app.  Accessibility is key for mind mapping because I often let content simmer and play with organization and content relationships for days, or weeks, (or months) before I head to the outline stage of development.
  1. Vittle: I just discovered Vittle and haven’t used it for any large projects yet – but I intend to. I played around a bit with the free version and then almost immediately purchased the full version.  Vittle is an iPad screen casting app that does, for less than $10, what I used to use Camtasia to do.  Vittle has a whiteboard pad that records audio and video explanations.  As I move my content from long 20-minute ten-year-old videos into short 1-2 minute focused segments, Vittle will be my go-to whiteboard “lecture tidbit” app.
  1. WordPress: I started my blog over five years ago, but it lay dormant for most of that time. Recently, I’ve begun to write about my teaching process and the tools I use for that process.  I also have used my blog to write out longer-form answers for questions I’m frequently asked by students.  Having a blog post, with step by step pictures available allows me to point students to help without needing to repeatedly explain the same thing in multiple emails.
  1. YouTube: I’ve been teaching online for over 15 years. In the early days, it wasn’t possible to share video content because most students (and teachers) were on dial-up internet modems. In 2007 I started sharing my first video lecture content – as Camtasia uploads into my LMS shells.  By 2012, any new video content I created was going into YouTube instead of into the LMS.  Students can access YouTube independently of the LMS, giving them more mobility and freedom to learn in a time and place that is most convenient for them.  My end of term evaluations always  have requests for more videos and YouTube is where most of those videos land.  Moving forward, I’m using Articulate Storyline and Office Mix to integrate short videos with other content (particularly with self-assessment quizzing) but YouTube will continue to be my go-to for longer form materials.

Inspiration and Information:

  1. Feedly: I’ve always been an RSS fan and the discontinuation of Google Reader years ago left me in a bind. I tried a couple of different replacement readers and Feely is the one that stuck.  I’m not a fan of content aggregators like Flipboard – I always feel like I’m missing something when I allow a service to curate content for me.  I prefer to curate my own sources and a RSS reader allows that.  However, I have recently become a fan of the Skimm and NextDraft newsletters so my Feedly reading had dropped off a bit as a result.
  1. Tweetbot: I created my Twitter account over five years ago, and then promptly ignored it. Recently, at a conference, I learned about Twitter backchannels and I discovered a world of content and interaction that brought together like minds from around the world in collaboration.  I’ve had to back off of Twitter a bit recently because it was sucking me in for hours at a time, but I still find ideas and inspiration every time I check it.  For me, the key to using Twitter is to actively curate my lists.  If someone I follow tweets repeatedly off topic, or their main posts are those status things about how many followers they added that week – they’re gone.  I curate my lists heavily in favor of those who share relevant, timely, content.


  1. America’s Navy Anatomy Study Guide: My focus is OER content and this Anatomy guide is the best free mobile app version I’ve found. It has multiple modes, including a quizzing mode, that allows students to drill the bones and muscles any time they have a few minutes to spare.  The key to retention is repetition and ongoing drill is beneficial.
  1. PubMed: Writing OER content requires constant fact-checking. PubMed is the go-to for up to date basic medical science research.  While most articles referenced are behind pay walls (grr…), the abstracts are generally sufficient for a quick fact check.  For deeper research, I’ll then go through Google Scholar to see if the relevant article .pdf has been posted online anywhere.

As an online teacher, I spend hours each day using technology as an interface to interact with my students as they learn.  Since online learning is most frequently asynchronous, I am always excited about tools that improve the learning experience for students when I’m not immediately available for contact.  I’m also always on the look out for OER resources and the tools to help me create them. It’s a happy day when I find an online tool that helps me and my students travel our education journey more effectively together.

Apps I use everyday…

3 01 2010

Apps I use everyday:

Organizer iPod app

Over the past 6 months I’ve road tested over a dozen to-do and calendar apps.  The one I use every day now is called “Organizer”.  This app is useful because it allows me to sync my calendar and to-do list together.  All of my lesson plans and appointments are entered into iCal on my school Mac and then I sync that with Google calendar, which automatically syncs with Organizer.  That lets me enter things in only one place (in iCal) and have them show up wherever I need to access them.  This app also lets me post pictures on the calendar pages.  This is very useful for remembering the events of the day and for organizing what I’m wearing (since the last thing I want to do when getting ready for school is to figure out what to wear – I plan that ahead of time using the TouchCloset app).  I check the Organizer app many times each day and it has earned it’s spot on the top row of my iPod home page.

Info:  Website:                        Cost:  Lite version is free; Full version is $5.99

Awesome Note App

Since I have so many projects in the works at one time, it’s crucial for me to have a flexible note keeping app to get it all organized.  I use the Awesome Note app daily for that purpose.  Within the app I have various folders.  One of the most useful folders has the contact info for the parents of each of my students.  Having email addresses close at hand is very convenient when I have a question or concern about a student.  It also allows me to track when I’ve sent notes and emails home.  Another folder in the app allows me to track what books I’ve read.  And, I have other folders for other home and school information.

Info:  Website:                 Cost:  Lite version for free; Full version $3.99

Disclaimer:  I always advise getting the Lite (free) version of any app!  I never download the full version until I know it’s something I’m going to use so much that I need the extra features.  Lite versions are definitely the way to go for apps!

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