Academic​ workflow with Things and Vitamin R​

12_05_18 at 12.52.44PM.pngThere is no shortage of Promodoro or todo apps in the Mac world. There are countless, systems, tools and the like. Very few of them are actually truly functional for an academic scholar. The nature of academic work is different from other tasks because it requires consistent reading and writing. We spent most of our time reading and writing; thinking about our research projects.

I have tried many promodoro apps for the last couple of years,  to manage my research projects and improve my working habits, for a better efficiency. None of them stick with me except Vitamin R.  The reason why I like Vitamin R is that it is specially designed to manage time (promodoro) as well as reflect on the task themselves. Vitamin R has these neat features called Scratchpads, Now and Then sections that help you write your thoughts (reflections) on the tasks. It is really very useful feature. If I get interrupted by a neighbor or get an urgent phone call while I am working; or get tired or have a headache, they are immediately documented in the Scratchpad.

Very few other apps offer features that help me to reflect on what I am working on. You can write a few comments on the todo entries themselves, in other apps such as Things and Omnifocus; but they really don’t have a place for extensive and deep reflection on your actual working process.

  • Did I accomplish the task?
  • Was I sharp in doing the task?(not all accomplishments are the same; just checking off the task is really meaningless).
  • Was there a distraction or disturbance? if so, how can I avoid it in the future?
  • So far as I can tell, only Vitamin R a system to reflect on how the task went.

The way the whole system is built on Vitamin R is different. In comparison to Vitamin R, I find other todo applications very shallow because they really don’t have a system on how I accomplish the tasks; and any means of recording relevant lessons learned in the process.

Assume I am planning to write a research article on topic X. That is my objective. The next step is to select materials that I need to read for the project. After collecting some reading material, I will skim through them, and choose the most important papers. Then, I need to do a deep reading to have an important understanding of the topic. Then, often I write short summaries of the articles. These summaries go to my concept mapping application (Tinderbox or Scapple) to compare the core ideas of the articles. Finally, I will bring my own data and construct a new analysis from the concept map.

Each step is connected. The whole process will probably take me months. What I need is not just a todo app that just lists todo tasks of the day; rather, enables me to construct the whole system into it. I also need to break down each of these tasks (reading article Y, for example) into smaller chunks to make them management.

Here is what the general plan looks like in Things:

12_05_18 at 12.25.38PM.png

Once you have this scheme, this is the time to get into action. My process is controlled with Vitamin R. Vitamin R shines because it helps me to chunk my tasks into time intervals.

I drag each of the tasks from Things to Vitamin R. Thankfully, these two apps work together beautifully. Dragged tasks are liked to their origins. You can also write additional notes in the objective part of Vitamin R if you have comments to add. Then, set your time and let it go. The timer kicks in, I am doing my work.

12_05_18 at 12.26.14PM.pngWhen the timer fishes, I will stop the task. That is the best part of Vitamin R. I take a couple of minutes to reflect. It is the best tool I find to reflect on how the task is going on. Sometimes I am sharp at my reading; sometimes I get distracted. If I am feeling focused today, I will elevate my game. I will write short notes on how things are going, and increase the workload and time interval as a response. If I am feeling distracted, I will write (still in Vitamin R) why I am feeling so. Most importantly, I will plan ways of avoiding the problem for the future. For me, the problem is often related to my sleep. I will plan to go to bed in different time, or earlier. That way, I use Vitamin R to manage my tasks, as well as my health conditions at the same time.


Bookends vs Zotero vs Mendeley vs Jabref

I have been very dismissive of Mendeley for many years now. For one good reason: the data is always extracted from Google Scholar. I get the worst, most incomplete reference from Mendeley.  Being an early adopter (staring from its beta stage; around 2008), I was left with frustrations with Mendeley. Now, it is time to appreciate one great quality of Mendeley that no other reference manager can emulate: its attempt to do the undo-able. That is, Mendeley tries to get the reference information by reading the PDF file directly. This technology is unique to Mendeley, so far as I can tell. While both Bookends and Zotero can extract some identifiers like DOI and ISBN, they never try to get the Title, the author and the date by directly reading the PDF file.  Mendeley does that. As a result, it is a life saver when you have a lot of junk to clean up.

I recently downloaded more than 3400 pdf files from a linguistic archive. Importing them to any of the references gives not a single relevant reference data–both Zotero and Bookends gave me zero result. I also tried Papers3. Quite interestingly, Papers was able to pick some of them. But, the data it gets was less than 20% success rate.

Then, I dragged them to Mendeley, majority of them get their references filled. Most of them get junk reference, of course, as usual. But, hey, this is technology. We have to do a lot of trial and error. Cleaning the junk library was much better than inserting references, one by one, for 3400 item. For that, I am now grateful of Mendeley.

But, ultimately I cannot live with Mendeley because it gets data from Google Scholar only–always junk data. That is why I have to move back these partially filled references to either Bookends or Zotero.

Completing the incomplete references in Zotero is a nightmare, I learned by the hard way. Zotero excels at getting data from browser (internet) and the attach the PDF over the reference. Having PDFs with incomplete reference or no DOI, however,  Zotero is a huge pain.  I  am a PDF guy. I rarely pick the reference from the web page. I always go to the pdf; and  attempt to fill up the reference when I have some extra time latter. For that, Bookends is much better. BE has a feature called Autocomplete (similar to the Targeted Browsing feature in Sente) which helps me highlight the Title of the book (article) from the pdf and tell it to search it somewhere in the web engines (google scholar, World Cat, or my local library website). That way, I don’t have to write the reference manually.

For Zotero, if you have missed to get the data from the website first, or that the PDF contains no DOI, the only option you have is to manually write the reference. Jabref is even better on that because you can copy and paste references from Google scholar to the existing PDF.

But, I find Zotero  better than Bookends on these two aspects.

  1. Direct syncing of the Bibtex file: using the Better BibTex plugin
  2. Automatically  getting the ISBN of the books. Zotero picks the ISBN of the books almost always correctly. This feature is coming to Bookends as well. But, BE is not really effective at yet.


How about Jabre?

It excels at manipulating references in the bibtex format. Furthermore, it as one unique feature that no other reference manager yet implemented–embedding the XML metadata into the pdf files. There are two good reasons to write metadata into the PDF files.

  • it improves searching: you can search Spotlight by the author or the Title of the book; or order the books by their date of publication. This is specially very useful if you use more advanced searching tools like FoxTrot, or (DTsearch in the windows)
  • you can lose the reference, or share the pdf without losing the reference data about it. If your library is lost or  corrupted, you don’t have to fill the reference data again. You can just drag the pdf and Jabref will populate the reference data for you.

The conclusion is: every reference manager has its own strengths and weakness. Each of them have their own niche users; and niche features. Bookends and Jabref are my all time favorite reference managers. I think I will keep all the 3 reference managers me for now. Some people own three cars, just for sheer fun of it, even if one car is usually enough. I don’t have to chose among these great softwares. I will use Zotero for the books, Bookends for everything else and Jabref for bibtex.

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