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.


Time-lining software to manage projects

I generally don’t like mind mapping softwares. I rarely have a pre-made, hierarchical data that I will list down into the nodes of a mind-maping software. My data is usually messy; unstructured. It is my job to collect and structure them.  The rigid structure that mind-mapping softwares imposes puts me off. It is ironic that they call them “mind mapping” tools as I find them the least mind-friendly of my tools.  My brain just doesn’t work with this kind of rigid structure. My brain works with connections, and fussy boundaries. That is reality of the human mind as we know it. 

I am a linguist. I know this as a matter of fact because I know the boundary between the word ‘like’ and ‘love’, ‘meet’ and ‘gather’ even between ‘map’ and ‘structure’ etc is as fuzzy as it gets. Fuzzy connections, or associations is how human brain works–not by rigid hierarchical structures.  

I have considered  mind-mapping  software as irrelevant to my work flow. I just gave up with them very early on. 

There is one exception thought. I tried them for managing projects. Very few of these applications have the capability  to manage projects. The first of these tools I have tried was Xmind. Xmind has Gantt chart. I like the gantt and many of the other views like the Matrix. 

But, it didn’t stick with me that much because the application is a bit cumbersome. It is very hard to pull an application everyday if it puts a bit of burden on my processor. 

I used Tinderbox a bit for this kind task. I used Tinderbox longer than Xmind for managing projects. I specially used it a lot for Agile system. 

Tinderbox also swamped me with large number of notes: as every pieces of task should be dropped with an individual note file. A simple task managing file immediately grew to hundreds of notes because every task requires its own individual note. 

I recently tried MindView. It is a lot better than Xmind because it supports both gantt charts as well as timeline. I specially like the Timeline. It also has dedicated project management system: like managing resources; tasks: etc. I found that Mindview is much more potent system for managing project than any other mind mapping application out there. 

The fact that I like the timeline a lot led me to further investigations to the applications that have this feature. In the process, I discovered Aeon Timeline. It is very neat application. Very fast and efficient. 

Timeline and Gantt are unified into a single system. Best of all, zooming into the details and out to the general overview has never been easier. This guy is the first software I so far discovered that successfully showed me the big picture of my project while still seeping into the details. 

In all other softwares, the choice is either or. You have to get to the details—losing the big picture; or lose the details and see the big picture. Tinderbox itself has this weakness. You have to either go to the top of the map; or zoom into one corner of the map. There is no both ways. In Aeon Timeline, flying from details to granular structures is just a matter of scrolling on your mouse; or simple punching on the touchpad. It is very beautiful. I love this easy way of zooming in and out of the details. 

Where Bookends sucks

I am now checking out other alternatives as the fate of Sente is looking dismal. The best alternative for the users of Sente looks like Bookends. I think there is some kind of communication between the developers of the two applications. One of the reasons that we suspected the abandonment of Sente came from the developments on the Bookends side. we have seen, the developers of Bookends have been preparing to grab the former users of Sente.In their latest updates, since June 2015, they have been modifying their application to import Sente references. But, still, there are a lot of glitches to move references from Sente.

But, personally, I am more worried about the capabilities of Bookends as a reference manager than the migration. The migration is a work of few days. But, if the application has some fundamental weakness, that will be a pain for a long time; that I am afraid the pain of migrating my references might not worth the effort.

First the strengths:

  1. Bookends seems faster than Sente; at least at the startup.
  2. It works well with a number of other applications such as Devonthink, Tinderbox and Scrivener.
  3. And, most importantly, it has some cool tools called **Global Change**  which seem very useful. These tools helps to make a change to a number of references in one sweep. Sente also has this system; implemented differently.I think the Bookends has an upper hand here. One of the worst footprints of Mendeley from the Windows that remained in my reference for ages was: the Titles of the references were placed in the place of the Journal. I don’t why Mendeley does that. But, the Titles were exported as Journal. I was not able to change that for a number of years within  Sente. Bookends does it in a sweep, just a couple of seconds to fix about 1500 references. Yes, that is great programming.


and the issues:

I think bookend is quite good reference manger. But, it has some really deep issues:

  1. The PDF reader is ugly; and not even comparable to the reader in SEnte. Sente gives the best PDF reading experience ever; not even the dedicated PDF readers like PDF Expert, iAnnotate, Acrobat Reader can reach it. Bookends has a mediocre PDF reader.
  2. Not well organized: the tools and features are jumbled here and there. It is really not clear which of the menus do what. At the first look, the app generally looks unattractive. But, honestly, I am less worried about that. I just think some people might not appreciate it. Personally, I just want my job done. I am not going to wear this app for  my birthday party.
  3. But, the real issue, and the true depth of shit of Bookends is on the reference detection and downloading part. The whole focus of the Bookends seems on the MedPub. Generally, most reference managers can detect references from the major databases (search engines) like PubMed and Google Scholar. But, Sente has been efficient in doing it from a broad array of sources: that I cannot list all here. The most important of them, for me have been: Worldcat and  Stanford University Library. Sente made the process perfect by its feature called Targeted Browsing. The two sources offer the cleanest references while Google Scholar gives out the most incomplete metadata. So, when I was trying Bookends, I was hoping that Bookends would do the same.

Assume that I received a PDF book from a friend. I want to download the metadata. In Sente, I would drop the PDF to the library, Sente displays its Citation Lookup  dialogue box in which I will select the Title of the book and choose WorldCat.


The top 5 sources are the most important. The title of the book, “Italian Syntax…” is going to be automatically pasted in the WordCat. Now, look at the WordCat website.  gku8e

That Red Circle makes the insertion of reference so elegant. Clicking the red button populates the reference information. Worldcat gives a complete reference data; i rarely find a mistake. Note that these 5 sources can be expanded, if required. I used to have a large number of other sources including Stanford University.

Bookends has a similar feature. But, the implementation is inefficient because it is restricted to a few If I want to do the same in Bookends, the process is clunky and inefficient. The sources are not expandable that, if they don’t work for you, you will be stuck. The fact that I cannot grab references from the WorldCat database is really disconcerting to me because that is the number one source for me. All the references for books come from it. It gives the most complete metadata.


First, Bookends asks you to attach the PDF. You will get the citation window after  the PDF is attached. That is way step away. After you attach the PDF you will have the following window:


This is where I am frustrated. The part I marked with the big red rectangle is supposed to display the Title of  the book. But, it doesn’t. Therefore, if you have to put the title, you are supposed to do it manually. You have remember the title, or copy it before hand. That is strangely sluggish. Second, the sources at the right lower corner  are really useless to me.

Except Google Scholar, the rest are useless, really. I cannot modify or add a new engine either. So, I am stuck. The offer is Take it or leave it. You will be happy if you are a medicine student; fucked otherwise. Google Scholar is quite ok for articles. But, it is one of the most incomplete sources.

Bookends has another method of downloading references using an internal browser. But, I think that one is even worse. I put the title of an article; out of the total of 20 articles in google scholar, which Sente detected all of them, Bookends was able to detect just two.

All in all, I think Bookends is not really polished at downloading metadata.

The difference between Sente and Bookends might seem minimal here, from outside. But, for some one who will use the process thousands of times, even the tinies further step is one more pain. While I like many of the features of the application, I find it hard to adopt the app as my main reference manager  because of  this problem. So, I am contemplating either to stay with Sente to the last breath of the app, or check out other alternatives, Papers 3 probably.


2017-02-05: update

  • Now, Bookends has included further sources of data extraction. Now, I am now using Bookends as my main reference manager. Even if it has some weaknesses on the reading side, it turn out to be one of the most complete reference manager out there. I have noted my observations here.

Blog at

Up ↑