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.

MaxQDA vs AtlasTi

I was fascinated by these two applications, in addition to NVIVO.

I spend a couple of days learning about each of the software: trying with sample projects, watching tutorials etc. I tried all of them on the Macbook.

NVIVO is  useless on the mac

NVIVO is generally the slowest of all the three; and has the least features. It is clunky. The Pdf reader is mediocre: not that functional. The pdf reader lacks navigation features such as the bookmark and outline. Therefore, the easiest of the decision  was to dismiss NVIVO. Indeed, if not for the dysfunctional pdf reader, I won’t have to pay for QDA software as my university already offers NVIVO for free. But, man, NVIVO on the mac is a  joke.

MaxQDA for coding

The real comparison turns out to be between AtlasTi and MaxQDA. These two QDA applications are truly amazing. Maxqda is much faster when importing documents. I was impressed how fast it imports the documents in comparison to NVIVo specifically. Dragging a bunch of text files, NVIVO took more than 30 minutes; Atlas imported them in about 12 minutes: Max did it in just over 1 minute. It was a wow moment.  In addition, unlike the other two, Max can import RTFD files. MaxQDA is also extremely polished and clean. Even if there is a huge mess of menus and functions, I love the whole interface of Maxqda. It looks like a Windows application on the mac, in contrast to Atlas which is a truly Mac app. But, to be honest, I was totally in love with the interface of the Maxqda. I also like that it has many features. If one counts the number of features embedded into MaxQDA, they could be twice more than that of the AtlasTi.

But, as I dig deeper, I find some disconcerting worries. As it turns out, the application (the code) is brilliantly done. But, the software has some design directions that made it not so convenient for my use.  The whole focus of Maxqda is the code (=tags): not on texts and concepts. That might be fine for some people whose intention is an extensive coding of text.

Reading and annotating a document are second citizens with MaxQDA. There is no advanced document manager unlike in Atlas. As I understand the MAXQDA, the whole system is tuned to people attempt to put their materials into a structured spreadsheet-like system after coding (tagging) every bit of it. The application is tuned to manipulate the codes; not that much of the original texts. Almost every feature of the application is about the code.

My intention is mostly to use these applications to read PDF files, understand the concepts, reflect on them,  and develop them in new directions. I want to use them as a hub to knowledge management, not merely coding specific parts.

Coding is not the main focus of my workflow. Reading, understanding, and reflecting are my focuses. For these, the quotation-commenting system presented in AtlasTI is much more practical.

AtlasTi for gaining & breading ideas

Look at what this person says in this video, the value of quotation and reflection on a certain document.

AtlasTi  is designed to engage the user with the concepts in the text–for a deeper understating of your material. You can completely gate away with the whole notion of codes and live with Quotations, Comments, Titles of the Quotation and Networks. IN Atlas, you just have enough of the tools to understand complex network of ideas and arguments. AtlasTi can be used as a fully dedicated information manager as well as reading software. The closest I have seen similar to AtlasTI, is  a reference manager software in Windows known as Qiqqa. Sente in the mac was also close to doing the same. In Sente, we could quote, comment and Title the quotes. We, however, were not able to tag them. Sente was almost there.

I love the idea of reflecting on what I am reading. I often come up with a completely new idea that could potentially grow to completely new work by reading, commenting on and extending from the works of others. AtlasTI is a perfect tool for that. The pdf reader is fluid and brilliant. You can organize documents and group them. There is a lot of processes you can do about the documents themselves. Even if you don’t want to code them, you can still use Atlas for retrieving information: learn about your documents, writing summaries; comparing the main concepts of each of the documents (by reading the abstracts of article documents, for example).

Max has 4 types of memos; Atlas has just one. The memos in Max are intended to do different tasks.  They might even be conceived to do the tasks of the Quotations in Atlas.

So, one might ask, why not using Memos of Max to understand the concepts: just like the Quotations and comments are used in AtlasTi. I have understood that a whole bunch of Memos are designed in Max just to do that. Well, the problem with the memo in Max is not well integrated with the document. It is like a sticky note on the side of a pdf file. They cannot be presented in the map. They are just like the stickies in the PDF files: attached but forgotten.

But, the comments in Atlas are like much like the comment sections in Sente or Qiqqa. AS you click on the highlight, you will have it displayed,  you can also read the comments (reflection) in a column alongside the quote.

Be aware that Max also has this term “Quote”: but, it is a different thing. They use it as “quote matrix” which is another spreadsheet to compare different values of the codes. It has nothing to do with the actual quotation of documents/texts.

So, MaxQda or AtlasTi?

My conclusion is that Max is inclined to be a gimmick: focused on turning your documents into discrete spreadsheet-like data. Atlas is much better to dig deeper into intricate logical argumentation and conceptual twists. The link feature in Atlas gives you a glimpse of how the comments, quotations, notes (memos) and documents are related. It can also output analysis, spreadsheet just like Max. but, that doesn’t really interest me.

Atlas also has its own issues, however. Unlike the two other, direct editing of the document is not supported. Plus, exporting documents seems much convoluted and difficult process.

But, the most devastating problem for Atlas is the license. The licensing in AtlasTi is completely evil. It is very expensive. And, it works only for 2 years (student license), and you cannot use the old software again. It is like the online subscription system. Once you are done with your subscription time, you are locked out.

Update: Thanks for Susanne Friese, I am now told that AtlasTi can export the data even after the license has expired. That is good news.

How to convert scanned images to perfect ebooks

ScanTailor is better than  Acrobat and Abby Fine Reader

One  major challenge to convert phsyical books to ebooks is the cleaning up of the black marks on margines  left from the scanning process.

There are many tools out there that can help to reduce the problem. But, almost all of them have a problem of removing the shades or black marks fully.  That is where ScanTailor, a free software for mac and windows,  excels.

ScanTailoer is the most valuable pieces of software to turn junked, dirty scanned pages into  neat, readable pdf files. Even the most expensive software such as Acrobat Adobe and Abby Fine reader cannot compare with it. It has some magic to clean out all the marks, shades and black marks on the margins of the pages.

Once you process the images in ScanTailor, and OCR them with Adobe or Abby, you get an industry standard pdf files. If you have an old book that you want to convert it to ebook format and sell it, this is the right step to follow.

Scan it with any scanner to image files such as Tiff or PNG–>clean it up in ScanTailor –>OCR it with Acrobat or Abby. Abby can also export it to Epub and Mobi if you prefer these format.

At end of the process, you will  have a neat ebook that you can even sell it online.



If you have a DJVU  file you want to convert it searchable pdf file, for the macc, you need Cisdem Document Reader to extract all the pages to images (PNG or TIFF) so that StainTailor can import them. I used to follow a convoluted process of exporting them to pdf then converting them to image because my djvu reader (DjVuLibre) cannot extract all the pages to (PNG or TIFF) image.

This is one of the lessons I learned in the process of experimenting with different tools.


How to install ScanTailor

It is hard to find the mac version of ScanTailor. I have spent many hours trying to compile from the source code, and downloading from Homebrew. The Homebrew is failing to download some dependencies in the latest version of Mac OS.  If you are having issues to compile from the source code or install from Hebrew,  the best option you have is to to download the Universal version (thankfully the authors have compiled for us. This version seems to  lack some features in comparison to the Advanced version. But it works fine for the main functions I described here).

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. 

Extract Bibtex references from table of contents

I have been trying  different tools to extract bibliography references from table of contents of a pdf book.

Assume you have the pdf format of an edited book which contains 20 articles in it. If you want to have the reference data for all of the entries, you have to go to google scholar and extract the reference data for each of them. The process is hectic. Furthermore, google scholar usually offers incomplete data. You need to go and edit each of these references. it is a lot of work.

Won’t it be easier if you can just pick the reference data directly from the table of contents of the given pdf book?

Yes, in principle.

But, in practice, you need to understand a lot of programming and under-the-hood understanding of PDF files. I have none of it. Therefore, I came up with a simpler, but, equally plausible solution= using Keyboard Maestro and Jabref.

The process is a bit complex. But, the output is much better and faster than Google shcolar or any of the reference extraction methods.

  1. Fill up the reference data of the main book in Jabref (from Worldcat)
  2. Copy the bibtex of the edited book to a specific clipboard inside Keyboard maestro. (if you are importing my macro, simply hit CTRL+C; that will copy the bibtex and make some calculations to get the publication year)
  3. Copy the Title, Author and page number of each of the articles of the pdf book. Each of the references must be copied in that order.
  4. hit a shortcut (CMD+ALT+9) that calls a window of Keyboard maestro asking me for the number of copied references. I count the number of references I copied and answer the question. I typically copy 8 references at a time.
  5. click OK. KM magically turns the clipboard to references; calculates the page numbers for each entry, and crossrefs them with the mother book.

I magically get a perfectly formatted reference from the copied clipboards. Once you get how it works, it is very powerful script.

Keyboard maestro script

You can ask if you are interested in the script.

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.

Mirroring ‘Oxford Scholarship Online’ on your mac using Bookends


Oxford publications started up a sort of revolution on how printed books are accessed online.

Most other publishers put the exact same book, in a single PDF or Epub format, online for sale. Oxford makes an important change that seems to start a revolution on how we consume books online. In Oxford’s system, each of the chapters of the books stand by themselves as published articles. Each of the chapters of the collection gets their own DOI that they can be read, downloaded or referred independently of the main book.

Look at this video how it works.

Now, we are in a position to have the cake and eat it at the same time. The old conflicts on whether to keep books broke into their chapters and sections (as such a system facilitates searching and discovery on each of the chapters), or, keep it together to be able to see the work as a whole immediately disappears. We have both the whole and the individuals at the same time.

So, I have been wondering on how to mirror that system in Bookends. I experimented on how each of these independent chapters could be managed. Bookends has a mechanism to manage Chapters separately; while still linked to the main book.  Bookends is such a well-thought application: each of the chapters are able to live by themselves just exactly like they are presented in Oxford Scholarship Online. I am so impressed. I haven’t seen any other offline reference manager that is able to manage chapters like Bookends (Oxford).

The more I use each of the features, the more appreciate how well-designed Bookends is.

For me, I used to split PDF books into specific page ranges (page 1-50; 51-100 etc) just to keep the large pdf books easier for my searching tools like Foxtrot. I have already explained the system before.

Now, with Oxford Scholarship online and Bookends, I don’t need to split. I simply download each of the chapters and attach them as chapters into a single reference entry in Bookends. The pdf files of each of the chapters are attached to their corresponding entries. It is much better system because I won’t have duplication of information. I only hope that all other publishers offer books in the same way to the Oxford Scholarship online.


Jotting applications in the Mac

Jotting applications are my class of note writing apps which specifically focus on fast jotting of notes as  ideas strike my mind. They don’t have to be complete. They are measured by how they are efficient to feed to a full blown writing applications; and how they are easy to insert the notes. Here, I have the comparison of my favorite apps I tried recently.

Criteria Curiota NoteAway Tab Notes Unclutter NvALT TaskCard Devonthink sorter
Transparent file storage in Finder (library in Documents folder) x x
Supports RTF and RTFD it is a sort of rtfd; but it is ntRTFD extension x x x
Permits direct assignment of Finder tags x x x x
Transparent file naming (the title of the note is the file name) adds further junk x x x
menu bar icon for quick jotting
Quick note inserting shortcut


Curiota and Devonthink Sorter come at the top. If Curiota permits direct assignment of tags, it would be the perfect jotting app.

I would like to hear if there is an app that satisifies all the tests.


Switching from Day One to MacJournal

Day One has been a great application for writing daily journals. Now, they are moving to a subscription system. I don’t like a subscription-based software. One reason for this is I want to spend some months completely offline. In addition, thinking about some payment every month makes me feel miserable.

So, I am now trying to move to the old MacJournal for my journaling needs. I haven’t found any other better application than this app. Many of the note-writing applications do not encryption.

So, to export my journals, Day One can export to a handful of formats: html, plain text and json. The json keeps the most complete information. MacJournal doesn’t accept the sjon. I found a transitional application that natively imports the json=Bear.

I use bear as means to transit to Macjournal.

Day One—> export in Json format—> import the json to Bear—>expor it in RTF format—> import the rtf to JacJournal.

There are still two losses in this process:

The tags: the tags are transferred as in text tags: not true finder tags. As such, Macjournal cannot recognize them as tags

The images are lost; because RTF cannot keep the images

For the images, if you have many of them, a better strategy would be to have the pro version of Bear and export in Word format. MacJournal can import the word. But, for the tag, still, the word format is not a solution. We need some mechanism of converting the in text tags (marked as #tag) to finder tags so that MacJournal or any other appliation for that matter would recognize them as tags. Trying different methods, I now  have this [Hazel rule]( to convert those hashed texts to Finder tags.

Export the notes from Bear to a finder folder–> run the hazel rule on the folder. The rule assumes that the tags in each file are not more than 5. If each of your notes contain many more tags, you might need to modify it.

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