Workflow with Sente, Devonthink, Scrivener using Hazel and Dropbox as glue: part 1

Since I want to follow up informations on the internet on a few applications that I am interested in,  I have setup  google alerts for tracking  blog posts and articles into my email inbox. Under my Devonthink tag, today I get this small visual workflow in a website called Pinterest.


I have never visited Pinterest before; but the visual illustration looks beautiful.  There is no explanation on how to build the workflow in the visual maps; but the illustration is elegant, something I have been planning to design. Since this is the  workflow  what I am already using it for the last year, it seems good idea to put how I put these different apps to work together to have the “virtually perfect” kind of workflow for my research (phd dissertation, I am starting soon). I have already written short articles in my previous posts on  some of the connections I made between these four majestic apps. In this extended post, I will demonstrate how I developed my workflow using Sente, Devonthink, Scrivener, nvALT, xMind, Sublime Text and ultimately Latex. Hazel, the Automator, Dropbox and Keyboard Maestro are the core glues of the workflow. I will spell out how each app works together with the other applications to great a coherent and elegant workflow.

Now, have a loot at a pictorial overview of the workflow we will have by the end of this series.

research workflow
Click for larger preview

In the next few series, I will try to explain each step of the workflow; how I develop the connections and how the tools chosen talk to each other to build a solid workflow. (I didn’t represent Hazel in this drawing mainly because the tasks of Hazel. The role of Hazel  will be clear by the end of the post)

Let me start from the app I use to gather resources for research: Sente.

# Sente

For me, the most important organization burden is lifted by Sente. Sente has four crucial features which are the life and soul of my workflow: Targeted browsing, File renaming,  QuickTags and Status. I will explain how I use each of these features to download, store, rename and organize my PDF files; then, how I will incorporate the organized PDF into the Devonthink hemisphere using Hazel as a glue.

I am not going to explain how to do all the importing and referencing process in Sente. That is left for the user manual; my task here is to show how to use what I call above the crucial features and getting things done.

Let me start from setting up the Sente library:

## File naming

The library is setup to store PDF attachments inside the Sente bundle. Setting up the library inside the bundle is very important for syncing the library to iPad via the Sente server.

The attachments will also be named as:

[First author Last name] [Year of publication] [Title of publication]

The file naming  is  important because I find some of the PDF files hard to read inside Sente; hence, I have to open them in acrobat. If you have the files properly named based on the author and title, getting the file is just a matter of second, specially if you are using Alfred.

## Targeted browsing

After you setup your library, the next step is to search files and download or import them into your sente library. There are two ways of getting your PDF files into Sente library; both of which support of-the cuff-setting up the reference of the file. The first method is directly downloading from the internet. Sente has this wonderful feature called targeted browsing. The main advantage of the targeted browsing is you have a choice of downloading bibliography information from a plethora of websites; you are not limited to Google Scholar or MedPub (the main weakness of Mendeley, by the way is absence of such a choice; it can download only from Scholar and medPub). Even if Google scholar is one of the greatest data sources on the internet, the data you retrieve from it are usually incomplete. Many people like MedPub. But, for my field, MedPub is irrelevant. Therefore, for articles, I havn’t found any better source than Google Scholar.  To get both the reference and the PDF file from Google scholar to your library, what you do is first import the reference information into your library by clicking the red button in   scholar website; and then, download the related PDF file. I am sure you know how to do this; I don’t need to explain it in depth.

The second approach is to have the PDF file in your disk; and then drag it or import it into your library. Sente will present you a window to add reference information to your PDF file. At this point, what I usually do is: highlight the title of the PDF file and take the title to my favorite search engines. For research articles, there is no better choice than Scholar.

As for books, thanks for their ISBN numbers, there are a lot of choices; WorldCat being one of the most popular. I used to retrieve the data for the books from WorldCat for a while.  But, after some time, I leaned that it sometimes confuses Affiliations metadata with Author. Therefore, I have been looking for alternative sources for retrieving bibliography information for books. Google Books is quite good; but Sente Targeted browsing seems to have some kind of difficulty to retrieve data from google books; takes longer time. Finally, , to my surprise,  I discovered the library of Stanford has the cleanest data; and Sente is very happy about it.

The template you develop to modify your targeted browsing in Sente is called Autolink Templates. Here is how I setup my Autolink Template:

Autolink Templates in Sente


## Quicktags

Quicktags: are the tools for organizing your research resources into groups. I have three major classes of Quicktags:

a) the Class: this is the class of quicktags that I assign to the PDF’s inherent classes. I assign these tags to classify the paper into the basic inherent classes of my field: Linguistics. Linguistics has many sub-branches if study; and sub-topics of research. Therefore, whenever I download a PDF paper, I assign these classes into the paper so that I can easily search and look at whenever I am looking at certain sub-topics. I for example use tags like Syntax, Semantics, Pragmatics, Phonology, plus sub-topics such as  VPs, PP, RC, DP under Syntax which what they are. I also have hierarchies of tags for the families of languages that I am interested in.

Afro-Asiatic [Semitic[Classical[Arabic, Hebrew]][Modern]] etc

b) the Project: this is a group of tags that I assign to papers on project basis. The projects are usually transient tasks that I plan, finish and move on to the next project. They could be part of the specific Class; they can also run across many classes. I assign these transient tags to the papers I am downloading, or on those which are already in my library. I search down my library, google scholar and may other source to combine all the resources to finish under one project using these Project tags.

c) the third group of tags is what I call meta tags. They are organizational tags. Whenever print a PDF file, I assign a tag xPrint; whenever I am reading the paper in Acrobat reader, I assign a tag called xAcrobat; or, finished reading the PDF and exporting the annotations of the PDF,  mark it xExport.

The Meta tags are supporters while Project tags are brothers of the Statuses, which I will explain in a moment.

## Statuses:

I basically use Statuses are meta-tags and to track the progress of projects. As you can see from the following snapshot, I have about 12 Statuses that I assign to my PDF files:

Statuses in Sente

– To be read nextis for example a status that I assign to a paper that I want to read just immediately after I finish reading the current paper.

  • Must read: is another status for a paper need to be read by hook or crook before I finish my PhD; a paper that I believe can offer a significant and profound insight to my research.
  • Repelling is on the negative side: a paper hard to read; or written in a bad language; the point is: I am dropping that paper; and might delete it from my library completely.

you get the idea


Sync attachements of Sente via Dropbox

Sente  from thirdstreetsoftware is one of the best reference managers in the town. It has some unique features putting it in superior position to most of its competators. The quote-comment-annotate feature of Sente has no real alternative in any of other reference managers and  PDF readers. Most PDF reader softwares can annotate  PDF documents, but they do not create as such comfortable environment for the individual/academician to read the content and write down his/her own ideas as Sente does. Not only for reading the PDFs, Sente is also a brilliant reference manager. I have been using Mendeley for many years,  since its beta stage. Adding metadata to a PDF article has never been as simple as in Sente. Mendeley offers you to extract metadata only from Google Scholar while Sente offers unlimited choices for the user, google scholar, medpub, worldcat (personal favorite), even you can create your own customized Sente to search any obscure search  engines (database). There also many other elegant features in Sente such as: hierarchical tags (QuickTags), Status markers, Smart Search (filters), synchronization to ipad and other mac computers, etc that put the application as a perfect companion for the serious academician.

With all elegance and beautify, there are, however,  a few trivial issues bogging down the useability of the application; these could also be big turn offs for some people to try it in the first place. I have been using the app for the last few months. I totally love it. And for some of the problems, I have come up with my own solutions, and I am here to share my ways to you.
One of the problems of Sente is putting a 20MB limit for file synchronization. If your PDF is larger than 20MB, it will not be synchronized. One possible work around this issue is to keep your pdf files outside of the Sente bundle, inside dropbox, and let Sente sync only the references.   For many reasons, this approach found to be problematic. It is likely that the link between the PDF and the reference or the annotations will be broken.  is not the  Hence, many experienced Sente users and the developers themselves recommend users to store the PDF files inside its own bundle.

The problem of storing the PDF files is the file limit. The files with larger than 20MB will not be available from distance.  That is not a good idea, as many of our files will not be available, specially for those people who like to scan books, this is a bad news as most of the PDFs scanned from books are huge files.

I have solved this problem in two different ways:

1. Reduce the files sizes using Acrobat. If you have acrobat (not adobe), you can reduce the file sizes. Open the files that you want to reduce the size. Then, go to Files, Save As, then Reduced Size PDF. You can then follow the prompts to finish the process. Acrobat also gives you the option to batch process (multiple files at the same time) the files. That is great. Just drop all the files that are larger than 20MB and acrobat does its job. In my experience, it cuts down the files size by 7X smaller, specially if you configure it to make the PDF compatible with  7.0 and later.

2. Syn the Attachment folder in Sente into Dropbox.  Sente doesn´t allow you to put the bundle inside the dropbox folder. They said dropbox causes file corruption. That could be true as the bundle is a package of highly delicate XML files that could be easily corrupted during dropbox synchronization. But, synchronizing just the attachments is not a problem by itself as far as I can understand. So, I am using Symbolic link to synchronize only the attachments inside the Sente bundle. Here is how you can  do it.

Open the Terminal and write the following text it:

ln -s /Users/username/path to Sente library/SenteLibrary.sente6lib/Contents/Attachments SPACE
/Users/username/path to dropbox/Dropbox/

Make sure you replaced the username by the appropriate username, and the paths by the appropriate paths.

To make it   clearer, assume that my name is John and I store my Sente Library inside Sente folder of my documents folder.

John/documents/Sente is where I stored my Sente library
John/dropbox is where I want to link  the attachements of Sente

So the above command looks like like  the following for me:

ln -s /Users/John/Documents/Sente/SenteLibrary.sente6lib/Contents/Attachments    /Users/John/Dropbox/

This command will link my attachments (PDF files) existing in  the Sente library into my dropbox folder as Attachments. Then, every time I add new files into my Sente library, the PDF files will be available in my dropbox folder, synchronized to all my computers.

This creates a good working environment if you want to work from distance, or you want to access your file from everywhere, as the use of dropbox we all know. This also exonerates you from the 20MB file limit Sente puts on you.

I hope this helps sb.

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