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.

joudw

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:

txpz41

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.

is Sente abandoned?

Sente has been my favorite reference manger for the last couple of years. It has the most elegant reading interface; the annotation and quotation features are incomparable to any other PDF reader, let alone reference manger. I enjoyed every bit of the time I spend with Sente. Importing reference data, and downloading PDF files alongside, has never been as great. Unlike any other reference manager both in windows and mac environment (I have tried many of them), Sente allows downloading references from a very wide variety of sources. Its targeted browsing has been of utmost service for me. I really love how the application is designed; how it all is implemented. Sente is extremely well-crafted application; much better than Papers and Bookends in many aspects.

But, unfortunately, there is no update of any kind from Thirdstreetsoftware for the last few days. They shut down the blog, and stop replying emails. There are also some internal rummers that Sente might not bee see developments. I am truly worried if Sente is vanishing into nonexistence; all the time I spend on organizing my library; all the annotations and notes I made….I don’t know how to live without it. Very sad part of proprietary software;  the end is always ugly.

It also makes me wonder what kind of person would develop such a polished application for years; and ultimately abandon it. They have been developing it for IOS quite recently. There should be something seriously wrong!

 

 

Replace Tinderbox with Scapple

Tinderbox has been very proud of its mapping features. That feature is indeed the main selling point of the application. But, I just realize, one  doesn’t  need to go through the pain of learning an application as complex as Tinderbox to gain these benefits. A little sister of Scrivener, Scapple can do it the mapping of ideas with the smallest fraction of cost; with the easiest pace of learning. It is also better than mind mapping applications mainly because it is portable (that is, you can just drag your notes to Scrivener), and the rigid outlining forced in the mind mapping applications doesn’t exist in Scapple. It is just free, a clean piece of paper. Write, connect in a way you want your ideas to flow.

 

Go and try it. You don’t have to worry about learning a complex, arcane piece of software to graph your ideas.

 

Abandoning Tinderbox and wikis; sticking with plain text

On Note-taking, wikis and Tinderbox

General lessons:

  • Wikis are bad: they will be broken if u move something. So, never use them: history is the best teacher; hyperlinks are stupid for keeping information for a long time
  • Future proof plain text (markdown) files are the best.
  • Keep all the text notes in the same folder, inside Dropbox
  • plain files can be access them by different apps (as the need arises).
  • Use services such as Simplenote and Dropbox to access them via the cloud (syncing)

    these were the steps i used to sync my notes to various apps

  • Create the notes in nvALT
  • Store them in a folder in Dropbox
  • Index the folder in Devonthink
  • Sync nvALT to Simplenote
  • Sync Tinderbox to Simplenote
  • Sync Scrivener to Simplenote

    Work on any of the app, as the need arises. The changes will be reflected everywhere (windows pcs, ipad, iphone, all fetch from the same folder).

  • nvALT is the best for simple notes (drop what is in your head)
  • Tinderbox is best for creating connections of ideas
  • Scrivener is the best for drafting

After some more experiences and lessons, I realize that the syncing between Simplenote and Tinderbox is broken. Tinderbox adds some weird symbols to my text when I sync them to it via Simplenote. I have been waiting for Tinderbox six if it can solve the problem. It turns out that Tinderbox 6 is by no means better than the previous version in this regard. Its arcane nature, its little communication with other applications in Mac still remains a major issue.

Therefore, I am forced to abandon it for now< at least until the formatting problem is solved. (I requested Mark Bernstein, the developer of Tinderbox a number of times, to fix the issue. Even if he promised so many times, I haven’t seen him doing it for over a year now. so, I am losing hope with him too)

Abandoning Tinderbox also invalidates Simplenote’s fuction. so, I am also not using simplenote anymore.

The whole writing system is build around dropbox now (the nvALT) folder. For creating connections between ideas, now, I have to rely on Scrivener and Devonthink (and Scapple for visualization).

now, more simplified steps:

  • Create the notes in nvALT
  • Store them in a folder in Dropbox
  • Index the folder in Devonthink
  • Sync nvALT folder to Scrivener via Folder sync

Simpler and more efficient, at least until i need visualization of my notes (which happens rarely)..

Why you need to split your big PDF books

I have one secret tool that I bust all my class mates when it comes to digging down the nitty-gritties of small pieces of information. 

When we discuss some issue with professors or classmates, sometimes we come up with some wild ideas. We ponder about it; ask if anybody else has thought that before us. What they usually do is google.  I also sometimes google the ideas if anybody else thought them  before us (me). But, the fact of the matter is, google has a lot of noise out there with the same keywords but has little to offer the very specific information I am looking for. 

That is where a internal database comes to rescue. I collect as many books and article into my disk so that I can dig them whenever i want to find out specific ideas. The concept is known by “text mining” in a different camp of linguistics.

 Right now, I have over 2000 books and articles in my disk all of which deal with Theoretical Linguistics. 

If you have a collection of books and articles like me, and tried search a specific phrase into it; using Alfred, Spotlight or Devonthink, you will immediately learn that the biggest book always comes on top regardless of the quality of the material in it. The reason behind it is the word count. The larger the book, the more likely that it contains the queried word multiple times. If you collection specially contains gigantic Encyclopedia books, there is not chance that the short article comes out on top of your search result however relevant the article could be. 

Therefore, to make each small article as competent as any other material; and that your search tools could pick the small articles whenever they are relevant, you need to split the books into article sizes. 

I have experimented with different tools of splitting my books; beginning from Apple’s own Automator to a number of python and Shell scripts. Most of them work by bursting  the book by pages.

Bursting a book into single pages could be feasible when you have less than 1000 books. As you books grow, the bursting creates too many files to manage. In addition, the single pages won’t contain enough material to read within  the search result (FoxTrot for me). That is where splitting in 10-15 (article size) rage becomes crucial. 

Right now, I have shell script that breaks down my books in 10 pages ranges, a script that I adopt from a South African guy (I forget his name; I met him in Acadamic.edu). 

Any book or article I add to Sente library directly gets copied to another folder (using Hazel ) and gets splitted into article size page. All the pages finally move to another folder for ultimate archival; where my searching tools such as Devonthink and Foxtrot index. 

I will come back  to the  the full workflow and the scripts I use to achieve the task in another post. 

How to handle images in (Multi)Markdown text

Markdown is a language built for plain texts. The biggest weakness of plain texts is they can not hold images in them. To complement this fundamental weakness of plain texts, I have developed a system that works between Hazel, Dropbox and Keyboard maestro. The idea is simple. Create a permanent folder in Dropbox that you will maintain for the rest of your life. Whatever text you are writing in, whatever application you are using, always save and point to that specific folder. My folder lives in Dropbox. I call it simply Images. All of the pictures (images) that are part of my text notes are stored in this folder. Most of these images are made by snapshotting from the pdf files and online sources. For that matter, I made my mac to save all the screen-shoots  to automatically save in that folder. ok, let me write it like in steps:

  1. Make a folder in Dropbox: call it Images
  2. Make your mac to save the screen-shots in Images. Follow the steps in here to accomplish it

  3. Make a hazel rule to rename the screen-shots to a sequence of numbers (or some other pattern you like)

  4. Embed an applescript inside Hazel that will copy the file name of the image to clipboard

Look at the rule I made in Hazel: first only the rule;

ppic341

then with the script:

ppic342

 

Finally, use a Keyboard maestro macro to get the location of the image as well as the file name.

ppic343

That is it. What you need is just to snap the image from the PDF then, write “ppic” in your plaintext file. A link to your image will be inserted; and any markdown previewer (Marked for example) include the image in the preview.

Workflow with Sente, Devonthink, Scrivener using Hazel and Dropbox as glue: part 2

On Mirroring

In this second post, I am going to talk about a method, rather than a tool (software). I call the method “mirroring”. The method is a complementary approach for syncing. I generally like syncing files across my macs and iOS devices. The problem is: syncing is possible only when the app developers offer it. For Sente, for example, you can sync your Sente library to your Sente in IOS. But, you can not do so to other applications such as Devonthink; or Scrivener. The tags in Sente are not visible in Finder; and the notes and annotations, all are specific to the application. It is a locked application in that sense. Most reference managers are lock-down applications, unfortunately. I would be wise to avoid them; but they facilitate workflow.

 

Therefore, since I am relying on Sente and other locked applications, for my work flow, mirroring is a way around the locking weakness. What do I mirror? I mirror my projects.

My works are project based. I move from one project to another; writing small articles and developing small pieces of works for my dissertation is what I am doing, and will be doing for the next two years. I already talked about how I organize my PDF files based on projects. How do I mirror it? I mirror my project inside Sente to Finder by creating a folder. For example: if I am working on a project called “Object Shift”; i will have a tag in sente with the same name. All the PDF files that I will need to read will be tagged “Object Shift”. Look at the following picture: ppic82 When I double click the Tag, Sente hooks me to what I call the  project mood. The project mood is my favorite mood for reading in Sente. It also helps me to see the relationships and differences between the papers. ppic83

 

Now, I have all the papers I believe are important for the project. I then read and annotate them as fast as I can; and export the annotations to a Folder in Finder. The folder I create inside Dropbox is a mirrored folder; with the same name. The folder itself is inside a big folder called “Projects” which itself is inside Dropbox.  That mirrored folder (“Object Shift”) is where I keep all the notes I export from Sente  as well as the Tex file I will finally compile it to a finished paper. The “Project” folder is indexed inside Devonthink. Therefore, anything I add inside “Object Shift” is automatically available inside DT.  Now, you see I am in a good shape. My project files are in a separate folder inside Dropbox; but still in communication with the rest of my files inside Devonthink. The next step is  to develop a dozen of search algorithms (smart groups) inside DT that will hunt down all the relevant  files  to my topic. File selection and grouping in Sente is manual. Grouping inside DT is automatic. There are both pros and cons for for manual and automatic approaches of grouping files for project. I combine the two to get the best results.

 

As I have mentioned, I have “Object Shift” inside Sente, Dropbox (a folder) and Devonthink (indexed).  I also open a project under the same name inside Scrivener (I use it for some projects) and also a paper folder tagged with same name where I put all the papers relevant for the project.  That is mirroring.

It is a way of organizing myself wherever syncing is not available globally.

I mirror not only the projects and folder; but also the Statuses. The Statuses that I assign in Sente, demonstrated in the first post, are used across the board: inside Devonthink, Finder (Path Finder), Scrivener and even printed papers and books. Their application in the printed materials is actually quite interesting. I was a reading a book titled “How to Read a  Book”. In that book, the authors have a notion called x-raying the book.  X-raying a book is going through the major sections of the book, and evaluating the organization of the topics to evaluate the topics for your purpose. It is very effective method. I have developed the habit of examine the Table of Contents, the Sections and Sub-sections of the books before I read them. As soon as I finished examining the book, which takes just 2 minutes, I assign my statuses to the sections; with small notes; by attaching small stickers on them. That way, I will make sure that I l read the “Must Read” sections; and skip the “Repelling” sections (too much details or digressions) etc. As one can see from its multiple applications (on folders, projects, books and articles),  I can say that Mirroring is rather a habit; a useful habit to get things done.

You can make it your habit too.