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.

 

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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](https://www.dropbox.com/s/w5w597lz3emwyp8/ExportFolder.hazelrules?dl=0) 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.

Chronosync is Time Machine plus Git

Writing a very important document needs some care. A reliable backup is crucial.

In addition, versioning system is very helpful. It is different from the backup because you can go back in time and revert back to some of the changes you made. Not all the changes we make on our document are useful. We could make mistakes. You wish you have the old version of your file. Version is a great strategy to make a carefree editing. You can get the old version anyways: why do you worry to make the changes. It improves your productivity as you are relieved of wrong changes.

Subversion has been the most dominant system for ages. Now, Git  has replaced it. But, even if these tools are as useful for writers as for developers, they are less popular among writers probably because of the technical nature of them. I have been using Git for a while to keep versions of my latex files. My latex editor, TexSTudio even supports committing git commands.

After a while, I have however realized that I often forget to commit my changes. Sometimes, I want to revert back; learning that I have no version of that certain editing. I tried to supplement the git system with Keyboard maestro to automatically commit. It was working fine. Still, things become too hectic when I made a lot of changes distributed in many folders. The files are also not all  latex.  so, I need commit them with a separate program (via the Terminal).  So, looking around for other solution. One strategy is to rely on Time Machine, as many people do. The problem with time machine it that it is less configurable. I want more versions on some files and less on others. Some files are crucial: I wanted them versioned in every 20-30 minute because I often want to refer back the old versions.

In addition, as it tries to copy all the files in the disk, Time machine is a huge resource hog. When I was using it, it topped the applications which consume the most of energy of my machine. It sucks the battery juice from my machine. Furthermore, Time Machine doesn’t support bookable backups. They are very useful in case of crisis. That is where I started to check out Chronosync.

 

I have been using Carbon Copy Cloner for keeping bootable backups. CCC also keeps versions of files, to be fair. But, the versioning system in CCC is not really useful to keep track of changes in a file. That is when  I decided to migrate to Chronosync. This beast does both the syncing and the versioning like a pro.

 

Chronosyc permits a more fine-tuned backup and versioning schema. You can tell it to backup some folders just once in a day (say the downloads folder) while versioning the most active, working folder, Projects folder, every 30 minutes. Best of all, you will never feel the pressure on your mac. Since you can dissect your backups to your like, Chronosync doesn’t eat up your RAM or heat up your machine.

Chronosync is like Swiss army for both tasks of versioning and backing up. A money well spent. The saving I make on the battery pays back the price of Chronosync.

Comparing the 3 best pdf readers in Mac: Skim vs Highlights vs PDF expert

PDF files are the life of the academic. All information come with them. Of the time I spend reading, more than 95% of it goes by Pdf files. For that end, a good pdf reading application would be very important: much more important than any other application I use.

I have been looking for different tools for reading Pdf files.

Every one of them have strengths and weakness:

1. Skim

Skim: designed for the academic community: free and open source.

Strengths:

  • The ranked search is amazing.  of the  3, Skim has the best searching capabilities. PDF  expert comes next.
  • The annotations are more powerful and flexible: the anchored note is specially a wonderful tool. You can literally draft your next book using the anchored note. Reading triggers ideas; ideas breed ideas. Ideas cannot come out of the blue: they emerge during the reading. The best part of the anchored notes that you can give Titles to the notes. You can manipulate them so that the exported note will be much cooler.

I usually put ## on the title of the anchored note so that the title will come out as a true title when I exported the annotation using Markdown format.

  • The keep on top feature is very useful to compare ideas: any of the annotations can be kept on top.
  • Supports scripting
  • Export templates: you can modify these templates to your need. This is extremely useful.

But, there are some weaknesses with this all strength.

  • The non-standard format: if you want to read or see the annotations of the Skim, you have to export it. You cannot just open the pdf and keep on annotating. This is a deal breaker. Really. I am tied up to local system; this is like a prison. I like PDF expert for it adheres to the standard PDF specifications. I think it is the best mac reader with the standard formats next to Adobe’s own products.  Mac OS has this weird system comes by the name **PDFKit**: it gets broken, keep on screwing us all the time. Corporate greed seems the reason why we are suffering. Why doesn’t Apple adhere to the standard Adobe specifications? This same crap Kit also seems the  reason that saving pdf files in Preview and the rest of Mac local applications bulges up the size of the pdf.
  • The separate .SKIM file is a pain in the ass. It gets lost. If you export and import the pdf, all the annotations get duplicated. It is whole mess.

If Skim follows the standard PDF specifications; writing the annotations directly to the PDF itself, I would never look around.

2. Highlights

Strength:

  •  It follows the standard annotation system: annotations made in Highlights can be viewed and edited in other editors (both in the mac and windows)
  • The annotations are powerful. The annotation panel could be wide: therefore,  a long text can be directly inserted. Even if it is not as convenient as the anchored notes in Skim, the panel is generally convenient to drop longish texts.
  • Works great with other applications: like Devonthink, Bookends, and Evernote. This is one of its best features
  • the exported notes are in Markdown format: this can be taken as strength and weakness: depending on your interests.
  • Splitting annotations into distinct notes. This is the most interesting feature, for me, because I can keep single ideas as separate notes. I  have been using Sente annotations for this purpose.

Weaknesses

  • general clunkiness: the app contains a lot of bugs
  • the Splitting feature is not well worked out. I would have bought this app if I were able to assign titles to each of the annotations. The Titles are very useful for summarizing the concepts of each of the singular annotations. This is the most debilitating problem I have with Highlights. The spliced notes have no meaning: not life because they are not customized by titles or tags.

3. PDF expert

PDF expert is very fast and fluid application. I use it everyday. The developers are generally very responsible and fast guys. The code they write is amazing. The programmer talent in Readdle  tend to be very high. I participated in their beta versions for a long time now. I can tell you, their betas are more matured and reliable than the final releases that Apple sends out. There are some small details: specially its speed, which makes this app worth trying. I like it so much. I is the first app I open in the morning. The best part of the app is that it follows the standard Adobe system. The annotations made in PDF expert are visible on any other pdf reader. That is why I use it as my default reader.

Strengths:

  • I also like the new searching tool. It searches all the open files.
  • it automatically detects the true pages numbers of the pdf
  • blazing fast
  • follows the standard Acrobat annotation format
  • The annotation tools are generally ok

Unfortunately, PDF expert is also  the least creative of the 3 apps I am trying. The features it contain are most already in acrobat or other pdf readers.  The export features are very weak: even terrible. I tried to export in the Markdown format. It doesn’t permit me to customize on what types of text I want to export. Generally, the exported text turn out to be  vary bad containing unwanted stuff (like Date, author…).  Even if there is wondrous programming talent,  the direction they are taking are mundane and non-creative.There is barely a new feature in this reader that other readers, like PDFPen, Acrobat etc, do not have.   They don’t understand the areas of need. The annotation tools could  be better. The developers of Highlights have truly understood the needs of the scientific community.  It is only the implementation that is lacking in the latter.

My take:

After trying it on a couple of times, I have given up with highlights.

I am now using Pdf expert and Skim. I use Pdf expert for fast reading. When I have to just scan and take a few points, I open my file with it. I highlight a bit; clip a few lines to Curiota and close it down.

When I have to read a book or an article from the beginning to the end, for intensive reading, no reader offers the comfort that Skim offers. The exports are also much robust. Therefore, for in-depth reading, I am relying on Skim.

By the way, there is an other candidate that could offer a similar comfort for reading: the Marginnote. It seems to have some great annotation tools similar to anchored note: even better, mind mapping within the reader. I tried it for a couple of minutes. But, I dropped the app immediately because the annotations are in proprietary format: they will be a big lock down. While the annotation summary can be exported, the annotation and the annotated pdf are divorced forever. I am skeptic of apps that highly rely with proprietary file system.

Where Bookends rocks

Before, I wrote a few complains (https://dellu.wordpress.com/2016/03/28/where-bookends-sucks/) I have on Bookends as replacement for Sente. It has been almost 9 months since that post.

Now, I am updating my experience with the Bookends.

The good news: the latest version of Bookends (12.7.7) has solved one of the major complains I had on the application. That is: it can now extract references from a plethora of sources that the source of extraction is no more a problem.

In addition, I learned in the course of the previous months that the right method of finding references of PDF books is to use the ISBN associated with the books. Once you write the ISBN of the book in the ISBN field, Bookends happily can download all the reference data from Amazon using its Autofill feature. The Autofill feature is a super-feature. One day,  I put about 400 PDF articles collected over the years into Bookends watch folder; all of them have their DOIs printed in the first pages of the articles. It was just magic to see all the PDF files find their references filled automatically in a couple of minutes.

I also leaned that Bookends is much potent application than Sente when it comes to managing references. The tools embedded into it are unbelievably rich. It has organizational tools like: smart folders which support REGEX,  static folders,  labelling (color coding). It has a fully configurable Format Manager which enables the end user to import or export; rename the references in endless ways. The Format Manager in Bookends is the greatest feature I have ever seen in any reference manager. It is a dream come true. It is a liberating feature. I cannot say enough about it.

Bookends has other tools under Global Change. Finder replace that works across the whole library; batch changing of reference types, batch inserting data..and, other many types of manipulation tools.

Attachment handling and file renaming is superb in Bookends. The best part is: files are managed very transparently. You can explicitly put your files in a Dropbox folder without any hassle: while still they are attached to their references.

The Duplicate Finder tool embedded into Bookends is the best in the class. Jabref is great for finding duplicates. But it cannot reach the complexity and elegance of the duplicate finder in Bookends. You will never miss a duplicate with it.

If you are into Latex, it is also one of the most Bib friendly non-bib reference manager. It can assign unique Bibtex keys: and, the Format Manager can be manipulated to export in any of the Bibtex formats (Bibtex or BibLatex). You can also manipulate your format to export distinct (unique) bibtex fields. You don’t even need to export the reference to get your bibliography to work with Latex. You can make Bookends to work with your Latex file directly.

Bookends has  AppleScript dictionary. That again opens a world for who are into the scripting.

Integration with other super applications: I have never seen any reference manager as flexible as Bookends (I admit, Zotero could be even more flexible: I just don’t like that app; never tried it seriously.). For me, the fact that Bookends works well with Devonthink and Tinderbox is the best part of the story. Bookends is hand in glove with both Devonthink and Tinderbox. You can export and import in both directions; you can even directly sync them using some scripts (all the three are scriptable). Combining the three power tools is the nirvana for the knowledge worker. The world has never been greater.

The only feature I am still missing from Sente is the reading and annotating capabilities of Sente. The reading experience in Bookends is nowhere closer to Sente. Otherwise, as I am more using Bookends more, I am getting more surprises how a reference manager could be so rich and so capable. In an ideal world, BE would incorporate the annotation tools of Sente.

Powerful search tools in Windows & Mac

If you are an information worker (academic), having great support from powerful search tool is  crucial. Unless you have that sharp searching too, you will have trouble to pick that grain of information from the gigantic jungle of information coded in the form of data, sentences, or books.

There are great tools everywhere; but, some stand out in their capabilities than others.

The three giants in the Windows environment you might need to check are:

  1. Dtsearch (Windows)
  2. X1 search (Windows)
  3. Copernic desktop (Windows)
  4. FoxTrot Professional search (Mac)
  5. ? Devonthink (Mac)

 

Personally, I am not that much fond of Copernic mainly because it has no internal previewing tools; and, it seems to consume too much resource of my machine.

My number 1 pick is DtSearch. It is the best in its class in digging the tiniest of information. The proximity search is an invaluable tool to find associated ideas.

X1 comes closer. It is more of a document manager just like Devonthink in the mac than a specific searching tool. X1 also a wonderful application. It is cheaper than DtSearch.

 

As to FoxTrot, it is quite comparable to the DtSearch. But I like the preview system in FoxTrot even more.

The proximity search in DtSearch requires you to write the distances between the words(phrases) explicitly like Mary w/5 John (‘search Mary and John within the distance of 5 words’); while Foxtrot has a little scrolling window to search within a paragraph, within a sentence or less closer phrases.

One might put DT as a competitor to Foxtrot in the mac. But, I think FT is much superior on the search side while DT rocks for its AI and other organizational tools.

(Note, I don’t like giving links to the products because I don’t want to sound that I want to get a penny by associating them to my small, free, blog….I am dropping these notes because I believe these notes might help somebody out there; not because I have some other agenda. I used to keep these notes in my internal system; i put them out now in case somebody get sth useful out of these notes).