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.

Mendeley vs Citavi vs Qiqq (also Sente and Bookends)

I haven’t used my Windows machine for a while now. I was then curious how the reference managers progressed in these periods. I was specially curious about Mendeley because I struggled with that application for some time then.

So, here is my observation: Mendeley stayed the same for the last couple of years. There is no real development; nor any change of any relevant sort since I knew the application. All the icons, the settings, the menus; the features: I see no changes. It is as clumsy as used to be; in many areas. One of the properties that Mendeley sucks at is how reference is downloaded from the internet. It attempts to use Google scholar; combining with its metadata extraction too. What it does is: it attempts to detect some DOI or other identifier to the PDF in the first few pages; and then, use that information to download reference information from Google scholars. For me, the result is a total debacle. It has always been a debacle. Mendeley can detect the papers only less than 5% of the times; as my PDFs don’t typically have metadata information; nor are they always published articles. Many of them are books; or drafts of books, and earlier versions of published articles I received from friends.

My favorite feature of Mendeley, which had been, still is: the BibTex sync feature. I have to admit, I have been tempted to live with Mendeley because of that feature. But, heck, if you have wicked reference data, what is the point of syncing it to Bib file. You will have incomplete citations ultimately. You will be embarrassed in front of colleagues when you realize that your references are incomplete after you sent out the paper. Because of the importance of the feature, I will focus on this feature in comparing the reference managers.

Citavis is not very far better than Mendeley when it comes to reference extraction from the internet. It can even be worse. I was able to download references from the internet only if the book has ISBN numbers or the article has DOI number. Otherwise, manual insertion is the only way I am left with. Look at this tutorial to learn how the process is clumsy in this application: https://youtu.be/MyaW9q_464w?list=PLkLfx87WKrTZTfifTvttqgKwzyQSTDYY5

In Citativ, when you read a PDF file, you can highlight or quote a certain text: comment on it; or give a short title to the comment and the quote. I totally love the idea of giving a short title to the quotation I make from a PDF reading. This feature is also available in Sente. The idea is: you quote a certain sentence or paragraph from the PDF; then, give a title which summarizes the core point of the quote and tag it if you want to. These quotes serve as a short summary of the article. The titles are your reminds of the core points of the quote. It is like summarizing the summary. Very neat approach to reading articles. The neat part in Sente is each of these short quotes could be exported as a separate note file. That means, if you have 20 quotations from the article, you will have 20 short notes: titled appropriately in a folder in finder. The problem with Citavi is each of the quotations are not exportable to separate notes. They can be exported as single file only. That means, it is not any better than reading and annotating a PDF in Acrobat Reader or other PDF readers (PDF exchange; or Foxit in windows: PDF expert in Mac)  and exporting a summary.

Qiqq is very different. Its way of extracting references from Google scholars is comparable to Sente. You click the PDF; click BibTex sniffer: you will be given Google scholars to pick the references. If Qiqq failed to detect the title of the PDF correctly, you can manually select the title. Qiqq immediately populates the scholar search with the selected text.

I have given the following book for all the three reference mangers: It was only Qiqq which correctly imported the full reference information.

gq4omd

I think the reference downloaded in Qiqq is much better than Sente. Sente has an advantage of downloading from multiple sources like WorldCat; Stanford, British libraries…very good results in some sources, weaker results in others. I used to get the most complete reference data from Stanford library website. But Sente sometimes fails to download the Publisher Field from many sources. Bookends can pick from Google Scholar, Justor and two other sources. But the process  of downloading a reference data (called Autocomplete in Bookends; targeted browsing in Sente; BibTex sniffing in Qiqq) is most elegant in Qiqq and Sente.

 

The other interesting feature of Qiqq is the brainstorming feature: absolutely brilliant tools to play with your references. It can also be used to track the positions one author took over time, how his/her ideas change in the long run. it can also be used to study the history of ideas: where a certain phrase appeared first; then, how other authors reflected that phrase in their publications. Look at these tutorials to see how the Brainstorming works in Qiqq:

 

My ratting of these reference manager’s capability of downloading references from the internet:

  1. Mendeley = 4/10
  2. Zotero= 3/10
  3. Citavi = 2/10
  4. Bookends = 7/10
  5. Sente = 9/10
  6. Qiqq = 8/10

Why is Sente higher in this ranking?

Because it offers much better choice than Qiqq on the sources. Qiqq does it elegantly on Google scholar; but, it cannot download from other sources which potentially offer more complete reference data.

Conclusion: if I ever have to move to Windows, I will definitely use Qiqq (in combination with OneNote or ConnectedText).

Scientific research workflow, mac

I am now starting up my PhD in linguistics. I have already collected more 1500 PDF articles and books (also did my MA in linguistics). So, I am trying to build up as perfect  workflow as possible  for my future research works. The university has given me a macbook pro, so , I am no more using windows OS. Even if there doesn´t seem to exist any comparable application in Mac as MS OneNote, I am discovering quite powerful apps in mac OS too. I have already learned a lot about Devonthink, Cirus Punies Notebook, Curio, Tinderbox and the like great apps. Therefore, I will be recording my experiences with each of the apps I am trying until I come up with the final, perfect system for my work flow.   I will write a detailed review of each of the applications here in the future. But, for now , I will just put only a short summary of my experiences with them.

1. File Organizer

My first task is to properly setup files organized in a specific folder, to make them easily accessible via Spotlight (or Alfred, I prefer the latter though). For file, organization, I use two tools; Dropbox folder and Mendeley. Dropbox doesn´t require explanation. I use mendeley not only to collect references, but also rename and organize my PDFs. It is such a powerful application to do these tasks. Here I use it.

a-I set a folder in Finder, I call it “agglomeration”, to mean, a folder where I drop all newly downloaded PDFs. All the PDF I download from internet directly go there. I use a download manager  called folx to force all the pdf files to go to this folder.  You can google it.

b-I have another folder in Dropbox, call it “AllLing”. This is the folder where I keep properly organized files.

c. Then, I setup Mendeley to suck-in all the PDFs available in the  “agglomeration” folder into its library, rename and then put them all into  “AllLing” folder.

As you can see from the above screenshot, the Mendeley is organizing my PDFs into a folder, inside Dropbox. Since the files will be renamed to Author-year-title, I can search the files using any of these attributes.  I also index the folder “AllLing” into Devonthink (see next). One main reason I want to use Mendeley is the fact that it live syns Bibtex files , even if it is not as elegant as I wish it to be. Other reference managers such as Sente and Papers are great by their own, but are weaker in their integration with bibtex.

2.Database manager:

Database managers are tools to  organize files and information in a manageable manner.  I use Devonthink this purpose.  Devonthink is one of the most powerful apps I have ever seen in the  mac environment. It has an artificial intelligence which looks inside the PDF files and establish content-based relation among the PDFs. That means, if I am reading an article on “Definiteness” , the software can scan its database, find and suggest relevant articles,  articles that contain the word “definiteness” or/and other  related words in the articles for me. It is also packed with many other interesting features such as  tagging system,   notes-taking tool; organize files into different folders, smart folders, duplicate detection, replication (aliases) etc. If you are staring to use the app, the learning could be a bit steep. I definitely recommend you to watch a screen cast in  a  website (it is under a paywall unfortunately) called screencastonline. Their screencast gave me a good ground on  Devonthink. (Note: I don´t have any affiliation with any of the links I mention here). Devonthink will be an    indispensable part of  to my workflow. I have tried some of the other database apps. I think no other app as good as Devonthink for managing scientific papers. Therefore, my database agenda is closed. The challenge I am facing is to make other applications to work with Devonthink.

So, Mendeley renames and puts the files in “AllLing”; Devonthink indexes them. I then group, replicate, organize, tag the files in the Devonthink so that I could organize them for my specific projects. I am right now writing a paper about Nominalization. Hence, I search and “see also” the related papers in Devonthink, Group them in one folder; I then drag them to Sente for reading and taking notes.

3. PDF annotation and note-taking:

Macadamec has already written a great post about Sent. I recommend visiting his  post; I am not going to repeat the whole story here. I will just shortly reflect my own experience with the application and its place in my work flow.

I  am considering totally leaving Mendeley and migrating to Sente because of the fact that the application has a more elegant tools of annotating PDFs. It can directly quite, snapshot, highlight and insert all these into the Notes panel. That is brilliant. It can also rename files, just like Mendeley. The notes then could be exported to Devonthink or Scrivener using some apple scripts. brilliant!

Sente  has some fundamental flaws, unfortunately, that makes me nervous to totally migrate my data from Mendeley:

a. it fails to import PDFs from other applications,

b. the link between the note and the pdf could also be broken. Some people have experienced this problem, and I had the same issue with a few PDF annotations.  Right now, I am using it only as PDF annotation, not as a reference manager. My references and PDFs remain in Mendeley while I temporarily import the PDFs I want to read into Sente.  (just search in Alfred and drag it to Sente because the files are properly renamed by Mendeley, or go to the folder “Allling” and drag the file; but, I usually drag them from Devonthink).

c. it is also bad for Latex integration

d. Annotations are not stored in the PDF: this the problem of almost all the note-taking tools in Mac; they store the annotations in their own database. If you open a PDF from Dropbox in another PDF reader or browser, you couldn´t see the annotation done in Sente (or Mendeley or Papers) while the annotation done in Acrobat or Foxit or PDFexchange are there, everywhere you have the pdf. Storing the annotation is good for long term use, as these applications could break. But, Sente couldn´t do it, unfortunately.

4.Drafting

Here, the choice is clear. Since all the notes are exported from Sente in either OPML or RTFD format, I just import them to Scrivener.

5. Final Polishing and Publishing:

I export my draft form Scrivener in Latex format, I import the text to TexStudio, a latex editor that I use to finally polish my work. Texstudio, and also TexShop, can automatically detect and insert my references  which are stored in Jabref (in sync with Mendeley).

Finally, a shinny PDF!

End

Must have windows 7 applications

Here, I will list some of the best windows application that, I presume, that every windows user “need” to have. Of course, there are a dozen of tech magazines and website that list a dozen of such stuffs. These sources can tell you all the powers that the applications can do, the features they come with. But, the writers of thee sources rarely tell you the actual experience they have with the applications. Yes, some many application these come crammed with so many great features. These so many features, however,  usually obscure the main objectives that the applications made for. That is what makes a pedantic application different from a usable application. Usability is what most tools lack these days. They cause you more confusion and annoyance than enjoyment and service.  Here, I will mention some of applications that I found to be more useful, based on my experience. Let me start from the academic tools

Academic Apps

LaTex (freeware) for writing your documents. If you have some serous academic paper to write, you have to get LaTex. But, for simple texts, stick with Microsoft Windows  or whatever text processing apps you have.

Notepad++(freeware) for text editing; TextStudio for LaTex documents; emacs/vim if you are a serous programmer.

Jabref: to manage your bibliography, if you are using Latex.

Mendeley Desktop to organize your PDF files: Currently there is no any alternative than mendeley to manage your pdf files. it is a great too. it can extract the metadata of the files, tag from Google Scholar, and even rename  and organize your files into groups.

PDF-Exchange to read PDF: you can also try Foxit. These two softwares are equally efficient for reading PDF files, though the former has more features in the free version than the latter.

Microsoft OneNote: for more serous notes. yes, Evernote is one of the greatest tools for clipping pages from websites and writing your own notes. But, after some practice and learning a lot about these two applications, I found OneNote to be better than Evernote, specially to write more serous notes. The way OneNote organizes the notes more intuitive and robust than Evernote. Now, it can also synchronize your note online (with SkyDrive).

Dropbox for your cloud computing needs. You already know it!

Calibre: to manage your ebooks. If you have e-reader like Nook or Kindle, the chances are you have a dozen of ebooks (EPub or Mobi) files. Calibre can help you to clean up the clutter. It can also convert from one format to the other. The best in the game!

Wordweb: desktop dictionary. No doubt, Wordweb is the most popular and the best dictionary application for windows. Lingoes is also great.

CutePDF: to convert your documents into PDF

Adobe Pro: to convert PDF files to other formats such as word, excel etc

Media Apps

MediaMonkey:for audio. MM is the best and probably the only software you need  to manage your music and audiobook. I know so many people use iTunes.  The main turn off for me with iTunes is the fact that it stores metadata about my files in a separate folder. That means, if you edit (tag) the name of the singer, the Album, the CD cover, all these information will be stored in iTunes library, not with your actual files. If you want to migrate to another application some time, you will lose all the editing you did on your files. You will not get the name of the artist, not the album…. That is bad. I want my files as clean and edited as I want. MediaMonkey can do it and store the information with the files. MediaMonkey also has better editing (tagging) tools than iTunes.

The KMPlayer: for videos. I know many people prefer VLC player. VLC is great for the fact that it can play almost all links of video/audio files you throw in to it. But, I found The KMPlayer more efficient in managing my video file. It can also play  all the popular video files.

Other Utilities

Google Chrome for browsing: I am sure you have already tried Chrome. it is a great  browser. It also seems a bit faster than Firefox.

UTorrent: small but efficient torrent downloader. you have to download the earlier version of uTorrent (2.1 or earlier)  if you what small size and efficient torrent downloader. The new versions have been damn shit!

IDM: for downloading files from internet: Internet download manager is  the fastest download manager in the market.  There are some other free alternatives to it. But, yah. I am not as such satisfied with them.

Revo Uninstaller: to uninstall applications. it removes all the junkie that uninstalled applications leave behind.

Ditto: to manage your clipboards. It keeps the contents you copied for latter use.

Everything: for desktop searching. Windows has its own desktop search engine. But, Everyting does the job faster. Switching off the search indexing of  the windows also helps your computer to perform  faster.

Directory Opus. Though  quite expensive, Opus is the best desktop explorer software. It has been two years since I used the regular explorer.

Avast free: for antivirus. Both avast and avira are great  antivirus programs. I prefer avast for two reasons. First, it doesn’t display adds ( Avira had been quite intrusive for some time. I am not sure right now if it still displays adds so aggressively as before). Secondly, it uses less resources than avira (in my pc)

Evernote: to clip webpages from website and write down notes.

7zip: to extract archive files: a free, fast  and powerful software! You get almost all the features of the expensive extractors such as winrar. Just wonderful!

Bulk Rename Utility: for renaming files, though its interface is ugly,  there is not better software than this one! It does the job very well

Tell me your favorite application!

Reading inside Mendeley, better to avoid it

I have already started writing about the great research tool, Mendeley Desktop. I believe, mendeley is one of the mandatory tools every academician need to have. Many people are using it for many things. As to me, however, its main virtue is the ability to organize the actual PDF files in a brilliant manner. In this post, though, I am going to tell you why you need to avoid reading and annotating PDF files inside Mendeley itself.

If you are familiar with the fast and efficient PDF readers as Foxit and PDF-exchange, you will face too many constraints with Mendeley’s internal PDF reader, which I found to be unbearable. Of course, you can read, annotate and write notes inside mendeley. But, the main downside of Mendeley’s internal PDF reader is the fact that your annotations will be saved in separate folder. Mendeley has a system called database where it saves information about the PDF files. That database is in a different folder from the actual PDF files. Hence, if you open your Mendeley annotated PDF files in another PDF reader, you will not get the annotations. This is bad. I want my PDFs annotated wherever I open them, whenever I want.

Mendeley team has tried to alleviate the problem by adding a feature to export the annotations of the PDFs. But, I found this to be a laborious task. Should I open and export the annotations of each and every file every time I want to see my annotations in another software? no, I will not do it. So, if you are like me, the best approach is to manage your files inside Mendeley and read them using more potent PDf readers as Foxit. Your annotations and notes will be saved embedded inside the PDF files that you don’t have to worry opening them in another software.  You will enjoy your annotations to the  end of time (unless you want to remove them of course) wherever you go, which ever software you use.  So, to  open the files organized inside Mendeley with external readers, you have to right clicking the file and choose “Open file externally”. Your default reader will be fired. Voila!

Cheers

Organize Mendeley’s Organizer using Duplicate File Detective

I have been using Mendeley Desktop for about two years now. Passing trough a lot of modifications, Mendeley Desktop has recently come out of its beta state. The best research project manager software now seems more stable and faster than ever.  Combing the potential of extracting the metadata of your PDF with the ability  organize and synchronize them with the cloud, no better application seem to exist that can satisfy all these needs.  Being a big fan of the application,  though, there are a few critical features that I am looking for implementation in its feature releases.  One of these is lack of Moving files while organizing files. If you use its file organization, it can only copy and rename  all the files in the library to a single folder. This means that, you should have a duplicate of files every time you use this feature. To alleviate this problem, I use an application called Duplicate File Detective. Of course, there are many duplicate removal applications out there. But, I prefer this application for one main reason; it can detect and delete only old versions of your files.

Here is how how to  do  it.

1. Open your Mendeley Desktop and make sure your  library as good as possible; Check the accuracy of the  metadata; check for duplicates in side Mendeley; check the dates, author, title of your files.

2.   After you make your library clean, go to Tools –>Option –>File Organizer. Check Organize my files. Click on Browse select a folder where you will store your whole library. You better select an empty ; otherwise, Mendeley will mix up your new files with the old files. You can also check Sort files into subfolders. But, I don’t recommend it. 

mendeley1

Check rename document files as the above picture, and finally Ok. This will copy all the files in your library to a folder (named AllLing in the picture). As you can see it I am also putting it in the dropbox folder. The reason is clear. Dropbox  gives more free cloud  space (2GB) than Mendeley (500MB). You can also get more free space by inviting your friends to it.

3. Since the above process copies all the files from their original folder to a new folder, you will have  two copies for each of your documents. To tackle this problem,  now you need to run Duplicate File Detective. In the DFD, select the disk where you store all your files and click Run Project.   When DFD finishes searching for duplicates, you will see all the duplicates in  a window. Go to Smart Mark (circled red in the picture below) –>mark Old files in Each Group –>Mark By File Created Date.

mendeley2

Now, give a glance on the list of files. If every thing is alright, all the old copies must be selected while the new copies stored in AllLing (in my case) remain unmarked. You can then either Move or Delete them. Now, you have cleared your clutter.

4. You can fix  a Watch Folder for Mendeley where you throw all new files that you will download from the internet. Mendeley will automatically import, extract the metadata , renamed and copy into  Organizer folder (AllLing in my case.).  After you make sure that the Mendeley has done its job, you can then manually delete the files in the Watch folder.