About OrganoGnosi

Organo and gnosi are the transliterated forms of the Greek words “όργανο” and “γνώση”, respectively, which can be translated as tool and knowledge. This blog is about tools (e.g. computer applications, scripts) and methods (e.g. automated digital workflow, hypertext writing) that a researcher can use in order to be more efficient in his/her efforts for finding and inventing new knowledge. The single most important element of my workflow is the creation and use of links or hyperlinks. A necessary condition for knowledge is the connection of at least two concepts. Moreover, in each academic work there are multiple references to previous works. These connections can be externalized, organized and saved for further study using links. The text in which there are links is called hypertext. The easiest way for writing hypertext is the use of a wiki program. Wikis are promoted largely as collaboration tools but they can be used in a personal setting as well. Unfortunately, the seamless use of links is not supported by the majority of the computer applications. This is the main reason for finding in my blog so many posts about how to create a certain kind of link. The programming language that I have written most of my scripts is called AppleScript and can be used only in Macintosh computers. However, a Windows user can still implement the core of my workflow, which is the writing of hypertext.

Oct 2012
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Send to clipboard the selected text in the browser, the source URL and the current date and time

Almost every day I find something interesting in a web site which I usually copy and paste it inside a wiki page. Moreover, I insert the URL of the web page and the current time and date. An example is the following:

AppleScript’s “big advantage” over other scripting languages (which, frankly are much better to use for most tasks) is that it can automate the action of other applications on your Mac (as long as the developer has provided an AppleScript dictionary). (http://stackoverflow.com/questions/1317497/what-is-applescript-and-what-is-it-used-for/1317498#1317498 – [[2013-02-22]], 12:56)

I enclose the date in double brackets because that way a link is created to the page with the title “2013-02-22” in which I keep my journal for the specific day. An additional bonus created from the link to the specific date is that when I visit the wiki page of that date, I can see a list of all of the pages that have a link to that page. This list is a good indicator of the subjects that I dealt with that day! This list is created by the following DynamicPageList query: {{#dpl: linksto = 2013-02-22 }}

Naturally, I wanted to automate the whole process so I created one bookmarklet for Firefox and one AppleScript for Google Chrome. The only difference between the two is that the AppleScript sends all the data automatically to clipboard while in Firefox the data will be shown in a separate window and then you need to press control + C and close the widow by pressing either Ok or Cancel.

The AppleScript is the following:

Click here to open the source code in AppleScript Editor

Update (2014-06-22): the above script at the moment does not work on Google Chrome. Actually you cannot execute any JavaScript code using AppleScript. For example the following simple script does not compile:

The same AppleScript for Safari is the following:

Click here to open the source code in AppleScript Editor

The same AppleScript for Firefox is the following:

Click here to open the source code in AppleScript Editor

Finally, the bookmarklet is the following:

You can drag and drop the bookmarklet to your bookmarks bar.

Presentation: Digital Tools for Academic Research

Digital Tools for Academic Research by

Tomorrow I will have the honor to make a presentation at Saint Edmund’s college of the University of Cambridge.

Presentation - St Edmunds

Mar 2013

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My favorite MediaWiki extensions

  • DynamicPageList is the single most useful extension that I use. It creates mainly list of pages satisfying various criteria (e.g. category, notcategory, linksfrom, linksto, title, uses, usedby, namespace). For more information you can read its extensive manual.
  • Labeled Section Transclusion allows selective translusion of marked-off sections of text. When it is used in combination with DynamicPageList you can synthesize the existent wiki content and create new dynamic pages according to specific criteria.
  • MathJax provides an easily installed way for typesetting LaTeX formulae in MediaWiki pages.
  • Wiki2LaTeX converts Mediawiki syntax into LaTeX.
  • WolframCDF allows cdf files generated by Mathematica to be shown in MediaWiki pages.
  • BreadCrumbs shows a trail of visited pages during the user’s session.
  • QuickLink makes easier and faster the searching and insertion of internal links.
  • SyntaxHighlight_GeSHi displays formatted source code written in more than 120 programming languages.
  • ReplaceText provides a special page to allow administrators to do a global string find-and-replace on both the text and titles of the wiki’s content pages.
  • MultiBoilerplate allows a boilerplate to be selected from a drop down box located above the edit form when editing non-existent pages.
  • Semantic MediaWiki helps to search, organise, tag, browse, evaluate, and share the wiki’s content.
Nov 2012
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Control the brightness of your monitor with DarkAdapted

At night I find the minimum brightness level of my MacBook Pro too intense. In order to solve this problem, I use the DarkAdapted app.


I have created the following custom presets:

My custom settings

Each preset corresponds to a different level of ambient darkness (dark, dart+, dark++, dark+++, dark++++ and brightness reduction (70%, 60%, 50%, 40%, 30%). The absolute color values for each level are shown below:

Level Red Green Blue
Dark 70% 180 180 180
Dark+ 60% 150 150 150
Dark++ 50% 125 125 125
Dark+++ 40% 100 100 100
Dark++++ 30% 75 75 75


Unfortunately, the developer has passed away and the official website is down. However, you can still download the app from here. The standard version of the DarkAdapted is free. At the moment you cannot buy the Pro version.

Nov 2012

all my posts, Mac

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How to copy the frontmost Skim PDF document to Dropbox and iCloud

For reading PDF files on my iPad I use most of the time the PDF Expert app combined with Dropbox. Moreover, I am experimenting with PDFpen apps for iOS and OS X which use iCloud in order to synchronize the PDF files and their annotations. Undoubtedly, the automatic and on the fly synchronization of my highlights and notes is quite impressive but I still consider Skim to be the best Mac application for reading PDF documents. As a result, I wanted an easy and fast way to send the PDF files, which I would like to read on my iPad, from Skim (more precisely from my DEVONthink databases) to my Dropbox and iCloud folders. This can happen with the following AppleScripts.

The first script sends the frontmost Skim PDF document to my Dropbox folder (:Users:MB:Dropbox:0 PDF files:) and the second to the iCloud folder for PDFpen (:Users:MB:Library:Mobile Documents:7PKJ6G4DXL~com~smileonmymac~PDFpen:Documents:). You should customize the variables which store the above paths in order for the scripts to function in your computer.

The Skim annotations are automatically embedded in the PDF document and you can see and edit them without any problem using either PDF Expert or PDFpen.

Click here to open the source code in AppleScript Editor

Click here to open the source code in AppleScript Editor
Nov 2012
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