Recent changes to FAQ

FAQ modified by Jason Winning

Jason Winning — Wed, 04 Feb 2026 02:57:01 -0000

--- v19
+++ v20
@@ -62,7 +62,7 @@

 **Hypernomicon is a Java application. I heard that Java should be avoided?**

-That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets were made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 22), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.
+That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets were made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 25), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.

 **From watching the video, Hypernomicon seems to assume that information will have a fixed, rigid hierarchical structure. But philosophy debates and relations between concepts aren’t rigid and don’t fit into a neat hierarchy.**

FAQ modified by Jason Winning

Jason Winning — Sat, 02 Aug 2025 20:44:31 -0000

--- v18
+++ v19
@@ -62,7 +62,7 @@

 **Hypernomicon is a Java application. I heard that Java should be avoided?**

-That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets were made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 17), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.
+That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets were made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 22), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.

 **From watching the video, Hypernomicon seems to assume that information will have a fixed, rigid hierarchical structure. But philosophy debates and relations between concepts aren’t rigid and don’t fit into a neat hierarchy.**

FAQ modified by Jason Winning

Jason Winning — Wed, 03 Apr 2024 04:22:21 -0000

--- v17
+++ v18
@@ -62,7 +62,7 @@

 **Hypernomicon is a Java application. I heard that Java should be avoided?**

-That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets were made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 11), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.
+That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets were made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 17), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.

 **From watching the video, Hypernomicon seems to assume that information will have a fixed, rigid hierarchical structure. But philosophy debates and relations between concepts aren’t rigid and don’t fit into a neat hierarchy.**

FAQ modified by Jason Winning

Jason Winning — Wed, 04 Mar 2020 11:02:28 -0000

--- v16
+++ v17
@@ -62,7 +62,7 @@

 **Hypernomicon is a Java application. I heard that Java should be avoided?**

-That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets we made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 11), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.
+That is mostly a misconception from the old days of [Java *applets*](https://en.wikipedia.org/wiki/Java_applet). Browsers used to have the ability to show embedded Java “applets” on web pages, and at one time, these were notoriously associated with security vulnerabilities in browsers. But those days are long gone (applets were made obsolete first by Flash, then by HTML 5), and Hypernomicon is not an applet on a web page; it is a standalone desktop application like any other (e.g., Photoshop). Especially since Java version 8 (Hypernomicon requires version 11), Java applications are no more vulnerable security-wise than any other applications. In fact, a huge amount of the code running on web servers (i.e., powering your favorite websites) and on phones/tablets is Java. If you have a Mac or Windows computer, there’s a good chance you already run Java software on it without realizing it.

 **From watching the video, Hypernomicon seems to assume that information will have a fixed, rigid hierarchical structure. But philosophy debates and relations between concepts aren’t rigid and don’t fit into a neat hierarchy.**

FAQ modified by Jason Winning

Jason Winning — Tue, 23 Jul 2019 09:01:55 -0000

--- v15
+++ v16
@@ -28,7 +28,7 @@

 **What’s your angle in all of this? How do you (Jason Winning) make money off of Hypernomicon? (Or, how do you plan to in the future?)**

-I don’t. My motivation for creating it was purely selfish: I needed it for my own work (keeping information in physical notebooks, random documents on my computer, “notes” apps, and PDF annotations just wasn’t cutting it). But (encouraged by some other people in my dept. like Rick Grush, from whom I also got the word ‘Hypernomicon’) I eventually realized that it could be beneficial to others and decided to offer it free of charge, source code and all. There is no subscription service or anything like that. If even just a handful of people get 10% of the benefit I have gotten from using it, that is gratifying enough for me. But even if that didn’t happen, I would still keep using and improving it because it is a hobby I greatly enjoy.
+I don’t. My motivation for creating it was purely selfish: I needed it for my own work (keeping information in physical notebooks, random documents on my computer, “notes” apps, and PDF annotations just wasn’t cutting it). But (encouraged by some other people like Rick Grush, from whom I also got the word ‘Hypernomicon’) I eventually realized that it could be beneficial to others and decided to offer it free of charge, source code and all. There is no subscription service or anything like that. If even just a handful of people get 10% of the benefit I have gotten from using it, that is gratifying enough for me. But even if that didn’t happen, I would still keep using and improving it because it is a hobby I greatly enjoy.

 **I use [Scrivener](https://www.literatureandlatte.com/scrivener/overview) to write papers. If I use Hypernomicon, does that mean I can’t use Scrivener?**

FAQ modified by Jason Winning

Jason Winning — Tue, 23 Jul 2019 08:57:44 -0000

--- v14
+++ v15
@@ -18,11 +18,11 @@

 **Is this a competitor of [Zotero](https://www.zotero.org/), [Endnote](https://endnote.com/), or [Mendeley](https://www.mendeley.com/)? Why should I use Hypernomicon instead of those?**

-For the most part, no, it serves a different purpose. The main function of Zotero, Endnote, and Mendeley (and other “[reference manager](https://en.wikipedia.org/wiki/Reference_management_software)” software) is to acquire and keep track of bibliographic data and help you to generate a formatted bibliography. Hypernomicon does not attempt to provide this function (except for the acquiring; it can detect bibliographic information from the PDF file or the internet and sync it to Zotero) and leaves it to the “experts”. Instead, Hypernomicon is more specialized than other applications at keeping track of notes and other semantic information about philosophy debates, works, and authors, as well as organizing your PDF files and any other files and folders used in teaching or doing philosophy. Hypernomicon keeps track of associations between its data/PDFs and Zotero bibliographic entries and keeps their information synced. [Hypernomicon is better at managing PDFs and file folders than other applications (so for example, you should use Hypernomicon instead of Zotero for managing PDF files)](https://www.youtube.com/watch?v=uS3Fm3IGnkQ), but it can integrate with a reference manager so you can have the best of both worlds. I plan to add Mendeley integration this summer (EndNote integration is unlikely because they actively try to prevent other applications from being able to interact with its data—[they even sued Zotero](https://en.wikipedia.org/wiki/Zotero#EndNote_lawsuit)! Mendeley may start doing this in the future too now that it is owned by Elsevier, but I hope not).
+For the most part, no, it serves a different purpose. The main function of Zotero, Endnote, and Mendeley (and other “[reference manager](https://en.wikipedia.org/wiki/Reference_management_software)” software) is to acquire and keep track of bibliographic data and help you to generate a formatted bibliography. Hypernomicon does not attempt to provide this function (except for the acquiring; it can detect bibliographic information from the PDF file or the internet and sync it to Zotero or Mendeley) and leaves it to the “experts”. Instead, Hypernomicon is more specialized than other applications at keeping track of notes and other semantic information about philosophy debates, works, and authors, as well as organizing your PDF files and any other files and folders used in teaching or doing philosophy. Hypernomicon keeps track of associations between its data/PDFs and Zotero/Mendeley bibliographic entries and keeps their information synced. [Hypernomicon is better at managing PDFs and file folders than other applications (so for example, you should use Hypernomicon instead of Zotero or Mendeley for managing PDF files)](https://www.youtube.com/watch?v=uS3Fm3IGnkQ), but it can integrate with a reference manager so you can have the best of both worlds. (While Hypernomicon currently can integrate with Zotero and Mendeley, EndNote integration is unlikely because they actively try to prevent other applications from being able to interact with its data—[they even sued Zotero](https://en.wikipedia.org/wiki/Zotero#EndNote_lawsuit)!).

 **What does Hypernomicon compete against then? What else does what Hypernomicon does?**

-As far as I know, Hypernomicon is the only software that exists that is specialized for doing philosophy research. The closest applications to Hypernomicon might be [Docear](http://www.docear.org/) and [Qiqqa](http://www.qiqqa.com/) (the latter of which is Windows-only). One benefit of Hypernomicon is that by integrating with Zotero, you get to use a reference manager that is better than Docear or Qiqqa. Docear and Qiqqa also attempt to manage your notes and other semantic information, use visualization tools like [mind maps](https://en.wikipedia.org/wiki/Mind_map), help you draft papers, and manage PDFs. Hypernomicon can also perform these tasks, but it is more specifically specialized to doing academic philosophy and other theoretical or dialectically-oriented disciplines, since it revolves heavily around understanding how notes, concepts, theories, arguments, and works are related, and allows you to see all of your information and knowledge is related in one large scheme, even across multiple disciplines, instead of isolated project-specific mind-maps. Unlike most mind-mapping software, Hypernomicon predominantly organizes information *semantically*, not visually, although it allows you to visualize your data in various ways. Another big difference between Hypernomicon and Qiqqa is that Qiqqa tries very hard to include [all the functionality you would need in one application](https://en.wikipedia.org/wiki/Feature_creep) (it includes a built-in web browser, PDF reader that does OCR and annotations, bibliography generation, cloud storage, sophisticated full-text search, tries to guess what paper you should read next, etc., etc.) whereas Hypernomicon specializes in a smaller number of tasks but is designed to integrate well with other applications that excel at other tasks. [I don’t think Docear has been actively maintained since 2015](http://www.docear.org/software/history-changelog/).
+As far as I know, Hypernomicon is the only software that exists that is specialized for doing philosophy research. The closest applications to Hypernomicon might be [Docear](http://www.docear.org/) and [Qiqqa](http://www.qiqqa.com/) (the latter of which is Windows-only). One benefit of Hypernomicon is that by integrating with Zotero or Mendeley, you get to use a reference manager that is better than Docear or Qiqqa. Docear and Qiqqa also attempt to manage your notes and other semantic information, use visualization tools like [mind maps](https://en.wikipedia.org/wiki/Mind_map), help you draft papers, and manage PDFs. Hypernomicon can also perform these tasks, but it is more specifically specialized to doing academic philosophy and other theoretical or dialectically-oriented disciplines, since it revolves heavily around understanding how notes, concepts, theories, arguments, and works are related, and allows you to see all of your information and knowledge is related in one large scheme, even across multiple disciplines, instead of isolated project-specific mind-maps. Unlike most mind-mapping software, Hypernomicon predominantly organizes information *semantically*, not visually, although it allows you to visualize your data in various ways. Another big difference between Hypernomicon and Qiqqa is that Qiqqa tries very hard to include [all the functionality you would need in one application](https://en.wikipedia.org/wiki/Feature_creep) (it includes a built-in web browser, PDF reader that does OCR and annotations, bibliography generation, cloud storage, sophisticated full-text search, tries to guess what paper you should read next, etc., etc.) whereas Hypernomicon specializes in a smaller number of tasks but is designed to integrate well with other applications that excel at other tasks. [I don’t think Docear has been actively maintained since 2015](http://www.docear.org/software/history-changelog/).

 There are also applications that do “[argument mapping](https://en.wikipedia.org/wiki/Argument_map)” like [Rational and bCisive](https://www.reasoninglab.com/product-comparison-2/), both of which philosopher Tim van Gelder was involved in developing; Hypernomicon performs this function as well, but unlike other argument mapping software, it keeps information about arguments thoroughly integrated with your other notes, PDFs, references, and other files and folders.

FAQ modified by Jason Winning

Jason Winning — Wed, 17 Jul 2019 06:37:49 -0000

--- v13
+++ v14
@@ -14,7 +14,7 @@

 **Why does it have ‘Hyper’ in the name?**

-Because hyperlinks are a huge part of how it organizes information. It uniquely combines features of a relational database with automatic hyperlink generation and hyperlink-based indexing, so information is related and accessible in a highly diverse range of ways. Just as hypertext adds a dimension of relatedness to a set of pages of text, hypertext adds a dimension of relateness to the relational database of Hypernomicon (the original working name of this project was “Hyperdatabase”). I haven’t done an analysis myself, but I suspect that the usefulness of Hypernomicon may be because this combined way of structuring information naturally leads to the gradual emergence of a [heterarchical](https://en.wikipedia.org/wiki/Heterarchy) small-world semantic network, [like what happens in the brain](https://en.wikipedia.org/wiki/Small-world_network#Small-world_neural_networks_in_the_brain). See the explanation of the ‘hyper’ prefix [in this article](https://en.wikipedia.org/wiki/Hypertext).
+Because hyperlinks are a huge part of how it organizes information. It uniquely combines features of a relational database with automatic hyperlink generation and hyperlink-based indexing, so information is related and accessible in a highly diverse range of ways. Just as hypertext adds a dimension of relatedness to a set of pages of text, hypertext adds a dimension of relatedness to the relational database of Hypernomicon (the original working name of this project was “Hyperdatabase”). I haven’t done an analysis myself, but I suspect that the usefulness of Hypernomicon may be because this combined way of structuring information naturally leads to the gradual emergence of a [heterarchical](https://en.wikipedia.org/wiki/Heterarchy) small-world semantic network, [like what happens in the brain](https://en.wikipedia.org/wiki/Small-world_network#Small-world_neural_networks_in_the_brain). See the explanation of the ‘hyper’ prefix [in this article](https://en.wikipedia.org/wiki/Hypertext).

 **Is this a competitor of [Zotero](https://www.zotero.org/), [Endnote](https://endnote.com/), or [Mendeley](https://www.mendeley.com/)? Why should I use Hypernomicon instead of those?**

FAQ modified by Jason Winning

Jason Winning — Thu, 04 Jul 2019 06:32:46 -0000

--- v12
+++ v13
@@ -52,7 +52,7 @@

 **What if Hypernomicon stops being maintained/upgraded? Will my data eventually become inaccessible? Is there a “[vendor lock-in](https://en.wikipedia.org/wiki/Vendor_lock-in)” effect?**

-I don’t anticipate any reason why I would stop maintaining it; I am a philosopher and I need it! Even if I stopped trying to make a living as a philosopher I’ll always have philosophy as a serious hobby and I’ll always need to use Hypernomicon. I’ve invested so much time in it that I can’t possibly imagine walking away from it. I have always developed Hypernomicon in my spare time so there is no particular funding source that is in danger of drying out (like [what seems to have happened with Docear](http://www.docear.org/software/download/)). But in the worst-case scenario where I (and anyone else in the future who maintains Hypernomicon) get hit by a bus, since the data is stored in an easy-to-understand [XML format](https://en.wikipedia.org/wiki/XML), even with minimal coding ability anyone could easily write a script to export the Hypernomicon XML data to plain text files or convert it to other formats (if you just look at the XML file in a text editor, you’ll see what I mean). Hypernomicon does not use any kind of proprietary file format that would be difficult to export. Formatted description text is stored as HTML in the XML files so it would be easy to extract and convert to another format like RTF. Hypernomicon doesn’t try to keep track of PDF annotations in a non-standard way (like Mendeley) or anything like that, so there is less “vendor lock-in” than with other similar applications. And in terms of bibliographic data, assuming you use Zotero, that is one of the most interoperable reference managers out there.
+I don’t anticipate any reason why I would stop maintaining it; I am a philosopher and I need it! Even if I stopped trying to make a living as a philosopher I’ll always have philosophy as a serious hobby and I’ll always need to use Hypernomicon. I’ve invested so much time in it that I can’t possibly imagine walking away from it. I have always developed Hypernomicon in my spare time so there is no particular funding source that is in danger of drying out (like [what seems to have happened with Docear](http://www.docear.org/software/download/)). But in the worst-case scenario where I (and anyone else in the future who maintains Hypernomicon) get hit by a bus, since the data is stored in an easy-to-understand [XML format](https://en.wikipedia.org/wiki/XML), even with minimal coding ability anyone could easily write a script to export the Hypernomicon XML data to plain text files or convert it to other formats (if you just look at the XML files in a text editor, you’ll see what I mean). Hypernomicon does not use any kind of proprietary file format that would be difficult to export. Formatted description text is stored as HTML in the XML files so it would be easy to extract and convert to another format like RTF. Hypernomicon doesn’t try to keep track of PDF annotations in a non-standard way (like Mendeley) or anything like that, so there is less “vendor lock-in” than with other similar applications. And in terms of bibliographic data, assuming you use Zotero, that is one of the most interoperable reference managers out there.

 **How do I access my Hypernomicon data on my phone or tablet?**

FAQ modified by Jason Winning

Jason Winning — Mon, 01 Jul 2019 10:54:40 -0000

--- v11
+++ v12
@@ -1,4 +1,4 @@
-**Hypernomicon FAQ** (some of these questions/answers will make more sense if you have already watched the [Introductory Tutorial video](https://www.youtube.com/playlist?list=PLCDXooVJfr1JKHT83awarYoIOhp0Xqr-B)).
+**Hypernomicon FAQ** (some of these questions/answers will make more sense if you have already watched the [Introductory Tutorial video](https://youtu.be/JOTkAzh0qZE)).

 **So who is this for? Is this merely a learning tool for students, or would it be useful for someone who is already a tenured professor?**

FAQ modified by Jason Winning

Jason Winning — Mon, 01 Jul 2019 10:53:38 -0000

--- v10
+++ v11
@@ -1,4 +1,4 @@
-**Hypernomicon FAQ** (some of these questions/answers will make more sense if you have already watched the [Introductory Tutorial video](https://www.youtube.com/watch?v=JOTkAzh0qZE)).
+**Hypernomicon FAQ** (some of these questions/answers will make more sense if you have already watched the [Introductory Tutorial video](https://www.youtube.com/playlist?list=PLCDXooVJfr1JKHT83awarYoIOhp0Xqr-B)).

 **So who is this for? Is this merely a learning tool for students, or would it be useful for someone who is already a tenured professor?**