FAQ

Hypernomicon FAQ (some of these questions/answers will make more sense if you have already watched the Introductory Tutorial video).

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?

It is not intended primarily as a learning tool or as “training wheels”. It is primarily designed for doing research on philosophy or a similarly theoretical discipline at an advanced or professional level, so it is equally suitable for grad students and professors (and anyone “in between”—like me) to use. It can be used for teaching, writing papers, writing a dissertation, writing a book, taking notes from seminars or talks, organizing your thoughts, etc. It might also be used by advanced college undergrads, for example taking an upper-division philosophy class, to take notes and study for exams (or of course writing papers). It becomes more useful, and can accommodate an ever-growing body of knowledge and understanding, the longer you use it. The more information you have added to the database, the greater the benefits it will provide in helping you organize it and understand how things are related at various levels. It is a tool for your total knowledge organization, not just for managing individual projects. My intention in designing it was to be able to retain all my notes and ideas in a well-organized fashion during and long after my dissertation, while I am getting tenure and trying to “publish, not perish”.

Is Hypernomicon only for philosophy, or is it equally useful for other academic disciplines?

Hypernomicon is well-suited for keeping track of information that is connected to debates, positions, and arguments. This type of information is important for many different fields, like literature, history, economics, law, theology, theoretical psychology, etc., and at least at an abstract level, experimental fields as well, anytime those fields are concerned with theoretical concepts, arguments, and debates. However, Hypernomicon is not well-suited for keeping track of things like raw experimental datasets, computer code for models, etc. So it is well-suited for research that deals mostly with qualitative information structured by semantic relationships, and less well-suited for research that deals heavily in sets of quantitative information or highly structured formalisms like sets of equations or computer code.

Do I have to be highly tech-savvy or knowledgeable about HTML or databases to use Hypernomicon?

No. It is intended for casual users who do not have any training/experience in databases or in any particular software or IT skills. It is made to be user-friendly for anyone who does academic research to use. If you have the technological skills necessary to use basic productivity software like Microsoft Word, then you can use Hypernomicon. Unlike with something like a Wiki, hyperlink generation in Hypernomicon is fully automatic (as demonstrated here) and requires no formal symbolism at all. (There are a couple of exceptions to this that pertain to optional features.)

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 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 small-world semantic network, like what happens in the brain. See the explanation of the ‘hyper’ prefix in this article.

Is this a competitor of Zotero, Endnote, or Mendeley? 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” 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), 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!).

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 and Qiqqa (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, 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 (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.

There are also applications that do “argument mapping” like Rational and bCisive, 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.

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 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 to write papers. If I use Hypernomicon, does that mean I can’t use Scrivener?

No, those two applications don’t really do the same thing. Hypernomicon can be used, among other things, to organize your Scrivener files, although the content of what is in Scrivener will be separate from your notes in Hypernomicon. Hypernomicon can certainly help you to draft papers but that’s not really what it’s specialized for, the way Scrivener is. On the other hand, Scrivener is not well-suited to be your primary organization tool for PDFs or notes. So the two can coexist on your computer and be used just fine without competing or conflicting.

How do I use Hypernomicon to download PDF files from the Internet?

Hypernomicon does not automatically download PDF files, but it can usually find the website to download a given paper from and open it in a browser for you. It also uses the Internet to try to auto-fill bibliographic information. The reason it doesn’t auto-download files is because I find this to be a very hit-or-miss process that no automated system can do very well (at least at present). Some websites may or may not have the official published version. Applications like Mendeley, Endnote, and Zotero often download versions that are not the official published version (because the published version might be behind a paywall, or may not be the first listed in search results), so you may not get the latest or best version. Authors often post versions of papers on their websites that don’t have important corrections, correct pagination, etc. If it is worthwhile to download a PDF of a paper, then usually it is worthwhile to download it manually to be sure it’s the right version instead of letting your reference manager guess for you. Auto-downloading files is one of those features that sounds good on paper, but doesn’t work that well in practice if you really care about which version of the paper you get (which you should, if you are a serious researcher).

Does Hypernomicon provide a cloud service?

No. It is recommended that you use an existing cloud storage desktop application like Dropbox, iCloud Drive, Google Drive, OneDrive, etc. to sync your Hypernomicon data between computers. I will detail how to do that in a future video (this is a feature I have been hugely dependent on for the last 5 years). Since Hypernomicon stores its data in XML format, it will work with any such cloud service—many other applications don’t sync very well that way and require you to use their own cloud servers.

Do I have to register for Hypernomicon, create an account, or start a subscription?

No, there is no registration process and nothing to log into. The application does not try to get you to create any kind of account. There is no subscription service that Hypernomicon will badger you into buying.

So it is “free to use”, but once I download it, it will say I need to “upgrade” to a “version” that costs money, but has better features, right?

No, when you download the free version of Hypernomicon, you have access to 100% of its features. Hypernomicon is not freemium, trialware, nagware or crippleware.

What if Hypernomicon stops being maintained/upgraded? Will my data eventually become inaccessible? Is there a “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). 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, 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?

Hypernomicon requires a laptop or desktop computer (Linux, Mac OS, or Windows) and doesn’t run on Android or iOS devices. Personally I think this is a good thing; usually applications on your phone or tablet require you to store your information within the application’s own servers, and you end up giving that application permission to access all kinds of stuff it shouldn’t need to be able to access. With Hypernomicon, you are always in total control of your own data, it lives on your computer (and perhaps a cloud service that you set up yourself, like Dropbox or Google Drive), and there are no Hypernomicon servers. Hypernomicon does not collect, upload, track, or store any user information of any kind. Hypernomicon does not ever “phone home“, not even to analyze how people use it or for bug reports. This does mean that you have to have a computer with you to use Hypernomicon (I myself have a tablet but only use it for reading; Dropbox syncs versions of the PDF files, including annotations, between the tablet and laptop). Hypernomicon can sync information between multiple computers however, so updating your database on your laptop will also update it on your desktop computer (again, this requires using something like Dropbox, Google Drive, etc. on both computers). If using Dropbox (or something similar), Hypernomicon itself does not need to have access to your login credentials or anything.

I understand if you feel like it is a disadvantage that you would have to have your laptop with you in classes and talks to get the full benefit, but you will have much more powerful functionality with you than exists with tablets or phones.

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

That is mostly a misconception from the old days of Java applets. 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.

I totally agree, and Hypernomicon was designed with this in mind. Relations between records in Hypernomicon are not necessarily hierarchical; in a true hierarchy any given node cannot have more than one parent, but this is allowed for many types of information in Hypernomicon, including arguments, positions, and debates. Also, there are many mechanisms for capturing nonlinear relations between ideas, through hyperlinks in descriptions or embedded descriptions for example. Finally, you can “link” records themselves together, for example to indicate that a term record refers to the same thing as a position record. It may be embedded within a network of positions, as well as a very different network of terms. And they can also be linked to note records that have still different relationships with other note records. The possibilities for specifying how information is related are endless. The tree tab allows you to see the same record as it is organized into multiple different hierarchies.

How do I use Hypernomicon to collaborate with other people? Can a group of people share a database?

Hypernomicon is designed primarily for personal, solo use (like how a person will have their own physical notebooks with their own personal notes). This makes sense because different people understand philosophy in different ways. You could, however, collaborate and share files if the database exists in a cloud storage folder, for example a Dropbox folder, that multiple people could access. But in this case, only one person can have it open on their computer at a time (the other one will get a message that the database is “locked” if Dropbox is actively syncing on both computers; if they are not actively synching, there is a danger of data corruption if multiple users make edits at the same time. The reason why Hypernomicon checks whether there is internet access by default on startup is to help reduce the chance of this kind of thing). One feature I have thought about adding would be the ability to open a database in “read-only mode”, so that multiple people would at least be able to access the database at the same time. You could also send a copy of a database to someone else (optionally with or without the PDFs); this is a simple matter of copying the database folder (or zipping it and then copying it) to the other computer. But this would be different from 2 people sharing and interacting with the same database. It would be like giving someone a photocopy of your personal notes; edits made on one computer will not be synced to the other computer. Another possibility is that a teacher could provide a database to students or have it running on a projector while teaching with students following along to help them learn material and study.

You can also share a single reference manager account, that each person’s Hypernomicon could integrate with. When people collaborate, it can be a good thing if they work with their own personal Hypernomicon database; it means they are each thinking individually and offering their own unique perspective, which is the whole point of collaborating.