Tag Archives: pim

Review: Docear

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We’ve talked about Docear the Visual Citation Manager on the blog before, before my time, but it’s been a while we’ll revisit it. Though, the most recent major update to the software was in 2015, and based on the forums it seems that Docear has struggled with finding funding. However, the researchers behind this project are still active. That being said, in the worst case scenario, Docear is an open source project and if things went south, you could still get your information out. If you are considering relying on this software for organizing very long term research projects you need to use an external cloud backup service as their My Docear service is no longer available and supported if it ever existed at all.

Docear

Screenshot of Docear demo mindmap

Docear paper demo mindmap showing linked annotated PDF

Docear is an open source mind mapping, reference, and citation management software for those who want a visual way to keep their research organized. It is available for Windows, Mac, and Linux computers. Docear provides plenty of support and useful instructions through their official user manual. The examples on the app itself for trying out the mind map and PDF capability incorporate some of the research behind the product itself and makes for an informative, if somewhat meta, experience. Docear staff like to compare the software to Zotero and Mendeley, but it’s a very different type of beast. Specifically, a combination of Jabref (without the OpenOffice support) and Freeplane for mind maps, and, depending on what type of PDF viewer you use, a document annotation software. To enjoy the full capability of this software you also have to download PDF X-change viewer, though you can still do some annotating with other less supported PDF editors. Docear also uses Mr. DLib or Machine-readable digital library cataloging. While Mr. DLib has not really caught on elsewhere, it is featured as part of JabRef and specifically powers the article recommendation function. If they ever get their funding together, Docear could become a space where you can research, organize, and write an article. And unlike some of the software options discussed on this blog and in our LibGuides, you can download Docear from a zip file and run it to full capacity on Scholarly Commons computers.

Although Docear is not quite the all-encompassing research suite the creators envisioned, there are still lots of funky little features not found in other services. For example, in the Tools and Settings tab you can add map locations with OpenMaps (unfortunately there is no search function — you have to zoom and select your location) to add a geographic component to your otherwise mental map,which you can see by clicking on “View Open Maps Location” later.

Screenshot of Docear Open Maps features

You can also add time alerts for time management in Tools and Settings. But before we get ahead of ourselves, it’s easy to add a node with keyboard shortcuts and the node panel in the toolbar. You can add links to websites and other nodes right in your mind map by right clicking on a node. Apparently, you can add formulas to your mind map using LaTex but I didn’t try it, as I am not one of the people who cares about that sort of thing.

And while you do have the option of writing in Docear itself, there is a plugin for MS Word, but only on Windows. On the one hand, the plugin is old and hasn’t been updated in a few years, and it doesn’t work on the computers at Scholarly Commons. But on the other hand, since it’s based in BibTeX, if it actually does work the way they say it does, you should be able to use it with any BibTeX bibliography, and not just Docear. This means, it could give you that MS Word integration that you might be lacking with another reference manager.

Overall, if you wanted a reference manager and document annotator that is easy to get started on this is NOT the one for you, but for those patient enough to deal with the learning curve, Docear can be a good addition to your research strategy. I really hope this project gets the funding it needs to fully live up to its potential, but for now it’s still a solid option for researchers looking for a unique way to organize their work.

Scholarly Smackdown: Google Keep vs. Trello

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Looking for a very basic project management tool to create to-do lists, stay on-track, and maybe even get things done? On today’s Scholarly Smackdown we will discuss two possible options: Google Keep and Trello.

Both tools feature:

  • Bulletin board format that shows a page of lists
  • No cost options
  • Online-only web application with neither a desktop version nor a way to work offline
  • Good usability
  • Mobile versions for iOS/Android that you can sync across platforms
  • Limited customization

Both allow users to:

  • Make to-do lists and checklists
  • Incorporate images into lists
  • Collaborate with groups — with unlimited team members
  • Add due dates for list items to be completed
  • Archive your lists when you’re done
  • Pin lists to be a priority
  • Put all the things needed for a project in one place and share with folks who need to see it

Google Keep is Google’s app for note-taking and task managing for yourself and your groups.

Google Keep screenshot

Google Keep’s advantages are:

  • Built-in and included in Google Apps so it’s ready to use and available to Illinois students
  • The app version for Chrome has a web scraper capability, which allows you to attach things you’ve scraped to your lists
  • Integrates with Google Docs, so it is easy to send work you have in Keep to Google Docs
  • Allows you to draw in your notes
  • Fairly intuitive
  • Reminders and Notes are separate; Reminders are notes that include a time stamp
  • Voice notes on Android

Trello was developed by Fog Creek Software and is now owned by Atlassian, the wizards behind our wiki. It is a great software for staying on top of things.

Screenshot of Trello

Trello free version advantages are:

  • Easy to sign up for and get started
  • Easy-to-access documentation and instructions
  • Much more granularity possible at the free level than Google Keep; you can create cards within lists within boards
  • Attach files up to 10 MB to your boards
  • Due dates on cards
  • One Power-up which is a special feature and there are a lot to choose from, such as integration with Slack

The paid versions of Trello are:

Overall, both Google Keep and Trello are great products for basic task management for both yourself and your groups. If you want something simple and love all things Google then Google Keep is probably your best option. However, if you are planning something with a lot of sub-steps and you want to be able to create really detailed checklists then you probably will prefer Trello. And of course, let us know about your favorite digital tools for preventing scholarly smackdowns in the comments!

TiddlyWiki Review

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Here at Commons Knowledge we like to talk about all of the various options out there for personal and information management tools, so today we’re talking about TiddlyWiki!

“It’s like a hypertext card index system from the future” -Jeremy Ruston, in the TiddlyWiki intro video

To summarize: this is a British, somewhat tricky to use, free and open source note taking and information management linked web wiki platform made in Javascript. TiddlyWiki is mostly used for task management. Still, if you’re looking for a way to manage all of your information and feeling particularly adventurous (and not at all into aesthetics, as TiddlyWiki is an ugly website — though CSS customization is possible) you might enjoy TiddlyWiki.

Everything in TiddlyWiki is a small piece, a tiddler —  a British word for a small fish — which you can stack, arrange, and link however you like. Tiddlers are individual units that you can incorporate into larger tiddlers through a process called “transclusion.” To have a tiddler all you need is a title. This is very similar to Scalar CMS where all content is equal, and can be linked or embedded in each other to tell both linear and nonlinear stories. However, TiddlyWiki is not as pretty and is focused more on note-taking and information management than presentation.

An example of a Tiddler

There are a lot of options for customization, as well as an active community that keeps the project alive and adds new customization options for different purposes (such as for writing a thesis). There is a WYSIWYG editor and formatting options, though you will still need to become familiar with the WikiText language in order to use more interesting formatting and customization. The WikiText language is similar to Markdown. There is also a plugin that will let you write your tiddlers in Markdown if you are more familiar and comfortable with that. You can add images and scribble all over them, as well as save links to websites with a download and some difficulty. TiddlyWiki includes search functionality and tagging, which is especially useful, as you can click on a tag you get a list of pages that have that tag. There are encryption plugins, which I have not tested, to create password-protected tiddlers and offer some basic security (though neither I nor the creators of TiddlyWiki endorse putting sensitive information on one of these sites).

You can use TiddlyWiki with TiddlySpot, Tiddly Desktop, or various browsers as well as node.js or a variety of other options for saving the program. Get started here.

Setting up where your files save so you can find them again is probably the hardest part of setting up a TiddlyWiki. It creates one HTML file that you update as you save. If you’re using Firefox and using the Firefox plugin I recommend downloading an empty wiki and copying it from your Downloads and pasting it to your G:Drive or another place where files aren’t deleted automatically. After, you can click on the cat icon and set it to automatically save your changes to your file on the Desktop.

Clicking on

Note: Don’t save things to the Desktop on Scholarly Commons computers long-term, as files are routinely erased.

Let us know in the comments if you have any other personal information management systems that need more love!

Writing the next great American novel, or realistically, finding the “write” tools to finish your thesis

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The Scholarly Commons is a great place to write the next great American novel; in fact, I’m surprised it has not happened yet (no pressure dear patrons — we understand that you have a lot on your plates). We’re open Monday-Friday from 9-6 and enjoy a well-lit, fairly quiet, and overall ideal working space, with Espresso Royale and the Writing Center nearby. But actually getting that writing done, that’s the real challenge. Luckily, we have suggestions for tools and software you can use to keep writing and stay on track this semester!

Writing Your First Draft:

Yes, MS Word can be accessed for free for University students through the Web Store and you can set it up to better address your research needs with features like the Zotero and Mendeley plugins to incorporate your references. And don’t forget you can go to Word > File > Options > Proofing > Writing Style and select Grammar and Style and Settings to set what Spellcheck will check for so that passive voice gets underline. However, believe it or not, there are word processors, other than MS Word, that are better for organizing and creating large writing projects, such as novels, theses, or even plays!

Scrivener

Scrivener is a word processor created with novelists in mind that lets you organize your research and notes while you are writing. With an education discount, a license for Scrivener costs $38.25. Scrivener is very popular and highly recommended by two of the GAs here at Scholarly Commons (you can email Claire Berman with any questions you may have about the software at cberman2 [at] illinois.edu). To really get started, check out our online copies of Scrivener: An Absolute Beginner’s Guide and  Scrivener for Dummies!

Mellel

Unfortunately, Mellel is only available on Mac. An educational license for the software costs $29. To some extent Mellel is similar in style and price to Pages for Mac, but also shares similarities with MS Word for Mac. However, this word processor offers more options for customizing your word processing experience than Pages or MS Word. It also provides more options for outlining your work and dividing sections in a way that even MS Word Notebook version does not, which is great if you have a large written work with many sections, such as a novel or a thesis! Mellel also partners with the citation managers Bookends and Sente.

Markdown Editors like Ulysses

Ulysses is a simple and straightforward word processor for Mac, but you do have to write in Markdown without a WYSIWYG editor. It costs $44.99 for Mac and $24.99 for iOS. However, it has many great features for writers (such as built in word count writing goals for sections of a paper, and Markdown makes outlining work very easy and simple). We have discussed the value and importance of Markdown elsewhere on the blog before, specifically in our posts Digital Preservation and the Power of Markdown and Getting Started with Markdown, and of course, want to remind all of our lovely readers to consider doing their writing in Markdown. Learning Markdown can open up writing and digital publishing opportunities across the web (for example: Programming Historian tutorials are written in Markdown). Plus, writing in Markdown converts easily for simple web design without the headache of having to write in HTML.

Staying Focused:

Maybe you don’t want to buy a whole new word processor. That’s fine! Here are some tools that can help creating the “write” environment to get work done:

Freedom : costs $2.50 a month, so Freedom is not free, indeed. This is an an app that allows you to block websites and even the internet, available for Mac, Windows, iOS devices. This app also has a lock feature that will not allow you to make changes to what is blocked for a set period of time.

RescueTime : another app option. Taking a slightly different approach to the rest here, the lite version of this app helps you track how you use your time and what apps and websites you use the most so that you can have a better sense of what you are doing instead of writing. The premium version, which costs $54 a year, allows you to block distracting websites.

SelfControl: a Mac option but Open Source, with community built Linux and PC versions, and most importantly it’s free! This app allows you to block websites, based on their server, for a set period of time, in which there is basically NOTHING you can do on your computer to access these sites. So choose which sites to block and the time limit wisely.

Editing Tools:

Hemingway

Named after Ernest Hemingway, this text editor is supposed to help you adapt his style of writing, “bold and clear.” When you paste your text into the free web version, the applet gives you the text’s reading level as well as pointing out instances of awkward grammar, unnecessary or complicated words and adverbs, and sentences that are too long or too complicated.There’s a Desktop version available for $20 though I honestly don’t think it’s worth the money, though it does give another simple space on your computer to write and get feedback.

A note about Grammarly 

This is an alternative to MS Word spell check with a free version to add to your browser. As a browser add-in, it checks automatically for critical spelling and grammar mistakes (advanced ones cost a monthly fee) everywhere you write except situations where you’d really want extra spell check such as Google Docs and can be wonky with WordPress. You can always copy and paste into the Grammarly window, but at that point, you’re probably better doing spell check in MS Word. There are also only two versions of English available, American and British (take that Australia!). If you are trying to learn English and want instantaneous feedback while writing on the internet, or studying for high school standardized tests, or perhaps a frequent YouTube commenter in need of a quick check before posting, then Grammarly is for you. For most people at Scholarly Commons, this is a plugin they can skip, though I can’t speak for the paid version which is supposed to be a little bit better. If you uninstall the app they try to guilt trip you, so heads up.

SpellCheckPlus: It’s BonPatron in English! Brought to you by Nadaclair Language Technologies, this web-based text editor goes beyond MS Word’s spellcheck to help identify grammar errors and ways to make your writing sound more normal to a native (Canadian) English speaker. There is a version that costs money but if you don’t import more than the allotted 250 words of text at one time you will be fine using the free version.

Let us know what you think and any tools we may have missed! Happy writing!

And to learn more and find more great productivity tools, check out:

Personal Information Management LibGuide

Getting Started With Paperpile

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Did the Paperpile Review leave you interested in learning more?

To use Paperpile you need an Internet connection, Google Chrome, and a Google account. Since student/personal use accounts do not require a dot edu email, I recommend using your Google Apps @ Illinois account  for this because you can fully use and enjoy unlimited free storage from Google to store your PDFs. Paperpile offers one month free; afterwards, it’s $36 for the year. You can download the extension for Chrome here. If you already use Mendeley or Zotero you can import all of your files and information from these programs to Paperpile. In order to use Paperpile, you will need the app on each version of Chrome you use. It should sync as part of your Chrome extensions, and you can install it on Chrome on University Library computers as well.

You can import PDFs and metadata by clicking on the Paperpile logo on Chrome.

Paperpile import tool located just right of the search bar in Chrome

On your main page you can create folders, tag items, and more! You can also search for new articles in the app itself.

Paperpile Main Menu

If you didn’t import enough information about a source or it didn’t import the correct information you can easily add more details by clicking the check mark next to the document in the menu and clicking edit on the top menu next to the search box for your papers.

Paperpile

Plus, from the main page, when you click “View PDF” you can also use the beta annotations feature by clicking the pen icon. This feature lets you highlight and comment on your PDF and it saves the highlighted text and comments in order by page in notes. It can then be exported as plain text or as very pretty printouts. It is rectangle-based highlighting and can be a little bit annoying, especially when highlighting doesn’t always covered the text that was copied. Like a highlighter in real life you cannot continue to highlight onto the next page.

Highlighted and copied sentence split by page boundary

When you leave the app, the highlighting is saved on the PDF in your Google Drive and you can your highlights on the PDF wherever you use Google Drive. The copied text and comments can be exported into a very pretty printout or a variety of plaintext file formats.

Print screen of exported annotated notes on Paperpile

Not the prettiest example but you get the idea.

Once you get to actually writing your paper you can add citations to your paper in Google docs by clicking the Paperpile tab on your Google doc. You can search your library or the web for a specific article. Click format citations and follow the instructions for how to download the add-on for Google docs.

Paperpile cite while you write in Google Docs

I didn’t try it but there’s a Google Docs sidebar so that anyone can add references, regardless of whether or not they are a Paperpile user, to a Google Doc. I imagine this is great for those group projects where the “group” is not just the person who cares the most.

Troubleshooting

Paperpile includes a support chat box, which is located on your main page, and is very useful for troubleshooting. For example, one problem I ran into with Paperpile is that you cannot change the page number to match what it actually is in the article and page number is based on the PDF file in the notes feature. I messaged and  I got a response with a professional tone within twenty-four hours. Turns out, they are working on this problem and eventually PDFs will be numbered by actual page number, but they can’t say when they will have it fixed.

For other problems, there is an official help page  with a lot of instructions about using the software and answers to frequently asked questions. There is also a blog and a  forum which is particularly nice because you can see if other people are experiencing the same problem and what the company plans to do about it.

Scholarly Commons runs a variety of Savvy Researcher workshops throughout the year including personal information management and citation managers. And let us know in the comments about your favorite citation/reference management software and your way of keeping your research organized!

And for the curious, the examples in this post are based from the undergraduate research collection in IDEALS. Specifically:

Kountz, Erik. 2013. “Cascades of Cacophony.” Equinox Literary and Arts Magazine. http://hdl.handle.net/2142/89474.

Liao, Ethel. 2013. “Nutella, Dear Nutella.” Equinox Literary and Arts Magazine. http://hdl.handle.net/2142/89476.

Montesinos, Gary. 2015. “The Invisible (S)elf: Identity in House Elves and Harry Potter.” Re:Search: The Undergraduate Literary Criticism Journal 2 (1). http://hdl.handle.net/2142/78004.

Review: Paperpile Citation Manager

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Are you addicted to Google Docs and are looking for a citation manager, PDF reader, or research workflow system? Do you wish you could just cite while you write in Google docs like you do with Zotero or Mendeley in Word? Do you have an extra $36 a year to spare?

Then you might want to try Paperpile!

Paperpile App Main Menu

Paperpile is a simplified reference management system and research workflow program for Google Chrome created by three computational biologists based in Vienna.

Pros:

  • Easy to use
  • Can organize your sources when you’re trying to write a paper or doing readings
  • A lot of explanatory text in the app
  • Allows you to import metadata and PDFs from your browser (similar to Zotero’s one click import) and asks you if you want to add the item (PDF and details) to Paperpile
  • The annotations feature makes readings and notes for classes a lot of fun with very pretty colors
  • When the PDF is not encrypted, if you highlight the text it will copy the highlighted text into notes with your annotations that you can then copy and paste when writing a paper
  • Wide range of document types and citation styles
  • You can cite while you write in Google Docs
  • Provides look up to find similar journal articles to what you are researching, which allows you to do research through the app, especially if you’re doing research from science databases
  • Keyboard shortcuts
  • 15 GB of free space through Google
  • Good customer service
  • Thorough explanatory material
Highlighted text with annotations in the Paperpile app

Excerpt from Montesinos, Gary. 2015. “The Invisible (S)elf: Identity in House Elves and Harry Potter.” Re:Search: The Undergraduate Literary Criticism Journal 2 (1). https://www.ideals.illinois.edu/handle/2142/78004.
And check out Re:Search: The Undergraduate Literary Criticism Journal and more great undergraduate research in IDEALS!

Cons:

  • High cost ($36), especially compared to solid free options like Mendeley and Zotero
  • Requires Internet access
  • Although the company is in the process of developing a plugin for MS Word, currently, Paperpile is heavily reliant on Google and Google Drive
  • Paperpile is a proprietary software and a startup so there are risks that they will go out of business or be bought by a larger company
    • Though, should the worst happen Paperpile uses open standards that will allow you to get your PDFs, citations out — even if they are in an ugly format — as well as the highlighted text saved in your PDFs, which can be downloaded through Google Drive
  • Paperpile is a very new product and there are still a lot of features to be worked out
    • I will say however that it is a lot less buggy than a lot of comparable reference management / PDF annotation software that have been around longer and aren’t classified as in beta, like Readcube and Highlights

Paperpile is comparable to: Mendeley, iLibrarian, colwiz, Highlights.

Learn more about personal information management through our PIM Libguide, various Savvy Researcher workshops and more! Let us know about your strategies for keeping everything organized in the comments!