TiddlyWiki Review

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!

Learning how to present with Michael Alley’s The Craft of Scientific Presentations

Slideshows are serious business, and bad slides can kill. Many books, including the one I will review today, discuss the role that Morton Thiokol’s poorly designed and overly complicated slides about the Challenger O-rings played in why the shuttle was allowed to launch despite its flaws. PowerPoint has become the default presentation style in a wide range of fields — regardless of whether or not that is a good idea, see the 2014 Slate article “PowerPointLess” by Rebecca Schuman.  With all that being said, in order to learn a bit more about how to present, I read The Craft of Scientific Presentations by Michael Alley, an engineering communications professor at Penn State.

To start, what did Lise Meitner, Barbara McClintock, and Rosalind Franklin have in common? According to Michael Alley, their weak science communication skills meant they were not taken as seriously even though they had great ideas and did great research… Yes, the author discusses how Niels Bohr was a very weak speaker (which only somewhat had to do with English being his third language) but it’s mostly in the context of his Nobel Prize speech or trying to talk to Winston Churchill; in other words, the kinds of opportunities that many great women in science never got… Let’s just say the decontextualized history of science factoids weaken some of the author’s arguments…

This is not to say that science communication is not important but these are some important ideas to remember:

Things presentation skills can help you with:

  • Communicating your ideas with a variety of audiences more effectively
  • Marketing your research and yourself as a researcher more effectively
  • Creating engaging presentations that people pay attention to

Things presentation skills cannot help you with:

  • Overcoming systemic inequality in academia and society at large, though speaking out about your experiences and calling out injustice when you see it can help in a very long term way
  • Not feeling nervous especially if you have an underlying anxiety disorder, though practice can potentially reduce that feeling

For any presentation:  know your topic well, be very prepared, and actually practice giving your talk more than you do anything else (such as making slides). But like any skill, the key is practice practice practice!

For the most part, this book is a great review of the common sense advice that’s easy to forget when you are standing in front of a large audience with everyone looking at you expectantly. The author also offers a lot of great critiques of the default presentations you can churn out with PowerPoint and of PowerPoint itself. PowerPoint has the advantage of being the most common type of slideshow presentation software, though alternatives exist and have been discussed in depth elsewhere on the blog and in university resources. Alley introduces the Assertion-Evidence approach in which you reach people through presenting your research as memes images with text statement overlay. Specifically, you use one sentence summaries and replace bullet points with visualizations. Also you have to keep in account Murphy’s Law, where slide color or a  standard font not being supported can throw off a presentation. Since Murphy’s Law does not disappear when you create a presentation around visuals, especially custom-made images and video, you may need more preparation time for this style of presentation.

Creating visualizations and one sentence summaries as well as practicing your speech to prepare for these things not working is a great strategy for preparing for a research talk. One interesting thing to think about is if Alley admits that less tested methods like TED (Technology-Entertainment-Design) and pecha kucha work for effective presentations, how much of the success of this method has to do with people caring and putting time into their presentation than a change in presentation style?

Overall this book was a good review of public speaking advice specifically targeted towards a science and engineering audience and hopefully will get people taking more time and thinking more about their presentations.

Presentation resources on campus:

  • For science specific, the definitely check out our new science communication certificate through the 21st Century Scientists Working Group and the Center for Innovation in Teaching and Learning. They offer a variety of workshops and opportunities for students develop their skills as science communicators. There’s also science communication workshops throughout the country over the summer.
  • If you have time join a speech or debate team (Mock Trial or parliamentary style debate in particular)  it’s the best way to learn how to speak extemporaneously, answer hostile questions on the fly, and get coaching and feedback on what you need to work on. If you’re feeling really bold, performing improv comedy can help with these skills as well.
  • If you don’t have time to be part of a debate team or you can’t say “yes and…” to joining an improv comedy troupe take advantage of opportunities to present when you can at various events around campus. For example, this year’s Pecha Kucha Night is going to be June 10th at Krannert Center and applications are due by April 30!  If this is still too much find someone, whether in your unit, the Career Center, etc. who will listen to you talk about your research. Or if you have motivation and don’t mind cringe get one of your friends to record you presenting (if you don’t want to use your phone for this check out the loanable tech at the UGL!)

And for further reading take a look at:

http://guides.library.illinois.edu/presentation/getting_started

Hope this helps, and good luck with your research presentations!

Spotlight: JSTOR Labs Text Analyzer

JSTOR Labs has recently rolled out a beta version of a JSTOR Text Analyzer. The purpose of the Text Analyzer is different than other text analyzers (such as Voyant). The JSTOR Text Analyzer will mine documents you drop into its easy-to-use interface, and then breaks it down by topics and terms, which it will then search JSTOR with. The result? A list of JSTOR articles that relate to your research topic and help fill your bibliography.

So, how does it work?

You simply drag and drop a file– their demo file is an article named “Retelling the American West in the Museum” –, copy and paste text, or select a file from your computer and input it into the interface. What you drag and drop does not, necessarily, have to be an academic article. In fact, after inputting a relatively benign image for this blog, the Text Analyzer gave me remarkably useful results, relating to blogging and learning, the digital humanities and libraries.

Results from the Commons Knowledge blog image.

After you drop your file into JSTOR, your analysis is broken down into terms. These terms are further broken down into topics, people, locations, and organizations. JSTOR deems which terms it believes are the most important and prioritizes them, and even gives specific weight to the most important terms. However, you can customize all of these options by choosing words from the identified terms to become prioritized terms, adding or deleting prioritized terms, and changing the weight of prioritized terms. For example, here are the automatic terms and results from the demo article:

The automatic terms and results from the demo article.

However, I’m going to remove article’s author from being a prioritized term, add Native Americans and Brazilian art to the prioritized terms, and change the weight of these terms so that the latter two are the most important. This is how my terms and results list will look:

The new terms and results list.

As you can see, the results completely changed!

While the JSTOR Text Analyzer doesn’t necessarily function in ways similar to other text analyzers, its ability to find key terms will help you not only find articles on JSTOR, but use those terms in other databases. Further, it can help you think strategically about search strategies on JSTOR, and see which search terms yield (perhaps unexpectedly) the most useful results for you. So while the JSTOR Text Analyzer is still in beta, it has the potential to be an incredibly useful tool for researchers, and we’re excited to see where it goes from here!

Meet Eleanor Dickson, the Visiting HathiTrust Digital Humanities Specialist

Photo of Eleanor Dickson

This latest installment in our series of interviews with Scholarly Commons experts and affiliates features Eleanor Dickson, the Visiting HathiTrust Research Center Digital Humanities Specialist.


What is your background education and work experience? What led you to this field?

I have a B.A. in English and History with a minor in Italian studies. As an undergraduate I worked at a library which was a really fun experience. I also took an archival research trip to Florida for my undergraduate thesis research and realized I wanted to do what the archivist was doing. I have a Masters in Science in Information Studies from the University of Texas at Austin, and completed a postgraduate fellowship at the university archives / Emory Center for Digital Scholarship. And now I’m here!

What is your research agenda?

I research scholarly practice in humanities and digital scholarship, specifically digital humanities with a focus on the needs and practices in large scale text analysis.I also sometimes help with the development of train the trainer curriculum for librarians so librarians can be better equipped with the skills needed to teach patrons about their options when it comes to digital scholarship.

Do you have any favorite work-related duties?

My favorite work-related duties are talking to researchers and hearing about what they are up to. I am fascinated by the different processes, methods, and resources they’re using. With HathiTrust I get to talk to researchers across the country about text analysis projects.

What are some of your favorite underutilized resources that you would recommend to researchers?

I wish more people came to the Digital Humanities Savvy Researcher workshops. If people have suggestions for what they want to see PLEASE LET US KNOW.

(To see what Savvy Researcher workshops might tickle your fancy click here to check out our complete workshop calendar.)

If you could recommend only one book to beginning researchers in your field, what would you recommend?

Debates in Digital Humanities, which is an open access book available free online!

Need assistance with a Digital Humanities project? E-mail Eleanor Dickson or the Scholarly Commons.

Juan Pablo Alperin: Does Our Research Serve the Public, or Only Ourselves?

Juan Pablo Alperin.

Mark your calendars: Juan Pablo Alperin is coming to campus on March 9th to give a lecture titled, “Does Our Research Serve the Public, or Only Ourselves?” The Talk will place in Illini Union 407 at 4:00 pm.

Here is the official abstract for the talk:

Traditionally, scholarly efforts have focused on making research available and discoverable among scholars, scientists, and related professionals. However, with the onset of the digital era and the electronic circulation of research and scholarship, a new model of “open access” to this body of work has taken hold, one which is committed to making research freely and universally available online. The same digital era has given us the possibility of capturing and measuring how knowledge is produced, disseminated, and used, both within and beyond this traditional group of professional researchers. In his talk, Dr. Alperin will present research findings, gathered through novel strategies and tools, that the public is already taking advantage of the growing body of freely available research. However, despite the growing evidence and a stated interest that our work have societal impact, many of our scholarly publishing practices continue to keep the research out of the public’s hands. As it becomes easier to provide evidence of public interest even in the most obscure and esoteric topics, academics of all stripes will be increasingly challenged to ask ourselves if our scholarly publishing system is serving the public’s best interests, or simply our own.

And here is Juan Pablo Alperin’s bio:

Juan Pablo Alperin is an Assistant Professor at the Canadian Institute for Studies in Publishing and the Associate Director of Research with the Public Knowledge Project at Simon Fraser University. He is a multi-disciplinary scholar, with training in computer science (BMath, University of Waterloo), social science (MA Geography, University of Waterloo), and education (PhD, Stanford University), who believes that research, especially when it is made freely available (as so much of today’s work is), has the potential to make meaningful and direct contributions to society, and that it is our responsibility as the creators of this research to ensure we understand the mechanisms, networks, and mediums through which our work is discussed and used.

 

A list of his publications and presentations can be found at http://alperin.ca/cv, and he can be found on Twitter at @juancommander.

For more information on the event, see our Scholarly Commons Speaker Series page and the Facebook page for this event! Hope to see you there!

Scholarly Smackdown: StoryMap JS vs. Story Maps

In today’s very spatial Scholarly Smackdown post we are covering two popular mapping visualization products, Story Maps and StoryMap JS.Yes they both have “story” and “map” in the name and they both let you create interactive multimedia maps without needing a server. However, they are different products!

StoryMap JS

StoryMap JS, from the Knight Lab at Northwestern, is a simple tool for creating interactive maps and timelines for journalists and historians with limited technical experience.

One  example of a project on StoryMap JS is “Hockey, hip-hop, and other Green Line highlights” by Andy Sturdevant for the Minneapolis Post, which connects the stops of the Green Line train to historical and cultural sites of St. Paul and Minneapolis Minnesota.

StoryMap JS uses Google products and map software from OpenStreetMap.

Using the StoryMap JS editor, you create slides with uploaded or linked media within their template. You then search the map and select a location and the slide will connect with the selected point. You can embed your finished map into your website, but Google-based links can deteriorate over time! So save copies of all your files!

More advanced users will enjoy the Gigapixel mode which allows users to create exhibits around an uploaded image or a historic map.

Story Maps

Story maps is a custom map-based exhibit tool based on ArcGIS online.

My favorite example of a project on Story Maps is The Great New Zealand Road Trip by Andrew Douglas-Clifford, which makes me want to drop everything and go to New Zealand (and learn to drive). But honestly, I can spend all day looking at the different examples in the Story Maps Gallery.

Story Maps offers a greater number of ways to display stories than StoryMap JS, especially in the paid version. The paid version even includes a crowdsourced Story Map where you can incorporate content from respondents, such as their 2016 GIS Day Events map.

With a free non-commercial public ArcGIS Online account you can create a variety of types of maps. Although it does not appear there is to overlay a historical map, there is a comparison tool which could be used to show changes over time. In the free edition of this software you have to use images hosted elsewhere, such as in Google Photos. Story Maps are created through their wizard where you add links to photos/videos, followed by information about these objects, and then search and add the location. It is very easy to use and almost as easy as StoryMap JS. However, since this is a proprietary software there are limits to what you can do with the free account and perhaps worries about pricing and accessing materials at a later date.

Overall, can’t really say there’s a clear winner. If you need to tell a story with a map, both software do a fine job, StoryMap JS is in my totally unscientific opinion slightly easier to use, but we have workshops for Story Maps here at Scholarly Commons!  Either way you will be fine even with limited technical or map making experience.

If you are interested in learning more about data visualization, ArcGIS Story Maps, or geopatial data in general, check out these upcoming workshops here at Scholarly Commons, or contact our GIS expert, James Whitacre!

Getting Started With Paperpile

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

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!

 

Image of Research is Open for Submissions!

image-of-research-banner-1

In conjunction with the Graduate College, the Scholarly Commons is pleased to host the Image of Research competition for the 2016-2017 academic year!

The Image of Research is a celebration of the diversity and breadth of graduate student research at the University of Illinois at Urbana-Champaign. Graduate and professional students from all disciplines are invited to submit entries consisting of an image that represents their research (either concretely or abstractly) and a brief written narrative.

Submissions will be accepted through January 15, 2017, after which judges will select a list of semi-finalists. From the semi-finalists, the judges will award four prizes given as professional development travel funds:

  • First Prize: $500
  • Second Prize: $300
  • Third Prize: $200
  • Honorable Mention: $100

Awards will be presented at a reception on April 5, 2017 in conjunction with the Annual Graduate Student Appreciation Week. Attendees of the reception will have the opportunity to vote for a semi-finalist to receive the People’s Choice Award ($100).

For more information about this year’s competition, or to submit an entry, visit the Image of Research website. Past entries and winners can be viewed in the online gallery and in IDEALS.

Best Practices Resources: The Research Clinic

Mary Homans, John Staley and Edward Till, working on a model of a proposed NYA (National Youth Administration) training camp at the Landscape Architectural School. Iowa State College. Ames, Iowa

Jack Delano, “Mary Homans, John Staley and Edward Till, working on a model of a proposed NYA (National Youth Administration) training camp at the Landscape Architectural School. Iowa State College. Ames, Iowa.” Negative. May 1942. Library of Congress collection of Farm Security Administration/Office of War Information Black-and-White Negatives, http://www.loc.gov/pictures/item/owi2001004703/PP/. Accessed September 6, 2016.

As a researcher, it can sometimes be difficult to draw the line between what is and is not appropriate behavior while working with those participating in your project. That’s why the Office of Research Integrity (ORI) and the Office for Human Research Protections (OHRP) created “The Research Clinic,” an interactive training video, which can help researchers learn how to protect their research participants and to avoid misconduct.

Now, it’s not quite World of Warcraft, but you choose one of four characters (my personal favorite is Megan Boyle, “a research assistant who has difficulties obtaining informed consent and following research protocols” who has a lot of student loan debt) and work through different video scenarios as that character. The goal of the program is to go back in time, and figure out what steps your character should have taken in order to have done their research ethically. The tutorial also links the viewer to optional information about aspects of the research process they need some extra information on.

“The Research Clinic” manages to mix an ethics lesson with an online game that mimics a game of whodunit with engaging humor and personality. However, in order to use it, one needs an up-to-date version of Adobe Flash Player, as well as a good Internet connection, as the videos can take time to load. “The Research Clinic” has several accessibility options, including closed captions and text voice over, as well as several keyboard shortcuts for easy movement throughout the series.

An important aspect of “The Research Clinic” is the human aspect. Each character’s story begins with some information about their life and personality, which allows you to get to know them, and to sympathize with their situation. It humanizes the researchers, and reminds the viewer that people who engage in research misconduct may not necessarily be bad people, going out of their way to tamper with evidence as they laugh manically and twist their mustache. Rather, research misconduct can occur when people are put into stressful situations and make a bad decision (or three).

The right decision may not necessarily be the easy decision, but when you’re working with human participants, taking the time to think about what you will do can make all the difference.