Gamification for positive habits

For as long as I can remember, I’ve enjoyed video games.  If there’s leveling up, character optimization, or strategic battles to be had, I’m in.  At my worst, I can burn an entire Sunday; I’ll admit that I’ve banned myself from playing DOTA2 after one too many late nights.

At their best, video games can be a vehicle for me to work on my goals.  For example, I’ve been changing the language settings on my videogames to Spanish.  I’m not learning a ton of practical vocabulary, sure, but immersion is a great thing, even if it’s silly.

The vocabulary can be a little silly, but immersion is good.

A newer concept for me is Gamification.  At it’s core, gamification is about turning stuff that you want to get done into a game.  Duolingo is a simple example of this.  Complete vocabulary lessons to level up and unlock new lessons.  When accomplishing tasks results in leveling up and earning rewards, the same compulsion that lead me to waste my teen years playing Everquest will now work in my favor.  That’s the idea, at least, and I manage to keep up with Duolingo fairly well.

Duolingo tracks your daily language progress through experience points (XP).   The site encourages you to make progress every day.  Looks like I'm not too consistent this week.
Duolingo tracks your daily language progress through experience points (XP). The site encourages you to make progress every day. Looks like I’m not too consistent this week.

HabitRPG is MUCH more ambitious with this concept.  It goes all out, giving you an avatar with the ability to earn mounts, group up with friends, and fight bosses.  You get to choose your “quests” so it can be tailored for whatever purpose you’d like.  If you set a daily goal to study for one hour, you’ll gain experience points and gold for completing it, but take damage each day you feel to check it off.  You can then spend accumulated gold to buy rewards that you specify, or in-game swag.

HabitRPG takes a fantasy RPG approach to positive habit building.

There’s no doubt that consistency and repetition are the keys to setting up positive habits.  This is where a tool like HabitRPG shines- it rewards positive habits in a fun and imaginative way.

I’m setting up my HabitRPG account to encourage more productive use of my free time.  In a future blog post, I’ll reflect on how gamification can be used in the laboratory.

Lab notebook software

Last year, I wrote about using Evernote as my digital lab notebook.  With the release of Findings, a new digital notebook software from the people who created my favorite reference management software Papers, I thought I would reflect on my digital notebook needs.

A digital notebook should be:

  • Indexed and searchable, with both automatic (embedded text searching)  and manual (tags) search functions.  Evernote handles this quite well- I can easily manage what tags I have available and organize them how I wish, but searching my notebook will also find terms in embedded word documents and PDFs, for example.
  • OS integration.  The great thing about drinking the Apple koolaid is these apps can work well across platforms.  We don’t tend to have our laptop on our experimental benchtop; being able to pull up a notebook on my iPhone is great.
  • Multimedia friendly.  My notebook is a mix of text, snapshots, data annotated in Powerpoint, excel files, word documents, and PDFs.  Again, Evernote handles this quite well.  It falters a bit in flexibility when printing out my notebook- usually my images don’t come out formatted quite right and I end up with a single image per page.
A sample printout from my notebook.  Note that I have a mix of media types (annotated powerpoint files, notebook scans, raw text).  While Evernote holds them all seamlessly, printing to this PDF (and into a paper notebook) results in clunky blank pages.  There is also no support for printing header information: ie experiment name, tags, dates... I have to manually write the file name on each page afterwards.
A sample printout from my notebook. Note that I have a mix of media types (annotated PowerPoint files, notebook scans, raw text). While Evernote holds them all seamlessly, printing to this PDF (and into a paper notebook) results in clunky blank pages. There is also no support for printing header information: ie experiment name, tags, dates… I have to manually write the file name on each page afterwards.
  • Traceable.  Ultimately, a lab notebook is for tracing the lineage of data.  Whether this is at the troubleshooting or the writeup phase, I need to understand what the starting material, protocol, and resulting output were at each stage of the experiment.  Science is seldom perfect, and a good lab notebook can prevent some confusing mixups (was that DNA sample prepared before or after I optimized the pH of buffer X?)  Here is where Evernote isn’t perfect, largely because this is a science problem.

I’m looking forward to trying out Findings and reporting back how it improves on these key issues (and others I haven’t thought about).

Scoop.it! and content curation

In the past, I’ve written about the importance of setting up custom newsfeeds for current publications in your field, and using Citeulike to share references.  While these tools can be useful for discovering and archiving content, they are not ideal for sharing and disseminating it.  Gathering content and distilling it for others is an art: the art of content curation.

Lately I’ve been using Scoop.it for content curation and outreach.  I created two main channels: one for science stories in the news, and another for new research in my field of fungal genetics.  By picking a key paragraph from the discussion or abstract, as well as a catchy image, I can easily pin small blurbs for each article (called scoops) to a news stream.  Each feed is easy to skim through, can be tagged and annotated, and allows me to easily review articles I was interested in.  RSS feeds for each topic can be fed elsewhere, such as a flagship brand website.

Aggregated scoops on a stream.
Aggregated scoops on a stream.

Perhaps most importantly, Scoop.it integrates other social media quite handily.  By default, I tweet all of my scoops.  Articles of general interest (generally from my science news stream) I often post to Facebook, which sometimes trigger a discussion.  This keeps me engaged in science communication, as well as in practice using social media (that I might otherwise let lie fallow).

There are certainly other tools for content aggregation, but the free Scoop.it account works quite well (a subscription offers several handy features, including sharing curation duties for a topic with others).  Feel free to leave a comment recommending other services.

RSS readers

(This post is a continuation of my science RSS series, found here)

Once you’ve identified RSS feeds you’d like to follow, you need to choose an RSS reader.  This is where the fruits of selective RSS subscription are much sweeter than signing up for email notifications.  Notifications go to my inbox, where they are drowned out by the day-to-day requirements of the academic life.

RSS feeds, on the other hand, wait patiently in the reader, separate, sorted, and ready to be skimmed.  Flipping through my reader every few days, and posting  articles of interest to citeulike, or Scoop.it (which I haven’t written about yet, but will), I stay on top of the big news in the science world, and the details relevant to my research.  Your reader may sync up to the cloud, your social media, or other reading, storage, or notetaking apps.  You can use your RSS reader to skim headlines and send the interesting bits to other programs, or you can do all your reading in the reader, depending on your personal preference.

But what reader to use?

Google Reader used to be the reader of choice.  Unfortunately, Google is discontinuing reader, and several readers have risen to fill its shoes.

Screen Shot 2013-06-04 at 7.01.28 PM

I currently use Feedly.  It syncs with my Google account, and lives in my browser, in harmony with my work and home computer.  I have my feeds roughly divided into peer reviewed publication, science news, and play/misc., which is good enough for me.  Feedly sports an ipad app, which is slick and intuitive.  Oh, and it’s free, which is a huge plus.

The feedly ipad interface, standard issue.  I removed all the default categories.
The feedly ipad interface, standard issue. I removed all the default categories.

Cnet has reviews of other RSS readers. They come in all shapes in sizes, from feature heavy standalone apps to minimalist browser integrated readers.  Shop around and go with what feels good- the most important thing is that you can integrate it into your work flow.  I used to use RSSowl for my feeds, which is also free.  But, as a standalone app, I used it less and less, until I stopped checking my feeds all together.  The most important rule for any app is that you use it!

For me, I will use a program if it fits well into my existing workflow.  I skim headlines in my reader.  Items of interest are sent to either pocket, evernote, citeulike, or scoop.it, depending on if they are for my personal consumption, work-related, or science outreach and communication related.  I will expand on these specific avenues in a later post.

A digital notebook

When I first started graduate school, I kept an old-fashioned notebook.  A 4×4 quad ruled Roaring Spring Lab Notebook.

My first carbon paper lab notebook

It had gridlines, it had carbon paper (The carbon sheets remain, unperturbed, at the back of the notebook), it had Thomas Edison on the cover scienceing it up.  It was everything I thought science would and should be.

As a tool for keeping track of what I did for later reference, however,it was a complete disaster.

I’m not an organized person by nature.  I work in spurts, I don’t keep careful track of what I’m doing.  I often have to go back and fill in the details.  This means writeups I would intend to return to later were buried under experiments I would go ahead with in the meantime.

I also am not a linear person (or perhaps science is not a linear endeavor).  One day I would work on project X, the next, project Y.  Science works that way, sometimes, project X needs a week to grow, sometimes project Y sits in the fridge while the primers are synthesized and delivered in the mail.

Both of these traits make for a messy, and extremely confusing lab notebook.  Sure, I could have kept one notebook for each project I was working on.  But what about when I’d perform an experiment that fit into two projects?  Sometimes I will perform an assay using two sets of mutants, for two separate reasons.  Would I double-copy the experiment?  Perhaps this is when I should have actually used that carbon paper.

No, instead, I switched to a standard 3-ring binder after my first year in graduate school.  I could re-define the boundaries of a given project easily, add and remove page dividers for each project, and easily add in printed pages.

Looking back on my research project (and looking forward to where I may be next), I think if I could do it again, I would keep a digital notebook first and foremost.  I did keep a digital notebook, using the app Mori.  Unfortunately, development on Mori ceased long ago, and I used it exclusively for digital notes.

No, I think the ideal thing to do would be to keep a purely digital notebook, with printed backups of results and summaries in a three-ring notebook.

A digital notebook is searchable.  It doesn’t have to be linear.  I can look for all projects with a given gene or technique, and pull them all out.  A good notebook is tagable (and hopefully well tagged.)  I don’t have to decide if an experiment goes in notebook A or notebook B.  It just gets tagged AB, and goes into the digital notebook.

I also don’t have to wait until my results are processed to add them to the notebook.  This is a big one.  Raw unprocessed data files (such as .nexml tree files that are a finished product, but need to be visualized, or microscopy experiments that take a fair amount of post processing effort) go right in the notebook.

A sloppily generated note on media generation gets filed away digitally.
A sloppily generated note on media generation gets filed away digitally.

Scanning in the above sheet, for example, lets me find it no matter what project I’m working on in the future, rather than digging through years of failed and succesful experiments in different notebooks when writing my materials and methods later.  Note that I added a minimal number of tags, but wrote out the key media ingredients (different forms of iron) for search purposes.

I’ll talk more about the best way to organize a digital notebook and tips for making the most of it (for example, sharing and compiling status updates for the boss).

Multitasking help: Slicer

Sometimes it’s the little things that make a big difference.

Slicer is a tiny app.  Its sole function is to reduce the active screen window to 50%, 33%, or 66% of the screen height.

Screen Shot 2013-06-07 at 1.34.47 PM

What do I use Slicer for?  When I’m copying data from a figure or excel file into a text writeup.  When I’m browsing the internet and taking notes at the same time.    Reorganizing data folder structures, dragging from one window to another. Anytime I’m multitasking.   Or half-tasking (procrastinating and working at the same).  And when am I not doing one of those two things?

Slicer makes hopping between apps, and working with multiple apps at the same time, so much easier.
Slicer makes hopping between apps, and working with multiple apps at the same time, so much easier.

This blog is really about ways to be a better scientist; efficient use of technology is one of them.  Slicer is one of those apps that I can’t believe I rely on so heavily- was it  so bad to drag and resize manually?  All I can say, working in a post-Slicer environment, where all of my windows fit into one of my designated work zones perfectly, I could never go back to my primitive ways.

Get your work on the cloud: Dropbox

Dropbox is simple and intuitive.  Make a folder on your computer that is automatically backed up to a cloud storage account.  Suddenly, the files you work on and the data you access syncs across devices, at home and at work.  Plus, you can dropbox folders with others.

Screen Shot 2013-05-18 at 5.04.58 PM

Write at home, go in to work, and the latest version is on dropbox without passing it between USB sticks.

Collaborating on a manuscript?  Keep the current manuscript and reference library in a shared folder.  No more emailing files back and forth (and, most frustratingly, losing comments or edits as versions are passed back and forth.  In theory, Microsoft Skydrive should be the ideal solution for this sort of thing, as it boasts seamless editing of word files as google drive does.  Unfortunately for both of these services, I wasn’t able to get it to seamlessly integrate as well without doing the word processing on the web interface.  Fun fact: if it doesn’t work easily for the boss, it isn’t going to happen.

Fortunately, collaborators tend to be elsewhere in the world, and while I’m a night creature, my advisor writes in the morning.  This means we aren’t all trying to edit the same Dropbox shared document at once.

Another nice use for papers is syncing my Papers library.  I wish that Papers had this kind of service automatically, but it’s a nice work around.  Keep your papers library on dropbox in a secure location, and you can sync it between macs.  Just be careful to close down Papers when you are done with it – otherwise, you’ll get conflicting libraries.

There are a million other uses for Dropbox, but these are the ones I regularly take advantage of.