MOOCs and me

MOOCs (Massive Open Online Courses)  are an interesting development in higher education.  At their most impressive, they are a way for brilliant educators to reach thousands of students at a time, all across the world.  MOOCs have the potential to remove educational barriers like learning disabilities, economic constraints, geographic realities, or busy life schedules.  My alma mater, Cornell, launched their first wave of MOOCs last semester.  Cornell prides itself on catering to “any person, any study” and its not hard to see how MOOCs can drive this mission forward.

Of course, MOOCs are entering the scene at a time when higher education is reconsidering its educational tenets.  A traditional classroom brings to mind stuffy tiered lecture halls with esteemed professors reciting knowledge to enraptured students (Tom Wolfe’s I Am Charlotte Simmons comes to mind).  Educators have long suspected that these teaching methods are not ideal, but recent high profile publications have provided clear evidence that there are better ways to engage students.  Active learning is a broad term, but it encompasses classrooms where students participate in activities or discussions. Instead of tuning out a professor (intentionally or not), a student must engage the material.

MOOCs certainly don’t have to embody one form of education or another.  They have the capacity to be very active educational formats.  Discussion boards, problem sets, live text or video chats, course projects, and peer review all require students to work alone or together to master material.  On the other end of the spectrum, a MOOC can be a string of youtube videos or reading assignments, with multiple choice quizzes at the end of each section.  The value of such courses is questionable.  When a MOOC is offered for free, it’s not a big problem.  But as institutions offer “online certificates” for participation, the issue becomes an important one.

I’ve been participating in the Data Science course track on Coursera, and am rounding the bend on the second module.  This sequence of courses is put together by Brian Caffo, Jeff Leek, and Roger Peng at John Hopkins University.  I think that theres a lot of positive examples in this course.  The community message board is quite active, with attentive TAs who field questions.  Much of the coursework is active- each week I’ve been asked to write my own code to accomplish certain tasks.  The course itself is crowdsourced for grading, a sort of peer-review lite.  The swirl() modules deserve a special commendation- these educational R packages teach you how to perform tasks in R right within the R environment.

On the other hand, the weekly video lectures don’t offer very much beyond some light structure for the course.  Skipping them and relying on a search engine for the quizzes is more economical and less frustrating (nothing is worse than listening to a lecture series and taking extensive notes, only to be quizzed on what I view as minutiae).

Overall I’m very grateful to the professors for putting the course together, and even more grateful that they offer it for free online (coursera offers an optional paid certificate).  Where the course succeeds, it exemplifies the potential for active learning in MOOCs.  At the end of the day, we have to remember that this is the internet.  There are seemingly limitless resources for education available.  What we demand from formal instruction is mentorship, guideposts, motivation, and accountability.  We can watch a video lecture any day- coursework should ignite our curiosity to work with the material ourselves (or at least hold a deadline over us to demand we do!).  Ultimately, we won’t learn unless we’re motivated and take the time to do so.

If you’re interested in learning more about active learning practices, I recommend using the resources that “Centers for Teaching Excellence” at various universities (including Cornell) have put together.

Bioinformatician’s Pocket Reference !!

Handy coding reference guide.


It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core IT toolkits on their plate. It has become mandatory to be able to mould different code snippets to build our own custom workflows, and thus keeping syntax at our fingertips has become essential.Although Google is best way to get syntax problem solved, it is not a bad idea to keep reference sheets is our smartphones or stick out some printed sheets on the back of your door, in the old fashion way!!
1) Apache

2) Awk/Gwak

3) C

4) C++

5) Debian

6) Git


8) Java

  9) LaTeX

10) Mathematica

11) Matlab

12) MySQL

13) Perl

14) PHP

15) Python

16) R

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Scientific writing is dry (but that’s OK)

This morning I was delighted to come across the IMA Fungus journal.  Put out by the International Mycological Association , the journal title (which primarily publishes species announcements and descriptions) playfully introduces each organism with a friendly “Hello, I’m a fungus!”  The truth is, scientific literature is seldom so fun and informal.

When I submitted my PhD dissertation draft to my committee, perhaps the most common complaint I got was that I was having too much fun with the writing.  Given the choice, I  always prefer to be playful than bland in my writing.  In science, this isn’t necessarily a good thing.  Primary scientific writing values clarity and correctness.  In trying to evoke vivid descriptions, I like to describe science with flair, pushing my metaphors to the absurd.  For example, I wrote that fungi forge weapons to wield against the parapets of plant defense, or that they brew novel molecules in musty cellular laboratories.

The problem is that while I have a lot of fun writing statements like this, it empowers organisms with sentience and intent.  It is incorrect.  So such statements are refined to purge embellishments (fungi produce molecules that specifically target host defenses, and produce diverse secondary metabolites in specialized cellular structures).

Me being dangerously informal during my exit seminar.
Me being dangerously informal during my exit seminar.

Obviously we should strive to be correct in our communication of science.  When publishing, it must be clear what we did, what we observed, and what we believe these results mean.  We must write knowing that english is not the primary language of those who are interested in our experiments.  But does this mean that we can’t have any fun?  I can’t speak for all scientists, but my love of biology is not sterile and precise.  It is colorful and messy.  It is most certainly anthropomorphized (despite my higher faculties being well aware that fungi are not sentient creatures).

We scientists are a fun bunch.  This fact is more than evident from any academic conference (take the raging party that is the Fungal Genetics Conference).  But our writing is often denser than German fitness bread.  Maybe it’s impossible to get away from that in our formal writing without introducing ambiguity or compromising our professionalism.  I suppose some day I’ll find out.

How many copies of my thesis/dissertation should I order?


You’re finished!  You’ve spent hours writing and rewriting your thesis or dissertation (such semantics!), braved your defense, and spent even more time addressing your committee revisions (to say nothing of the years of hard work that got you here).  Congratulations.  Time to submit and watch Buffy the Vampire Slayer for eight days straight, right?

This sums up my feelings on graduation nicely.
This sums up my feelings on graduation nicely.

A couple of issues I hadn’t thought about came up before I clicked submit, however.  One of these was how many copies of my dissertation I should order.  I had no clue, and I was pretty braindead by this point.  So I thought I’d list some people who might want a copy for future generations of sleep-deprived and deadline flaunting scholars.  If you forget somebody, that’s OK- I was able to re-order a single copy for ~$80.


Your parents, and perhaps grandparents, are a given.  After 4+ years of not being able to explain your work to anyone, having a 5 pound coffee table book to gesture at is going to make their day.  Don’t forget to include them in the acknowledgements!


I didn’t order a copy for any friends, but that doesn’t mean you won’t want to.  Finish before a friend who started the same year?  Nothing rubs it in their face quite like a printed copy of your dissertation.  It sure is an expensive snub, though.

Your advisor

Do not forget a copy for your advisor.  Again, write something nice in the acknowledgements or pay the price.  I learned the hard way that “To my favorite advisor” isn’t acceptable.

Your committee

Did you receive a lot of guidance from your committee, or shed a lot of tears in their office?  This can be a nice gesture of thanks.

I keep my thesis on my person at all times (if only to stop bullets).
I keep my dissertation on my person at all times (if only to stop bullets).

Your lab

This is the one place where someone might open your dissertation for very practical purposes.  Over the course of my time at Cornell I’ve consulted the dissertations of others surprisingly often, be it for a unique perspective on the literature or to see the nuances of methodology not written out in peer-reviewed publications.

The library

Your campus library probably prints a copy of your dissertation for its own purposes, but its worth checking that this isn’t expected of you.  How else could you perform the infamous $20 experiment, hiding a crisp bill in the meat of your dissertation and returning year after year to see if its disturbed?  Also, some departments keep separate dissertation collections- see if you are expected to contribute!


This probably goes without saying.  You may feel like you never want to see this cursed book again, but you probably will.  Even if its only to drag it out as a war story, or to prove to your date that you really can run a southern blot.

Celebrity burgers a reality

Back in September last year, I explored some possibilities that the “Stem Cell burger” opened up.  Perhaps the most far-fetched idea I had was to produce meat from cloned celebrity stem cells.

It seems this idea wasn’t as absurd as I thought.  A new company has launched called Bitelabs, claiming they will produce celebrity-derived meats in salami-form.

Always push the boundaries in taste

So is it a hoax or a real company?  The internet isn’t quite sure what to make of it.  My previous post covered the feasibility of such an endeavor, but the ethics remains a gray zone. In the meantime, I fully support the discussion, and I applaud Bitelabs’ understated strategy.  Personally I’d be interested in trying a cloned meat product, regardless of who the donor was.! 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 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, 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 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.