Monday, April 28, 2014

Just starting: Epigenetic control of Gene Expression, at Melbourne University

So there's a new MOOC over at Coursera starting up today.

Why take this MOOC?

Because I really liked the genetics part of MIT's 7.00x Introduction to Biology, and wanted to learn more. Someone on the forums there pointed to this course, and here I am.
Plus, I'm kind of in an Australian mood, what with the Astrophysics course at ANU.

What's epigenetics anyway?

It's the study of how protein synthesis (from DNA by way of RNA) varies, between individuals, between cells in a specific individual, and at different points in time for a specific cell, without changes to the actual genome (the DNA sequence).
Basically that's why monozygotic twin cats may have completely different colours.

Sounds complicated.

That's right. Though you may spell it "fun".
I guess that'll be the real test, whether the instructor (Dr Marnie Blewitt) can make it easily understood. Based on the first 2/3rds of the first week's lecture, I'd say she does a good job of presenting the subject matter in an organized way that conveys the important information in a digestable package.

Right; let's go!

Sunday, April 27, 2014

Courses I wish I'd taken

There are only so many hours a week one can devote to learning. Especially when one has a full-time job (indeed, one where official work-hours laws are something of a joke) and a family. So while I am quite involved in my MOOCing up − I do not own a television, I only watch Game of Thrones every week, and I've all but stopped reading fiction − I can't take all the courses that take my fancy; I make choices. And sometimes, in retrospect, they're not the best. So, here's a quick list of courses I didn't take, but wish I had:
  • Stat2.2x: Introduction to Statistics: Probability I did take Stat2.1x and did sort of enjoy it. I mean, while I did study statistics in school many years ago, it had always been the fifth wheel of the horse-carriage (as the − French − saying goes), meaning that in the French prepa-engineering school system, stats have always been underemphasized when compared to, say, algebra or calculus. So it's the mathematical field I'm the least familiar with, although I've grown convinced it's by far the most important one to know if one wants to make sense of the world. So the UC Berkeley course was a welcome refresher (and Prof. Adhikari has a very nice conversational tone). Yet, I don't necessarily want to become a statistics expert, so stopping at Descriptive Statistics sounded like a good idea; besides I was gearing up for Mount Sinai's Introduction to Systems Biology, which promised to be very intensive, and Harvard's Data Analysis for Genomics. As it happens, I dropped from both, and it may have been wiser to stick to the Stats curriculum.
    Actually, I just checked: I've still got time to take the course. I'm two weeks late in a 5-week course and having missed one homework and the midterm it's going to be slightly more difficult to get a certificate, but still; if my experience with Stat2.1x applies here, I can probably speed through the first three weeks. Registered.
  • China − all six parts, from Harvard. It's now well-established that for most of history, the world has been dominated by China. The recent era of European predominance is only a parenthesis that's closing as I am typing these words; yet I hardly know anything about China, its culture and history. Maybe it's a good idea to get some perspective. That's the kind of courses I view as "background culture" more than something directly useful, much in the same way as the Economics course I took from Caltech; these tend to take a backseat. That's rather unfortunate.
  • 14.73x The Challenges of Poverty from MIT. Sort of the same thing; also, Esther Duflo and Abhijit Banerjee are very-well-regarded figures in the economics blogosphere (that I follow more or less closely). I am quite convinced that world inequality is − well − indecent and, rationally speaking, completely inefficient; and I am certain that Duflo and Banerjee have some very interesting insights to give on that subject. Yet I somehow missed that February course.
  • Functional Programming Principles in Scala from EPFL. Besides the fact that I've driven through Lausanne a number of times and therefore consider it as part of my backyard, Scala is a language that's gotten a lot of traction recently, and that I've been meaning to look into sometime − and who can talk about it better than the creator of Scala? Sadly, my schedule is already overfull in April/May and so, it will be another time.
Of course, I may still take the courses out of schedule. But I am weak, and need the momentum from schedules, homework, finals, etc. to get going.

Dropping PH525 - Data Analysis for Genomics

Yesterday I wrote that it was "extremely unlikely I [would] get a certificate" for that course.

Well, it's official: I'm dropping out of PH525 - Data Analysis for Genomics (from Harvard via edX). It's not that the material is bad in any way; I just can't commit the necessary time and attention to the course. It's too close to what I'm doing with MIT's Analytics Edge class; there's only so many hours I can do R in a week.

Besides, next week (aka "tomorrow") I start both the Epigenetics course at Melbourne University and the MongoDB Advanced Operations course at MongoDB. If I'm already struggling to watch the Harvard lectures now, I dare not think what it will be in a few days.

So, well. I'll watch for repeats (or watch the archived course in due time).

Saturday, April 26, 2014

Current MOOCs Rundown: April 2014 edition

Right, so, I'll try to make a fixture of this summary of my current MOOCing situation.

MIT - 15.071x: The Analytics Edge


"Analytics" is a fancy name for "data mining", or perhaps it is the other way around? Anyway, it's the science of applying basic statistics to make sense of data, and/or to make better informed guesses. Examples include Amazon's smart suggestions, medical prevention (based on a number of variables, estimate the probability that a given person develops a serious condition), or risk assessment (what insurance premium should a 81-year-old male who drives 6000 km per year in an Audi but has had no accidents in ten years pay?) It includes such trendy sub-fields as machine learning and data visualization.

This course is a hands-on introduction to the field and R, a widely-used open source data-analysis-oriented programming language (sort of the open source alternative to SAS). As such it's pretty good, although at times I am slightly annoyed with the dumbing-down (they don't have to tell us every time to "Hit Enter" after typing a command − after 8 weeks, you'd think the students who hanged on had got the idea).

One of the better ideas they had was to hold a competition during week 7: based on a training set, students are supposed to submit predictions for a testing set; they are graded on the "Area Under the Curve", sort of a measure of the accuracy of the predictions. That week has probably been the one when I've learned the most; basically we've been thrown into the sea and had to learn to swim by ourselves. However, having this as a competition (students are ranked) is not such a great idea: with only a handful of tools at our disposal, all students are within a few percent of each other, which makes random fluctuations (estimations do include some randomness) disproportionately important. With a score of 0.727 I am currently ranked in the 642nd (out of about a thousand students who have submitted predictions); but the best student only has a score of 0.75 or so. While I have no doubt that he has a slightly better model than mine, I feel it slightly discouraging to be ranked according to a randomness-including metric.

Anyway, I fully intend to follow the course through to the certificate.

ANU − ASTRO1x Greatest Unsolved Mysteries of the Universe


An introduction to astronomy and astrophysics, by two very high-level researchers from the Australian National University, one of whom has won a Nobel prize no less.
This course is very introductory, so aimed squarely at students with little math or physics baggage, and that's fine for me (while I can do the math involved here with my eyes closed, I haven't really ever studied quantum physics beyond reading pop-science books; I dimly remember a chemistry professor writing down the Schrödinger equation on the blackboard, but it may have been only to scare us away from the subject.)

This course I am taking for fun, and for bragging rights (I've been taught by a Nobel winner, can you say the same?) I'm doing the homework while it's easy and not too time-consuming, but I guess I'll stop at some point, and doubt I'll be taking the final exam.

University of Copenhagen − Diabetes, a Global Challenge


My 4-year-old son has Type 1 diabetes mellitus, so I am naturally interested in the topic. This course however mainly discusses Type 2, which is an altogether different (and more poorly understood, although much more prevalent) disease. The approach is "panoramic": each week, a different professor gives a lecture on a particular aspect of the diabetes challenge; so far we've had an epidemiological overview, a biochemical rundown of the metabolic processes involved, a lecture about physical exercise and diabetes prevention, and one about "the clinical manifestations of diabetes".

Obviously, each week will be variably interesting. While the first three were very involving, the fourth was a lot harder to follow. Still, I find it worthwhile to stick to it. I don't, however, give special importance to getting a certificate for this course so I won't do anything beyond lectures (homework, peer-reviewed essays, etc.) that takes me more than, say, half an hour.

Harvard − PH525x Data Analysis for Genomics


Another R / data mining course. It's deeper (and more focused) than the MIT one, so potentially more interesting (but harder). Besides, the instructor is the author of Bioconductor, the most-widely used biological data analysis package for R, so it's nice to have him talk about this stuff (he's a good teacher too).
However I don't really have the mental bandwidth to keep up with the course (on top of the other ones plus work). It's extremely unlikely I'll get a certificate or even listen to all lectures; I haven't decided whether to drop the course altogether or stay registered to go back to the archived course whenever I feel ready for it.

All MOOCed Up

Hullo. This is a blog about MOOCs, or rather, about the MOOCs I take.

Why MOOCs?

This will be the topic of a full post, I believe, but generally: partly because I wanted to find out if at my advanced age (36) I still had the mental agility that led me through rather successful studies fifteen years ago, partly because I wanted to broaden my horizons.

What MOOCs?

I have taken eleven MOOCs to date (and passed ten of them; the remaining one I decided I couldn't care less about getting a certificate for, but it was still one of the more enjoyable courses I did take). Three more are still running, and I am registered for a further nine-ish. (All this in eight months; I don't believe in doing things halfway). I'll list them all in a minute, but generally they tend to fall in the following categories:
  • Biology, medicine and life sciences − because I loved bio but dropped it after high school graduation, perhaps the worst mistake I ever did, or perhaps not;
  • Computer science − because that's my day job and it's always good to learn new tricks;
  • Data mining, data analysis, statistics, economics − because it helps me making sense of the world I live in;
  • Any other things that strike my fancy.
Also, I favour interdisciplinary courses − e.g. bioinformatics, or statistics applied to genomics.

Where MOOCs?

Now that's a twofold question. I have taken, and am taking, MOOCs from both edX and Coursera (I am trying to fit a Udacity course into my schedule too; since it's self-paced it's the one that tends to slide). Mostly, I came to MOOCs after following a course at MIT OpenCourseWare, so I was naturally led to edX and that's where I took the vast majority of my classes (nine out of eleven finished courses so far).

In terms of institutions, that's been a mixed bunch. Only MIT, Harvard and Berkeley have I taken multiple courses from (I'm registered for a second course at Rice, but that's "only" the second part of the first course so doesn't really count). Generally, while last fall all courses I took were from US institutions, this year I'm doing courses from China, Australia and Europe as well. The US is still over-represented, but I guess it's only natural: they've basically invented MOOCs.

Who's MOOCing?

I'm a French software engineer (my full title is "Java Integration Team Leader" − means I do more presales, management and troubleshooting that actual coding nowadays, sadly). I have a fully European background, with British and Irish ancestry and a couple of years spent working in Sweden. In that respect I'm a little bit more cosmopolitan (and speak vastly better English) than your average Frenchman, but I wouldn't consider myself "well-traveled" by a long stretch. Education-wise, I'm a graduate from École Centrale de Nantes, where I majored in Engineering with a Computer Science specialization (nowadays ECN students are required to take two majors, one in an engineering field and one in a cross-disciplinary, "professional" subject, for instance project management, industrial design, etc.; but this didn't exist in my time).

Curriculum (ye olde virtual CV if you like)

Right, so, a quick rundown of the courses I've taken, am taking, and am registered for (at the time of this writing), in chronologicalish order:

Finished courses (unless specifically noted I have obtained a certificate of some sort for each, or the certificate is upcoming):
In addition, I'm registered for the "Intro to Hadoop and MapReduce" at Udacity, but can't quite fit it in the schedule so it keeps sliding; and I have started, but dropped after a week or two (for various reasons), a bioinformatics and an introduction to systems biology at Coursera (University of Toronto and Icahn School of Medicine at Mount Sinai respectively), as well as M101J MongoDB for Java Developers at MongoDB (too little time, too much redundancy with the DBA course, and anyway I was just beta-testing it to decide if I should send some of my team at work to take it).

About this blog

So what should you expect from this blog? I hope to write down some notes about, in no particular order:
  • each of the course I'm taking − the idea is to give my personal feeling about the course, how it fits in my "curriculum" such as it is (i.e. put it in relation with the other courses), etc.
  • the various platforms − it's quite interesting to contrast edX and Coursera (we'll see about Udacity later!)
  • the various types of certificates, and why get a certificate anyway?
  • the MOOCs I'd like to see, the MOOCs I'd like to take
  • how I organize my schedule, the various planners, mobile apps, etc.
  • some generalities, whatever goes through my mind
While I try to be generally informative, let me be clear that this is a blog about my MOOCs and how I feel about them. Subjectivity is unavoidable.

Do not expect reviews such as:
This course is rubbish.
But do expect to see, occasionally, things like:
This course isn't what I was expecting. Given my current workload and energy level, it's better I drop it.

Anyway… enjoy.