Make It Stick: 5 Steps to Designing a Syllabus That Promotes Recall and Application | Harvard Business Publishing Education


Make It Stick: 5 Steps to Designing a Syllabus That Promotes Recall and Application | Harvard Business Publishing Education
— Read on hbsp.harvard.edu/5-steps-to-designing-a-syllabus-that-promotes-recall-and-application/

May be we can learn a thing or two following this article from Harvars Business School, when designing a curriculum for bioinformatics students or medical students. Example curriculum included in the article above.

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A non-linear world.


The world is not linear.

Most of the time you need multiple variables.

Sometimes you would need a square, a cube, or even a log.

Even with lots of trials, it might still be difficult to fit in.

And, if you try to hard, you might end up being too over-fitting.

After all, it is quite a curvaceous world.

The Mexican Mestizo populations genome


Accidentally stumbling upon this paper about the Mexican genome study.

The Mexican people have already ventured into their genome since 2009! Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico, published in PNAS 2009.

Although the sample size was not very big and the genotypes were done on a platform with only 100000 SNPs, they started this nine years already.

Anonymous blood samples from 300 non-related and self-defined Mestizos and 30 Amerindian Zapotecos were collected in 7 states in Mexico: Guanajuato, Guerrero, Sonora, Veracruz, Yucatan, Zacatecas, and Oaxaca (ZAP). Genotyping was performed according to the Affymetrix 100K SNP array protocol…

May be there are several other publications coming out after this one?

HFS+ File system is NOT case-sensitive but case-preserved!


  • On MacOS system, cloned a git repository with two directories: 1) Assignment and 2) assignment. [Notice the A vs a].
  • Couldn’t find the folder “Assignment” locally
  • Remote git seems to have this folder.
  • Tried to find out whether local git repository was not updated or not.
  • Checked the commit ID, checked the log and confirmed that the local repository is up-to-date!
  • OMG … what happened!!!!!!!!!!!!!!!!!!!!!!!!!!!
  • Tried to check whether the correct git command was used. Read about git fetch, git pull, etc, etc.
  • Feeling frustrated.
  • Got no work done.
  • Suspicious that may be there’s some problem with case-insensitive on MacOS. Therefore, tried Google “macos filename case sensitive”.
  • Finally, found the answer to the problem on Google https://apple.stackexchange.com/a/22304/179773

Really?!

See the result below.

 

case insensitive macos
case-insensitive but case-preserved

Reviewing NGS Variant Call with IGV


Although I don’t really support doing a brute-force approach doing manual variants review, if you only have some of your top signal that you would like to confirm for further wet-lab experiment validation, IGV might still proves helpful. 

This review by Robinson, et al from a group at UCSD shed some lights and detail into how you can do the manual review in IGV: http://cancerres.aacrjournals.org/content/77/21/e31

I also found the IGV manual describing all the options in the preference menu to be quite useful: https://software.broadinstitute.org/software/igv/Preferences

Quick start on “Creating a new docker container”


As a bioinfomatician, one might get into the situation that requires you to run that software in certain environment again and again, unfortunately, on various computers.

The good news is there’s this thing called “Docker”, a container technology that might allow you to do so easier. If you are a fan of “Singularity”, you already know what I’m talking about here.

Without further ado, here’s what you will need:

  1. You’ll need to install Docker on your computer. Also, get a docker hub account. You’ll need this to deposit your docker image.
  2. Get the source code or the pre-compiled software that you want to run
  3. Create a new working directory to store your Dockerfile (see below)
  4. The most important step, which will determine how complicate your life will be authoring a Dockerfile​ is how you choose your base image.
    • Assuming you are trying to run java application, your best bet for the base image would be this image family java:openjdk-8-jre

Consider the following example (stolen from Broad’s Institute tutorial for FireCloud https://software.broadinstitute.org/firecloud/documentation/article?id=9453)

Continue reading “Quick start on “Creating a new docker container””