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.
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.
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?
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
Aug 09 (GenomeWeb) Geisinger team announced their approach to return secondary finding the genomic tests to participants.
Read the full article on AJHG at https://www.cell.com/ajhg/fulltext/S0002-9297(18)30236-2
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:
- You’ll need to install Docker on your computer. Also, get a docker hub account. You’ll need this to deposit your docker image.
- Get the source code or the pre-compiled software that you want to run
- Create a new working directory to store your
Dockerfile (see below)
- 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
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””