Running R in samsung tab pro 12.2

It's been a long time since I have wrote anything on this blog. I came home for a break and decided to work on some things other than school work!

I have always wanted to turn my samsung tab pro 12.2 into fully running linux machine with working python and R. This will allow me to work / study in cafes with more ease :) Here's what I have done

1) Gain root access.
- Among various sites out there, I found this procedure to work for my machine
 (http://androidxda.com/root-samsung-galaxy-note-pro-12-2-sm-t900). After this was done, I accessed SuperSU app and disabled KNOX.
- I also find this site useful for my set-up. This includes remapping the key and fixing wifi setup (http://graemehill.ca/turning-a-galaxy-note-pro-into-a-linux-laptop/).

2) Disable SELinux permission
- using "Terminal Emulator for Android" app, I typed

$ su
$ setenforce 0

- I checked whether the permission setting by going "Setting" --> "General" --> "About Device". "SE for Android status" is now changed to "Permissive".

3) Install Linux Deploy
- I found this method more intuitive than others. I followed instruction here (http://www.linuxuser.co.uk/features/run-linux-on-android-part-2) For more detail, here's what I have done.

- I created a new profile and changed the profile to

Distribution: Ubuntu
Distribution suite: trusty
Installation path: "/data/media/linux.img"
Desktop environment: LXDE (I tried GNOME, but wasn't successful)
Select components to install: (Check for "Desktop Environment", "SSH server", "VNC server"; DO NOT CHECK "X server"... It doesn't work, at least for me)

- Then, I clicked "Install at the top of the profile setup page. This allowed me not to see any "fail" next to functions that gets mounted.

- Clicked "Start" button on the top

4) Use JuiceSSH app to access the linux that has been deployed
- I used the instruction in the link above (http://www.linuxuser.co.uk/features/run-linux-on-android-part-2). Here's a gist of it.

1. To access the distro from a terminal, launch your SSH app and (if using default settings) log into android@ with the ‘changeme’ password. You can now enter standard Linux commands from the terminal.

5) Install R
- Now, here's the problem.. For some reason, R doesn't get installed fully but I got it to work just enough for now. I will need to keep on searching or whoever is reading this have some insight on this. Here's the problem and what I have done

what's done
- I used vim to add "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" in "/etc/apt/sources.list" file. One can pick any CRAN mirror of choice by following the instruction here (http://cran.r-project.org/bin/linux/ubuntu/). The link to the CRAN mirror sites are here (http://cran.r-project.org/mirrors.html).

- I added the key by typing

$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 

- One can also follow the instruction here for adding key (http://cran.r-project.org/bin/linux/ubuntu/). 

- After the above, I installed "r-base-core". One may be wondering why I didn't install "r-base" and here's the problem. It won't work. There are broken packages which I cannot identify. But, "r-base-core" will get R 3.0.1 in the machine and that's good enough for now until this site updates? (https://launchpad.net/ubuntu/+source/r-base)

$ sudo apt-get install r-base-core

- The machine doesn't have some packages I need, so I manually installed some.

$ sudo apt-get install gcc make

- Now I have R 3.0.1 running (also python but haven't fiddled with it too much yet). I also installed bioconductor tools too so it's all good for me now.

problems

- "r-base" doesn't get installed in simple "sudo apt-get install r-base" method
- R 3.1.2 doesn't get installed
- tablet rebooting randomly (but I think I have a fix currently..)

As a computer novice (I study genetics), above is what I have done (for fun!!). If anyone have a better solution, let me know! Hope my experience help those who are trying to do a similar thing.


*** Edits 2014.12.19
7) In order to fix tablet restarting problem, I flashed in the recovery and factory reset the tablet. For some reason, the superuser access was still present. I updated all my apps including linux deploy and others used above. In conclusion, the restarting problem was gone and I still had root access with all the keyboard fixes :)

8) I re-did installing ubuntu trusty in the Linux Deploy and installed R as above. Interestingly, "r-base" installed normally without any issues!! :)

9) The R version was still 3.0.1 so I decided to do some fiddling.

- add ppa repository
$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install software-properties-common
$ sudo add-apt-repository ppa:marutter/rdev

- install r-base
$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install r-base
--> no error but r-base, r-base-dev are kept back. I think I will just wait until (https://launchpad.net/ubuntu/+source/r-base) site updates.

my days in phd program

So what do I do for my phd studies?

Wake up really late. Go return a Harry Potter DVD to Redbox. Go to gym. Eat lunch(?) for 1hr and 30min at home. Then go to lab to change cell media. Act like I'm reading papers. Go to beer hour in 3hrs that's on every friday. Go home to eat dinner. Play sc2 with my brother.....

:D

Need a break? pursue a phd program...

jk. don't do it.

Two hit model and de novo mutation

Even though there are arising evidence that autism may be caused by environmental factors, many still believe that there are strong genetic influence in autism (Deletions and duplication of 16p11.2 is single most common cause of autism in genetic analysis and duplication of 7q11.23 also correlates with the cause of autism). In my search for my phd project, I looked into what genetic mechanisms may contribute to this increasing incidents of Autism and I found Two-hit model and the influence of de novo mutation.

If there is a molecular-phenotypic pathway, single mutation in that pathway may cause a change in phenotype (e.g. intellectual disability, depression, etc). Then, a second mutation (that may be caused from spontaneous mutation, de novo) can push the phenotype to autism or more severe neurological disorder. Even though it's only a model at this point, I thought it was very convincing. It supports the fact that autism is oligogenic disorder and also it's a partially heritable disorder. Partially heritable because there are high concordance rates between siblings in a family or twins in regards to ASD. Also, two-hit model explains how autistic kid can be born from a perfectly behaviorally normal parents (excluding environmental factors)...

so what do I do with this information...? Find these recessive genes? Breed mice with multiple known autism contributing genes to see the rate of autistic progeny? I don't know....hahaha.... :(

Autism, autism, autism!!!!

Autism? yes, that will be the topic I will be studying for next 4-5 years since I joined the lab that studies autism like crazy.

http://www.einstein.yu.edu/labs/brett-abrahams/default.aspx?id=28778

Here's the info on the lab that I am part of for my phd years. The lab is pretty cool with chill PI, a nurse, post-doc, and another student. People are nice. My other fellow phd student baked me ice cream/oreo brownies. I get a nice desk and a lab bench. But, I have a serious problem.

I don't have my own project!!!!!!!!!

why is that a problem? maybe not too severe right now, but it will be bad if this continues for a long time as my qualifying exam approaches and my PI is not gonna like me for being dumb...aite, so i seriously need to find something to investigate...and i kinda got excited when i ran into this news article.

http://www.stanforddaily.com/2011/07/14/study-finds-environment-more-important-to-predicting-autism-risk-than-genetics/

People often thought that genetic components have a high effect in the cause of autism...and these papers came out saying environmental factors have higher effect than heritable genetic components in the cause of autism. So what? I thought this could be a lead to my thesis project. I don't know what this could go into, but I just need to read, read, and read. Let's see how this goes.

Benjamin Franklin's self eulogy.

The body of B. Franklin, Printer, 

Like the Cover of an old Book,

Its Contents torn out,

And Stript of its Lettering & Gilding,

Lies here, Food for Worms,

But the Work shall not be lost,

For it will as he believ'd appear once more

In a new and more elegant Edition

Corrected and improved 

By the Author.

- Benjamin Franklin

----
Dear Benjamin Franklin,

Your eulogy really excites me for that day when our creator will finally perfect us and raise us up!!I look forward to seeing the new edition of you on that day and thank you for encouraging me even when you are in the grave.

-YJ

This Graduate school stuff is making me more nerdy..

Everyday I catch myself turning more and more into a nerd. Why? Here's an example...During a sermon, the pastor was talking about how all four of his children are different in many ways even though they are from same mom and dad...ok, normally I would just think, "Hmm, ok whatever" and will go back to listening to the sermon... 

But, not this time. I spent next five minutes thinking about homologous recombination and how that may lead to expression of varying genes, and finally result in the development of four children that are very very different, etc...yea, it's pretty nerdy and even I can't believe I just did that. I didn't tell anyone that I did it too...but why am I recording it here? Someone told me it will be funny looking back at these kind of things later in the future. Even though I'm really bad at blogging, I guess I will give it a shot.

Farewell, my ET prayer group. It was fun :)

Perfect for the cold rainy day~! with Kimchi and some....Kkakduki...

Johnny orders Bibimbap at the Gomtang restaurant....