Bioinformatician’s Pocket Reference !!

It is amusing how the brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5-minute discussion with neighbors (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 mold different code snippets to build our own custom workflows, and thus keeping syntax at our fingertips has become essential.Although Google is the 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

7) HTML

8) Java

  9) LaTeX
latex

10) Mathematica

11) Matlab

12) MySQL

13) Perl

14) PHP

15) Python

16) R
R

17) Screen

18) Ubuntu

19) UNIX

20) Vim

These are handpicked reference sheets and you may encounter various other versions of these over Internet. If you find any version of reference sheet which is worth sharing, feel free to paste the link below.

At the end, I sincerely acknowledge the authors who have put their efforts in designing these informative reference sheets and made them available to us.

Creating ‘Swap’ [‘Virtual’] Memory on Linux/Unix Operating System

Here’s some help for when you have too little RAM/memory and are trying to do memory-intensive steps, like indexing the human genome reference or doing other NGS-related processing.The way to do it is to create a ‘swap file’, as follows:

1) Check disk/drive usages:

df

2) Create the space. This step is long if you select a large amount of space. In this example, 512MB is created under root (/), given that block size (bs) is 1024 bytes:

sudo dd if=/dev/zero of=/swapfile bs=1024 count=512k

3) Switch it on:

sudo mkswap /swapfile

*This will only last until you restart the operating system, so, useful as a temporary measure. To make the swapfile permanent, do the following:

4) Open the following file:

sudo nano /etc/fstab

Paste in the following:

/swapfile    none     swap     sw     0     0

 

Article by: Dr. Kevin Blighe