Lecture 1: Learning Linux/Unix Operating System

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[00:00:14]Good morning everyone.

[00:00:17]Welcome to the course buying formatics for biologists. I am Rakkesh Pande faculty at bingformatics Banarash Hindu University. I'm going to uh introduce you the Linux system which is uh very important for biologists because most of the programs if you see they come for Linux systems or the other popular programs um uh on which operating system you get is Mac OS and the third one the operating system on which you get um most of the bionformatics programs and tools is window this course um basically um it jointly offered by me and Dr. Goro Pande from department of geology Banarash Hindu University.

[00:01:18]So before I start the my lecture I would like to give an outline of the course.

[00:01:27]So basically this course is designed for eight weeks and there are um certain uh lectures by me and Dr. Goro Pande. In week one I'll be introducing Linux and R programming concepts.

[00:01:48]In second week Dr. Goro Pande will talk about running a file in R and using of uh bioconductor and installation of that. Then in week three um again Dr. Goro Pande will uh explain how to use uh different pipelines to analyze irony sequencing and transcrytoic data. In fourth week I'll be back um with lecture on systems approaches in biology mathematical modeling techniques for biologist and different approaches of modeling.

[00:02:32]Again in fifth week I will explain how to develop mathematical models for biological systems.

[00:02:41]After that in week six again Dr. Goro Pande will uh explain how to use Cytoscape and UCSC browser for visualization of biological networks.

[00:02:55]Again in week seven I'll explain computational method to visualize protein structure and prediction of protein structures. And in last week Dr. Goro Pande will talk about protein and drug interactions.

[00:03:13]So today I'm going to talk about introduction to Linux. In today's talk I will introduce what is operating system, what is cell, what are command line interface and commands and cell scripting along with explanation of kernel. So let us start with understanding what is operating systems. operating system basically acts as an intermediary between user and computer hardware. And there are several popular operating systems. You can see uh the most popular you see around you is Windows which is a license based program. Another is Mac OS which is used mostly by Apple product.

[00:04:09]And the third most popular one is Linux.

[00:04:13]Linux is open-source software and it is Unix like program although uh it's look like Unix but it is not derived from the direct code of unique operating system and you can find different popular distributions of Linux the the most popular um distributions s I'm going to explain are Ubuntu, Fedora, SOUS and Red Hat. So now let me tell you what is command and what is command line interface. So when somebody say that okay go to the terminal and write a command we mean by uh just going to this kind of window which is called terminal where we can write Linux commands and Linux commands are basically text instructions which are given by users to interact with the your operating system which is here uh Linux X and this interface um on which we give the command line instructions is called command line interface and um this can be accessed through genome terminal or X terms or console.

[00:05:45]You can see here I have a um window um which shows the prompt at terminal. Let me explain that whatever the Linux operating system you use that uh comes with a sale program and sale is a program that describe receive that receives user commands from keyboard and passes them to operating system for exe execution.

[00:06:16]And there are mainly two type of sale programs in Linux distribution. you will find there will be either bass or SH cell and the um hierarchical location of cell is explained here. So basically cell is the program which which is basically gives interacts um gives basically instructions through kernel to hardwares to perform particular task. I'm going to explain the term sales scripting. When somebody say sales scripting, he means that in a text editor, you write all the sale commands and you can run that or rather you can say you can execute on the terminal. So basically when you say script it's a um many commands are given here. For example, um we are developing a sales script and we have created div ops script cell script file and now we are editing inside that welcome to my blog and in down by dot /develops.sh we have um executed this script file. Of course, all the commands will be executed together and you will see the um output. Welcome to my blocks. Now, this is um a little bit more advanced sale scripting in which on top we have this line which is called Cbank or Hashbank and then uh with H has you can give um comments also. So here is a um typical cell script. Now I'm going to explain another term which is very important to understand that is called kernel. Uh you can think that the kernel is brain of your operating system and the kernel basically manages your hardware, memory, different processes and devices and the kernel basically directly interacts with hardware and also it gets input from users.

[00:08:49]kernel and sale are two different terms which is very important to um understand and distinguish between them. So as we saw that the kernel is the core of your operating system. The sale is basically um provides an interface between user and kernel. Due to its existence, user are able to interact with system by entering different commands and basically cell translates your um users command into a form that kernel can understand and this happens through a command line interpretator relation among kernel cell command line and operating system. So you can think of that user which is typing some commands. The cell gets that instruction interpret that command to kernel and kernel executes those commands using hardwares and basically the performance or the process actually done is by the hardware. You can think of um the relation between kernel sale command line and operating system by this schematic diagram. Here you can think that your engine a car is basically a kernel and the steering of the car is cell the driver which is basically user.

[00:10:31]So that's how these terms are interrelated. Now I think I would like to summarize my lecture and provide take-home messages. So we learned that what is operating system. Basically that is an intermediary between a computer user and the computer hardware. There are different kind of operating systems you can find around you. Windows, Mac OS and Linux. Also there are different distribution of Linux like Ubuntu, Fedora, Red Hat and SU.

[00:11:13]Also Linux distribution SL program also all Linux distribution system have a kernel and cell scripting. you can provide instructions to kernel which will be executed by hardwares. So with this I would like to end my this lecture. Thank you very much for your attention.