1. Dedan Githae, d.githae@cgiar.org BecA-ILRI Hub Introduction to Linux / UNIX OS MARI eBioKit Workshop; Nov 24- 28, 2014

2. Importance of informatics to biology Functional aspect: Involves representation, organisation, manipulation, distribution, maintainance and using information – Design, data formats,, databases, simple scripts to assist handle data Developmental aspect: Develop analytical tools to get information from data – Comparing sequences to infer function of newly discovered gene – Compare 3D protein structure to know how protein folding takes place – How protein – metabolites; protein- protein interactions for cell function

3. Why unix Optimal for developing, compiling and running programs and scientific research tools- used in hi-performance computer systems. Has been in use in industry and academia (i.e. the software developers). Most programs are command- line (i.e., launched by entering a command in a terminal window rather than through GUI) Versatile scripting and system tools readily available on Linux allow customization of any analysis Free softwares! Did you know ? The world-wide web (www) runs on unix? Sotware that powers internet was invented on unix; thus most servers are unix-based.

4. Moving about Do not use your mouse The file system The terminal

5. Basic commands ls – list stuff in the present directory (folder) pwd – present working directory cd [folder_name] – change directory- navigate to the [folder_name] cd.. change directory to the parent cd ~ change directory to default 'home' head [filename] – list first few lines. tail listst last few lines less [filename] – read contents of a file in bits cat [filename] – display contents of the file cp [source] [destination] - copy file / directory from source to directory mv [source] [destination] – Move... i.e. Cut-&-Paste rm : remove Question : Why do you avoid spaces in filenames and folder_names

6. Command line - options Command line options – extended functionality to the command ls – l : list the files in the directory in long format ls -t : list sorted output by modification ls -S : sort output by size ls -r : reverse sort the output ls -R : List recursively in directory below current level ls -1 : list output one per line ls -p : helps identify directories by adding a / mkdir [dir_name]: Make a directory called dir_name rmdir -???

7. More helpful commands Question : Why do you need to avoid spaces in file names and folder names? Split/ csplit – splits a (big) file into smaller files cut – seperates parts of the file using preset delimiters eg tabs paste – combine portions from several files into one file sort – sorts a single file, group of files and simultaneously merge into one file cmp / diff [file1] [file2] – list first few lines. tail listst last few lines wc – word count Grep – search for pattern in file(s) Kill – stop a process Tar – to compress / extract archives

8. Special characters Question : Why do you need to avoid spaces in file names and folder names? / denotes directories. present directory.. Parent directory > redirect output to a file >> Append (add to the end) the output to existing file # Comment (ignored by computer) | redirect output of a program into another program < read as input [] defines a set of characters Regular expression- regex \ is called ‘escape’: the next char has special meaning ? match a single character matches zero or more

9. Thanks