Beginning Unix - Revision history

WikiSysop: /* Required course material for the lesson */

2026-02-02T12:01:34Z

Required course material for the lesson

← Older revision		Revision as of 14:01, 2 February 2026
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	== Required course material for the lesson ==		== Required course material for the lesson ==
	Powerpoint: [https://teaching.healthtech.dtu.dk/material/~~22113~~/~~22113_01~~-Unix.ppt Introduction to Unix]<br>		Powerpoint: [https://teaching.healthtech.dtu.dk/material/22118/22118_01-Unix.ppt Introduction to Unix]<br>
	The videos are not entirely in sync with the powerpoint, as it has been updated.<br>		The videos are not entirely in sync with the powerpoint, as it has been updated.<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation]<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation]<br>

WikiSysop: /* Exercises to be handed in */

2026-01-26T15:22:00Z

Exercises to be handed in

← Older revision		Revision as of 17:22, 26 January 2026
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	# Make a directory ''test'' and move the three files to it.		# Make a directory ''test'' and move the three files to it.
	# Make a directory ''data'' and move the three files to that instead.		# Make a directory ''data'' and move the three files to that instead.
	# Remove ''test' directory.		# Remove ''test'' directory.
	# Change directory to ''data'' and confirm that you succeeded. Go back to the home/work directory afterwards.		# Change directory to ''data'' and confirm that you succeeded. Go back to the home/work directory afterwards.
	# Make three new directories ''newtest'' - one inside the other, like a Russian doll.		# Make three new directories ''newtest'' - one inside the other, like a Russian doll.

WikiSysop: /* Exercises to be handed in */

2025-11-07T13:16:30Z

Exercises to be handed in

← Older revision		Revision as of 15:16, 7 November 2025
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	# How many genes belong to the rat, and how many of those are precursors ? (9) Note: A Swissprot ID looks like 'PARG_HUMAN' or 'TF1A_MOUSE', with the gene being before the underscore and the organism after the underscore.		# How many genes belong to the rat, and how many of those are precursors ? (9) Note: A Swissprot ID looks like 'PARG_HUMAN' or 'TF1A_MOUSE', with the gene being before the underscore and the organism after the underscore.
	# From the file ''ex1.res'' find the lines with positive numbers and put then into ''ex1.pos''. The lines with negative number go into ''ex1.neg''.		# From the file ''ex1.res'' find the lines with positive numbers and put then into ''ex1.pos''. The lines with negative number go into ''ex1.neg''.
	# Calculate ((356+51)*123-12765)/56 on the command line.		# Calculate ((356+51)*123-12765)/56 on the command line. Design your command so when you press ENTER to execute, it computes the result and shows the prompt waiting for your next command.

	== Exercises for extra practice ==		== Exercises for extra practice ==

WikiSysop: /* Exercises to do after Monday */

2025-11-07T13:14:15Z

Exercises to do after Monday

← Older revision		Revision as of 15:14, 7 November 2025
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	Note: Data files can be found in the [[collection of files]].		Note: Data files can be found in the [[collection of files]].

	~~===Exercises to do after Monday===~~
	It is assumed that you have downloaded the 3 files; ex1.dat, ex1.acc and orphans.sp before you start the exercises		It is assumed that you have downloaded the 3 files; ex1.dat, ex1.acc and orphans.sp before you start the exercises
	# First list the files in the directory.		# First list the files in the directory.

WikiSysop: /* Required course material for the lesson */

2025-11-06T11:14:42Z

Required course material for the lesson

← Older revision		Revision as of 13:14, 6 November 2025
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	Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix]<br>		Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix]<br>
	The videos are not entirely in sync with the powerpoint, as it has been updated.<br>		The videos are not entirely in sync with the powerpoint, as it has been updated.<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation] ~~Monday~~<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=88cb52db-1c77-4a98-94db-af270127d0dc Coping, Moving, Renaming files. Changing permissions] ~~Monday~~<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=88cb52db-1c77-4a98-94db-af270127d0dc Coping, Moving, Renaming files. Changing permissions]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fa98c15f-5c50-4ea3-8c85-af270127aedf Using shortcuts in Unix - making it easier] ~~Monday~~<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fa98c15f-5c50-4ea3-8c85-af270127aedf Using shortcuts in Unix - making it easier]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=7f775d1b-2788-45ee-b4ac-af2701279221 File inspection and editor in unix. 1½ min silence at the end] ~~Monday~~<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=7f775d1b-2788-45ee-b4ac-af2701279221 File inspection and editor in unix. 1½ min silence at the end]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=16f1e9bd-8044-4a97-b033-af27012771e2 Manipulating files: wc, paste, cut & sort] ~~Monday~~<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=16f1e9bd-8044-4a97-b033-af27012771e2 Manipulating files: wc, paste, cut & sort]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=5ecff806-b2de-42f7-ab97-af2701274f66 Manipulating files: grep and pipelines] ~~Monday~~<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=5ecff806-b2de-42f7-ab97-af2701274f66 Manipulating files: grep and pipelines]<br>
	Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=0679c534-a422-4ed6-9f52-af27012730b2 Touching upon various relevant subjects] ~~Monday~~<br>		Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=0679c534-a422-4ed6-9f52-af27012730b2 Touching upon various relevant subjects]<br>
			Youtube: [https://www.youtube.com/playlist?list=PLIhvC56v63IJIujb5cyE13oLuyORZpdkL NetworkChuck's Unix course.] Maybe you find him more entertaining than me.<br>
	Resource: [https://teaching.healthtech.dtu.dk/unix The resource on Unix for many courses at Health Tech]<br>		Resource: [https://teaching.healthtech.dtu.dk/unix The resource on Unix for many courses at Health Tech]<br>
	Resource: [[Biological knowledge needed in the course]]<br>		Resource: [[Biological knowledge needed in the course]]<br>

WikiSysop: /* Subjects covered */

2025-11-06T11:05:49Z

Subjects covered

← Older revision		Revision as of 13:05, 6 November 2025
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	* Understanding and navigating the file system.		* Understanding and navigating the file system.
	* Many different Unix commands		* Many different Unix commands
	* Scripting in bash

	== Exercises to be handed in ==		== Exercises to be handed in ==

WikiSysop: Created page with "NOTOC {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Programme |Next: Intermediate Unix |} You did do the Course preparation, right!! Otherwise all of this matters not. == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix]
The videos are not entirely in sync with the powerpoint, as it has been updated.<..."

2025-11-06T11:05:05Z

Created page with "__NOTOC__ {| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;" |Previous: Programme |Next: Intermediate Unix |} You did do the Course preparation, right!! Otherwise all of this matters not. == Required course material for the lesson == Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] The videos are not entirely in sync with the powerpoint, as it has been updated.<..."

New page

__NOTOC__
{| width=500 style="font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;"
|Previous: [[Programme]]
|Next: [[Intermediate Unix]]
|}

You did do the [[Course preparation]], right!! Otherwise all of this matters not.

== Required course material for the lesson ==
Powerpoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] 
The videos are not entirely in sync with the powerpoint, as it has been updated. 
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=110b2544-db60-4491-95cd-af270127f161 Unix intro and navigation] Monday 
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=88cb52db-1c77-4a98-94db-af270127d0dc Coping, Moving, Renaming files. Changing permissions] Monday 
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=fa98c15f-5c50-4ea3-8c85-af270127aedf Using shortcuts in Unix - making it easier] Monday 
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=7f775d1b-2788-45ee-b4ac-af2701279221 File inspection and editor in unix. 1½ min silence at the end] Monday 
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=16f1e9bd-8044-4a97-b033-af27012771e2 Manipulating files: wc, paste, cut & sort] Monday 
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=5ecff806-b2de-42f7-ab97-af2701274f66 Manipulating files: grep and pipelines] Monday 
Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=0679c534-a422-4ed6-9f52-af27012730b2 Touching upon various relevant subjects] Monday 
Resource: [https://teaching.healthtech.dtu.dk/unix The resource on Unix for many courses at Health Tech] 
Resource: [[Biological knowledge needed in the course]] 
Resource: [http://www.ee.surrey.ac.uk/Teaching/Unix/ UNIX Tutorial for Beginners] from University of Surrey 
Resource: [http://www.tutorialspoint.com/unix/ UNIX/LINUX Tutorial] from TutorialsPoint

== Subjects covered ==
* Basic file handling in UNIX.
* Understanding and navigating the file system.
* Many different Unix commands
* Scripting in bash

== Exercises to be handed in ==
Use a text editor to to create a file mycommands.txt where you write all commands and observations you do in the following exercises. Use copy/paste to copy the commands. 
Note: Make sure that we can easily see which exercise you attempt to solve. 
Note: You should work from your home directory, or a work directory that you specify explicitly in the top of your hand-in. 
Note: Data files can be found in the [[collection of files]].

===Exercises to do after Monday===
It is assumed that you have downloaded the 3 files; ex1.dat, ex1.acc and orphans.sp before you start the exercises
# First list the files in the directory.
# Copy ''ex1.acc'' to ''myfile.acc''.
# Look at the content of both files to ensure they are identical.
# Copy ''ex1.dat'' to ''myfile.acc''.
# Check that the content of ''myfile.acc'' changed.
# Delete ''myfile.acc''.
# Make a directory ''test'' and move the three files to it.
# Make a directory ''data'' and move the three files to that instead.
# Remove ''test' directory.
# Change directory to ''data'' and confirm that you succeeded. Go back to the home/work directory afterwards.
# Make three new directories ''newtest'' - one inside the other, like a Russian doll.
# Move the data directory to the innermost ''newtest'' directory.
# Confirm that the three files are moved along with the data directory.
# Copy the three files to your home (your top directory).
# Remove all ''newtest'' directories and ''data'' in the with a single command.
# Count the lines in ''ex1.acc'' and ''ex1.dat''.
# Con'''cat'''enate ''ex1.acc'' and ''ex1.dat'' in the file ''ex1.tot'', i.e. copy the content of two files into one new file. Verify that all gene IDs comes first followed by numerical data.
# Merge/Paste ''ex1.acc'' and ''ex1.dat'' together in ''ex1.tot'', thus destroying the old file. Verify that corresponding gene IDs and numerical data are put on the same line as the data.
# Extract (cut) SwissProt ID and 3nd numerical data (column 1 and 5) from ''ex1.tot''. Put results into a file ''ex1.res''.
# Find the 3 SwissProt ID's in ''ex1.res'' which have the largest number(s) in column 2, i.e. the top 3 entries. Display only the ID's.
# Find the lines (using grep) in ''orphans.sp'' which contain a GenBank accession number. There are 85, verify this. Note: An accession number is one or two capital letters and looks like this 'AB000114.CDS.1', i.e. Some letters followed by some numbers. The .CDS. part is kind of optional.
# How many human genes with SwissProt IDs in ''orphans.sp'' exist ? How many of those are hypothetical ? (11)
# How many genes belong to the rat, and how many of those are precursors ? (9) Note: A Swissprot ID looks like 'PARG_HUMAN' or 'TF1A_MOUSE', with the gene being before the underscore and the organism after the underscore.
# From the file ''ex1.res'' find the lines with positive numbers and put then into ''ex1.pos''. The lines with negative number go into ''ex1.neg''.
# Calculate ((356+51)*123-12765)/56 on the command line.

== Exercises for extra practice ==