Difference between revisions of "The bioinformatics lab SS 2011"

From Rost Lab Open
(Modules in programming, development and design - packages (Laszlo))
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== External media / installing a Linux OS / Debian stable / Linux kernel (Laszlo) ==
+
== External media / installing a Linux OS / Debian stable / Linux kernel (advisor: Laszlo) ==
# date: 2011 / 05 / 02
+
# date: 2011 / 05 / 09
  +
# topics: Linux distributions, rpm vs. deb, stable vs. bleeding edge; decisions to make at the time of system installation. Partitioning, LVM, cryptsetup; kernel modules, boot loader, initramdisk; dpkg, apt, aptitude, apticron; sysctl, /proc, /sys
# responsible: XXX
 
# topics: XXX
 
 
# links for preparation:
 
# links for preparation:
#* abc.com
+
#* google.com: popularity of Linux
  +
#* http://distrowatch.com/
  +
#* http://debian.org/ http://ubuntu.com/ http://redhat.com/ etc.
  +
#* http://kernel.org/
  +
#* http://www.gnu.org/
  +
#* http://www.gnu.org/software/grub/
   
 
=== Programming Challenge ===
 
=== Programming Challenge ===
  +
XXX
 
==== Hints and tips ====
 
==== Hints and tips ====
  +
XXX
   
 
=== Advanced challenge ===
 
=== Advanced challenge ===
  +
XXX
   
 
=== Materials and methods ===
 
=== Materials and methods ===
Line 27: Line 34:
   
   
  +
== Shell scripts, command line (terminal) editors and compilation (Markus) ==
 
  +
== Shell scripts, command line (terminal) editors and compilation (advisor: Markus) ==
# date: 2011 / 05 / 02
 
  +
# date: 2011 / 05 / 16
# responsible: XXX
 
  +
# topics: vim, emacs, shell scripts, gcc, makefiles, automake, autoconf, kernel and module compilation
# topics: XXX
 
 
# links for preparation:
 
# links for preparation:
  +
#* http://www.linuxlinks.com/article/20080824052425167/Editors.html
#* abc.com
 
  +
#* http://en.wikipedia.org/wiki/Compiler
  +
#* http://gcc.gnu.org/
  +
#* http://kernel.org/
  +
#* http://www.opussoftware.com/tutorial/TutMakefile.htm, http://www.amath.washington.edu/~lf/tutorials/autoconf/
   
 
=== Programming Challenge ===
 
=== Programming Challenge ===
  +
XXX
 
==== Hints and tips ====
 
==== Hints and tips ====
  +
XXX
   
 
=== Advanced challenge ===
 
=== Advanced challenge ===
  +
XXX
   
 
=== Materials and methods ===
 
=== Materials and methods ===
Line 48: Line 62:
   
   
  +
== Virtualization (Laszlo) ==
 
  +
1. Command line test
 
  +
== Virtualization (advisor: Laszlo) ==
# date: 2011 / 05 / 02
 
  +
# date: 2011 / 05 / 23
# responsible: XXX
 
 
# topics: XXX
 
# topics: XXX
 
# links for preparation:
 
# links for preparation:
 
#* abc.com
 
#* abc.com
  +
  +
  +
=== Linux Command Exam ===
  +
There will be a Linux Command Exam today, at the beginning of the practical session. The exams takes 10 minutes and you will get 25 to 30 questions about Linux command lines. You are allowed to use the computer and Internet.
  +
==== Example test questions ====
  +
What command would you use to:
  +
* remove an empty directory
  +
* remove a potentially filled directory
  +
* remove all files with '.pl~' extension in a directory tree
  +
* switch the group write permission on on all files that match the '*.pl' extension in a directory tree
  +
* list a directory with files sorted on modification time in reverse (newest on bottom)
  +
* copy a directory tree to another location in an 'archiving' way
  +
* copy a directory tree to another computer in an efficient way
  +
* create the directory /tmp/test/src/linux with one command when only /tmp exists
  +
* open a man page file in your present directory that is not within the regular man path
  +
* print your PATH? What is the function of the PATH environment variable?
  +
* add your present working directory to your path
  +
* look at the contents of a text file (name at least two tools)
  +
* compare two text files
  +
* list your environment
  +
* list variables in your environment that are exported
  +
* kill a process
  +
* list all 'bash' processes running on your system in user-oriented format
  +
* temporarily suspend a process
  +
* resume a temporarily suspended process
  +
* look at the top processes with respect to memory usage or CPU usage
  +
* list all ext3 type mounted file systems
  +
* temporarily mount a fat file system from device sdb1 to a temporary mount point
  +
* bind-mount /srv/raidarray/project to /srv/nfs4/project
  +
* eject a cd-rom
  +
* power off your computer
  +
* reboot your computer
  +
* examine the exit status of the last foreground command you executed
  +
   
 
=== Programming Challenge ===
 
=== Programming Challenge ===
  +
XXX
 
==== Hints and tips ====
 
==== Hints and tips ====
  +
XXX
   
 
=== Advanced challenge ===
 
=== Advanced challenge ===
  +
XXX
   
 
=== Materials and methods ===
 
=== Materials and methods ===
Line 71: Line 122:
   
   
  +
== Amazon EC2 (advisor: Markus) ==
 
  +
== Amazon Web Services (advisor: Markus) ==
1. VI test
 
  +
# date: 2011 / 05 / 30
AWS services supported in the grants include Amazon EC2, Amazon S3, Amazon SimpleDB, Amazon RDS, Amazon SQS, Amazon CloudFront and Amazon Elastic MapReduce. Cluster GPU Instances for Amazon EC2 are only available for grant recipients on a limited basis by written consent of the program administrator.
 
  +
# topics: Amazon EC2, Amazon S3, Amazon SimpleDB, Amazon RDS, Amazon SQS, Amazon CloudFront and Amazon Elastic MapReduce.
# date: 2011 / 05 / 02
 
# responsible: XXX
 
# topics: XXX
 
 
# links for preparation:
 
# links for preparation:
#* abc.com
+
#* http://aws.amazon.com/
  +
  +
  +
=== Vi Exam ===
  +
There will be a Vi exam today at the beginning of the practical session. The exams takes 10 minutes and you will get 25 to 30 questions about Vi. You are allowed to use the computer and Internet.
  +
==== Example test questions ====
  +
* How do you start vi?
  +
* How do you start vi and automatically open a file at line 22?
  +
* What is the command to save a file?
  +
* How do you quit vi without saving the file?
  +
* What is the command to jump to line 33?
  +
* What is the command to junp to the middle row of your current window?
  +
* What is the command to delete a complete line?
  +
* What is the command to delete one word (including the spaces)?
  +
* How do you copy the a word?
  +
* What is the command to replace all name '/tmp' to '/var/tmp'?
  +
* How do you open a new file?
  +
* What is the command to delete the next 10 lines?
  +
* What is the command to move the courser to the next occurrence of 'tmp'?
  +
* What is the shortcut for undo?
  +
* Which key stoke gives you information (e.g. number of lines) about your file?
  +
   
 
=== Programming Challenge ===
 
=== Programming Challenge ===
  +
XXX
 
==== Hints and tips ====
 
==== Hints and tips ====
  +
XXX
   
 
=== Advanced challenge ===
 
=== Advanced challenge ===
  +
XXX
   
 
=== Materials and methods ===
 
=== Materials and methods ===

Revision as of 11:31, 18 April 2011

This practical is a hands-on training that will make you successful in a Bioinformatic lab! This term we have a focus on virtual systems and Cloud Computing.

More details can be found at the http://rostlab.informatik.tu-muenchen.de/cms/biolab2011/ website.

Materials from old courses are available at The_bioinformatics_lab. There you can find many hints and tips and the protocols and presentation slides from last year. You may use them, but especially the protocols and presentations you have to prepare with your own content and own style!


Contents

External media / installing a Linux OS / Debian stable / Linux kernel (advisor: Laszlo)

  1. date: 2011 / 05 / 09
  2. topics: Linux distributions, rpm vs. deb, stable vs. bleeding edge; decisions to make at the time of system installation. Partitioning, LVM, cryptsetup; kernel modules, boot loader, initramdisk; dpkg, apt, aptitude, apticron; sysctl, /proc, /sys
  3. links for preparation:

Programming Challenge

XXX

Hints and tips

XXX

Advanced challenge

XXX

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf


Shell scripts, command line (terminal) editors and compilation (advisor: Markus)

  1. date: 2011 / 05 / 16
  2. topics: vim, emacs, shell scripts, gcc, makefiles, automake, autoconf, kernel and module compilation
  3. links for preparation:

Programming Challenge

XXX

Hints and tips

XXX

Advanced challenge

XXX

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf



Virtualization (advisor: Laszlo)

  1. date: 2011 / 05 / 23
  2. topics: XXX
  3. links for preparation:
    • abc.com


Linux Command Exam

There will be a Linux Command Exam today, at the beginning of the practical session. The exams takes 10 minutes and you will get 25 to 30 questions about Linux command lines. You are allowed to use the computer and Internet.

Example test questions

What command would you use to:

  • remove an empty directory
  • remove a potentially filled directory
  • remove all files with '.pl~' extension in a directory tree
  • switch the group write permission on on all files that match the '*.pl' extension in a directory tree
  • list a directory with files sorted on modification time in reverse (newest on bottom)
  • copy a directory tree to another location in an 'archiving' way
  • copy a directory tree to another computer in an efficient way
  • create the directory /tmp/test/src/linux with one command when only /tmp exists
  • open a man page file in your present directory that is not within the regular man path
  • print your PATH? What is the function of the PATH environment variable?
  • add your present working directory to your path
  • look at the contents of a text file (name at least two tools)
  • compare two text files
  • list your environment
  • list variables in your environment that are exported
  • kill a process
  • list all 'bash' processes running on your system in user-oriented format
  • temporarily suspend a process
  • resume a temporarily suspended process
  • look at the top processes with respect to memory usage or CPU usage
  • list all ext3 type mounted file systems
  • temporarily mount a fat file system from device sdb1 to a temporary mount point
  • bind-mount /srv/raidarray/project to /srv/nfs4/project
  • eject a cd-rom
  • power off your computer
  • reboot your computer
  • examine the exit status of the last foreground command you executed


Programming Challenge

XXX

Hints and tips

XXX

Advanced challenge

XXX

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf



Amazon Web Services (advisor: Markus)

  1. date: 2011 / 05 / 30
  2. topics: Amazon EC2, Amazon S3, Amazon SimpleDB, Amazon RDS, Amazon SQS, Amazon CloudFront and Amazon Elastic MapReduce.
  3. links for preparation:


Vi Exam

There will be a Vi exam today at the beginning of the practical session. The exams takes 10 minutes and you will get 25 to 30 questions about Vi. You are allowed to use the computer and Internet.

Example test questions

  • How do you start vi?
  • How do you start vi and automatically open a file at line 22?
  • What is the command to save a file?
  • How do you quit vi without saving the file?
  • What is the command to jump to line 33?
  • What is the command to junp to the middle row of your current window?
  • What is the command to delete a complete line?
  • What is the command to delete one word (including the spaces)?
  • How do you copy the a word?
  • What is the command to replace all name '/tmp' to '/var/tmp'?
  • How do you open a new file?
  • What is the command to delete the next 10 lines?
  • What is the command to move the courser to the next occurrence of 'tmp'?
  • What is the shortcut for undo?
  • Which key stoke gives you information (e.g. number of lines) about your file?


Programming Challenge

XXX

Hints and tips

XXX

Advanced challenge

XXX

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf


User management / directory services (Laszlo)

  1. date: 2011 / 05 / 02
  2. responsible: XXX
  3. topics: XXX
  4. links for preparation:
    • abc.com

Programming Challenge

Hints and tips

Advanced challenge

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf


Mail, DNS (Laszlo)

  1. date: 2011 / 05 / 02
  2. responsible: XXX
  3. topics: XXX
  4. links for preparation:
    • abc.com

Programming Challenge

Hints and tips

Advanced challenge

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf


Webserver (Markus)

  1. date: 2011 / 05 / 02
  2. responsible: XXX
  3. topics: XXX
  4. links for preparation:
    • abc.com

Programming Challenge

Hints and tips

Advanced challenge

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf


Databases and SQL (Markus)

  1. date: 2011 / 05 / 02
  2. responsible: XXX
  3. topics: XXX
  4. links for preparation:
    • abc.com

Programming Challenge

Hints and tips

Advanced challenge

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf


Default web applications - CMS and Wiki (Markus)

  1. date: 2011 / 05 / 02
  2. responsible: XXX
  3. topics: XXX
  4. links for preparation:
    • abc.com

Programming Challenge

Hints and tips

Advanced challenge

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf



Computer Clusters and External Services : Excursion LRZ

  1. date: 2010 / 06 / 28
  2. responsible: Markus
  3. topics: computer cluster hardware, batch systems
  4. links for preparation:

Programming Challenge

We will get a guided tour in the LRZ to see all the server and services in live operation.

Hints and Tips

  • We meet at 2 p.m. in the rostlab!
  • Please be in time.
  • A photo identification is required.
  • There is air condition in the server rooms. Please dress appropriate.


Modules in programming, development and design - packages (Laszlo)

  1. date: 2011 / 05 / 02
  2. responsible: XXX
  3. topics: XXX
  4. links for preparation:
    • abc.com

Programming Challenge

Hints and tips

Advanced challenge

Materials and methods

  • Session1_debriefing.pdf

Report

By XXX XXX:

  • slides.pdf
  • protocoll.pdf