Commit ac38fac1 authored by Toby Hodges's avatar Toby Hodges

Merge branch 'exercise1fix' into 'master'

Exercise 1 hints

See merge request !6
parents 2d3a9aa4 5e660836
About Bio-IT
About Bio-IT
-------------
The Bio-IT Project aims to develop and strengthen the bioinformatics community at EMBL Heidelberg. It is made up of members across a range of disciplines in computational biology, in different Units and Core Facilities. The project aims to improve the standard of computational biology practised at EMBL Heidelberg, to encourage collaborations, and to provide a forum for discussion of issues and ideas relevant to bioinformatics here.
The Bio-IT Project aims to develop and strengthen the bioinformatics community at EMBL Heidelberg. It is made up of members across a range of disciplines in computational biology, in different Units and Core Facilities. The project aims to improve the standard of computational biology practised at EMBL Heidelberg, to encourage collaborations, and to provide a forum for discussion of issues and ideas relevant to bioinformatics here.
The activities of the project include:
- the organisation and delivery of training courses such as this one
......@@ -20,26 +20,36 @@ The Portal hosts information regarding upcoming courses and conferences/other ev
Centres
^^^^^^^
`EMBL Centres <http://www.embl.de/research/interdisciplinary_research/centres/index.html>`_ are 'horizontal',
`EMBL Centres <http://www.embl.de/research/interdisciplinary_research/centres/index.html>`_ are 'horizontal',
cross-departmental structures that promote innovative research projects across disciplines. All the EMBL Centres listed below
have a strong computational component.
.. |cba| image:: _static/img-cba.jpg
:width: 20%
:alt: CBA
:target: https://bio-it.embl.de/cba
.. |cbna| image:: _static/img-cbna.jpg
:width: 20%
:alt: CBNA
:target: http://bio-it.embl.de/cbna
:target: https://bio-it.embl.de/cbna
.. |csda| image:: _static/img-csda.jpg
:width: 20%
:alt: CSDA
:target: http://bio-it.embl.de/statistical-data-analysis
:target: https://bio-it.embl.de/statistical-data-analysis
.. |cbm| image:: _static/img-cbm.jpg
:width: 20%
:alt: CBM
:target: http://bio-it.embl.de/biological-modeling
:target: https://bio-it.embl.de/biological-modeling
|cba| |cbna| |csda| |cbm|
|cbna| |csda| |cbm|
Bioimage Analysis
"""""""""""""""""
The `CBA <http://bio-it.embl.de/centres/cba>`_ supports scientists in extracting quantitative information from images acquired with light- or electron-microscopy.
Biomolecular Network Analysis
"""""""""""""""""""""""""""""
......@@ -51,8 +61,7 @@ Statistical Data Analysis
The `CSDA <http://bio-it.embl.de/statistical-data-analysis>`_ helps EMBL scientists to use adequate statistical methods for their specific technological or biological applications.
Modeling
Modelling
""""""""
The `Centre for Biological Modeling (CBM) <http://bio-it.embl.de/biological-modeling>`_ aims to support people to adopt mathematical modeling techniques into their everyday research.
The `CBM <http://bio-it.embl.de/biological-modeling>`_ aims to support people to adopt mathematical modelling techniques into their everyday research.
......@@ -8,25 +8,25 @@ Exercises
Misc. file tools
----------------
#. Which tool can be used to determine the type of a file?
#. Which tool can be used to determine the type of a file? (Hint: if you don't know about an appropriate command to do this, think about how you might go about finding one...)
#. Use it on the following files/directories and compare the results:
A. ``/usr/bin/tail``
A. ``/usr/bin/tail``
B. ``~``
B. ``~``
C. ``~/exercises/SRC_HUMAN.fasta``
C. ``~/exercises/SRC_HUMAN.fasta`` (or the equivalent path to the ``SRC_HUMAN.fasta`` file in the ``exercises`` folder on your system.)
Copying / Deleting Files & Folders
----------------------------------
#. Navigate to your home directory
#. Navigate to your home directory
#. In your home directory, create a new directory named ``new_dir``
#. In your home directory, create a new directory named ``new_dir``
#. Change into this directory, create a new empty file in there named ``new_file``,
#. Change into this directory, create a new empty file in there named ``new_file``,
and make sure that the file was created.
#. Duplicate this file by copying it as a new file named ``another_file``
......@@ -47,87 +47,87 @@ View Files
Searching
---------
#. Which tool can be used to search for files or directories?
#. Which tool can be used to search for files or directories?
#. Use it to find all directories in the ``~/exercises`` directory
#. Use it to find all directories in the ``~/exercises`` directory
#. Search for the file named ``date`` in the ``/bin`` directory
#. Search for the file named ``date`` in the ``/bin`` directory
#. List those entries in the directory ``/bin`` that are bigger than 400 kBytes
#. List those entries in the directory ``/bin`` that are bigger than 400 kBytes
Misc. terminal
--------------
#. Which two tools can be used to redraw/empty the screen?
#. Which two tools can be used to redraw/empty the screen?
Permissions
-----------
#. Create a directory called ``testpermissions``
#. Create a directory called ``testpermissions``
#. Change your working directory to ``testpermissions``
#. Change your working directory to ``testpermissions``
#. Create a directory called ``adir``.
#. Create a directory called ``adir``.
#. Use the command ``which date`` to find out where the date program is located.
#. Use the command ``which date`` to find out where the date program is located.
#. Copy this date program into the directory ``adir`` and name it 'mydate'.
#. Copy this date program into the directory ``adir`` and name it 'mydate'.
#. Check the permissions of the copied program 'mydate'
#. Check the permissions of the copied program 'mydate'
#. Change the permissions on 'mydate' to remove the executable permissions.
#. Change the permissions on 'mydate' to remove the executable permissions.
#. Check the permissions of the program 'mydate'
#. Check the permissions of the program 'mydate'
#. Change the permissions back so that the file is executable.
#. Change the permissions back so that the file is executable.
#. Try running it as ``./mydate`` or ``adir/mydate`` (depending on your current working directory)
#. Try running it as ``./mydate`` or ``adir/mydate`` (depending on your current working directory)
#. Copy a textfile from a previous exercise into ``adir``, then change the permissions, so you are not allowed to write to it.
Test that you are still able to read the file via `cat`.
#. Copy a textfile from a previous exercise into ``adir``, then change the permissions, so you are not allowed to write to it.
Test that you are still able to read the file via `cat`.
#. Then change the permissions so you can't read/cat it either. Test this by trying to read it via `cat`.
#. Then change the permissions so you can't read/cat it either. Test this by trying to read it via `cat`.
#. Change your working directory to ``testpermissions``, and then try changing the permissions on the directory ``adir`` to non-executable.
#. Change your working directory to ``testpermissions``, and then try changing the permissions on the directory ``adir`` to non-executable.
#. What are the minimum permissions (on the directory) necessary for you to be able to execute ``adir/mydate``?
#. What are the minimum permissions (on the directory) necessary for you to be able to execute ``adir/mydate``?
Remote access
-------------
#. Login to machine "submaster1.embl.de" (using your own username)
#. Login to machine "submaster1.embl.de" (using your own username)
#. Use exit to quit the remote shell (Beware to not exit your local shell)
#. Use exit to quit the remote shell (Beware to not exit your local shell)
#. Use clear to empty the screen after logout from the remote server
#. Use clear to empty the screen after logout from the remote server
#. Use the following commands locally as well as on the remote machine to get a feeling for the different machines:
#. Use the following commands locally as well as on the remote machine to get a feeling for the different machines:
#. Copy the file ``/etc/motd`` from machine submaster1.embl.de into your local home directory (using scp)
#. Copy the file ``/etc/motd`` from machine submaster1.embl.de into your local home directory (using scp)
#. Determine the filetype and the permissions of the file that you just copied
#. Determine the filetype and the permissions of the file that you just copied
#. Login to your neighbor's machine (ask him for the hostname) using your own username
#. Login to your neighbor's machine (ask him for the hostname) using your own username
IO and Redirections
-------------------
#. Use date in conjunction with the redirection to insert the current date into the (new) file current_date (in your homedirectory).
#. Use date in conjunction with the redirection to insert the current date into the (new) file current_date (in your homedirectory).
#. Inspect the file to make sure it contains (only a single line with) the date.
#. Inspect the file to make sure it contains (only a single line with) the date.
#. Use ``date`` again to append the current date into the same file.
#. Use ``date`` again to append the current date into the same file.
#. Again, check that this file now contains two lines with dates.
#. Again, check that this file now contains two lines with dates.
#. Use ``grep`` to filter out lines containing the term "TITLE" from all PDB files in the exercises directory and use redirection to insert them into a new file pdb_titles.txt.
#. Use ``grep`` to filter out lines containing the term "TITLE" from all PDB files in the exercises directory and use redirection to insert them into a new file pdb_titles.txt.
#. (OPTIONAL) Upon inspection of the file pdb_titles.txt, you see that it also contains the names of the files in which the term was found.
#. (OPTIONAL) Upon inspection of the file pdb_titles.txt, you see that it also contains the names of the files in which the term was found.
A. Use either the grep manpage or ``grep --help`` to find out how you can suppress this behaviour.
A. Use either the grep manpage or ``grep --help`` to find out how you can suppress this behaviour.
B. Redo the previous exercise such that the output file pdb_titles.txt only contains lines starting with TITLE.
B. Redo the previous exercise such that the output file pdb_titles.txt only contains lines starting with TITLE.
#. The *third* column of the file /etc/passwd contains user IDs (numbers)
......@@ -159,13 +159,13 @@ You can find the famous BLAST tool installed at `/g/software/bin/blastp`.
#. Typing the full path is too cumbersome, so let's append `/g/software/bin` to your $PATH variable and ensure that it works by calling `blastp`.
#. When you run `blastp -help`, you notice that it has a lot of options!
#. When you run `blastp -help`, you notice that it has a lot of options!
Use redirections in conjunction with grep to find out which options you need to specify a *input_file* and *database_name*.
#. Now run blastp using the following values as options:
#. Now run blastp using the following values as options:
*database_name* = `/g/data/ncbi-blast/db/swissprot`
*database_name* = `/g/data/ncbi-blast/db/swissprot`
*input_file* = `suspect1.fasta`
*input_file* = `suspect1.fasta`
#. Use either ``less`` or redirection to a file to manage the amount of information that ``blastp`` prints on your screen.
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