[Debian Wiki] Update of "BOINC/ServerGuide" by dhananjay

[Debian Wiki]

Dear Wiki user,

You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification.

The "BOINC/ServerGuide" page has been changed by dhananjay:
http://wiki.debian.org/BOINC/ServerGuide?action=diff&rev1=100&rev2=101

Comment:
Moving autodock application creation to [[BOINC/ServerGuide/AutoDockApp]]

  
  If your background is not biochemistry you can still understand it all from the technical side. But you will barely come up with your own docking project. If you are interested to help out some drug researchers local to you, just find your nearest university and ask around. Even if you are still going to high school, you may run into someone to mentally feed you or even to offer some real collaboration.
  
+ The steps for creating the example project, is described at [[BOINC/ServerGuide/AutoDockApp]].
- == BOINCed variant of the tutorial for running AutoDock on Ubuntu ==
- 
- We took a nice publicly available walk through for AutoDock and the MGLTools and modified that. There original is [[http://users.ox.ac.uk/~jesu1458/docker/|here]] which you may decide to walk through to increase your familiarity with the technology (biochemist or not). As you will see, that script was split in three sections. The first and last are left untouched. The middle one, i.e. the invocation of the tool, this is now modified for BOINC.
- 
- === Step 1: Prepare the server ===
- 
- All the above instructions were basically preparing for this:
-  * follow the above description to create a working BOINC server web site
-  * follow the [[http://users.ox.ac.uk/~jesu1458/docker/|external online instructions]] to create the wrapper as an application
- 
-   
-  * do the following to get the autodock application as an executing tool
-   * Use the packaged binaries of autodock. ( Won't take much sense to a large volunteer run project)
-   * Build statically linked binaries for each platform.
-     {{{
- $ apt-get source autodocktools
- $ cd autodocktools-*/autodock
- $ ./configure LDFLAGS=-static && make
- }}}
- 
- === Step 2: Prepare the biology ===
- 
- This step was not changed with respect to the original ''docker'' script. A few file locations have been modified. This just slightly adapted version of its "upper half" is kept [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-pre.sh;hb=HEAD|here]] ([[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-pre.sh;hb=HEAD|download]]).
- 
-  * install Debian packages: autodocktools autodock autogrid
-  * follow the ''docker'' [[http://users.ox.ac.uk/~jesu1458/docker/|web tutorial]] for
-   * download receptor from http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=2RH1
-   * reduce to first 5 transmembrane helices
-   * prepare docking with AutoDockTools (start runAdt instead of adt)
-    * add hydrogens
-    * specify grid
-   * retrieving ligands
-  * follow the "upper half" of the ''docker'' script for preparing the receptor and the ligands for docking. It is suggested to really go through the script line by line and not to just execute it:
-   * split .mol2 ligand collection into many files
-   * name each correctly
- 
- === Step 3: Submit jobs to BOINC server ===
- 
- This step involves the specification of work units. This is not completely trivial, since one job involves man files that need to be available at compute time. Some are invariant to the ligand, e.g. the receptor and the grid representing its force field, some are varying with every ligand, here especially the ligand itself.
- 
-  * script to submit work units
-  * script to be executed to start autodock
- 
- The middle part of the ''docker'' script is to be executed on the server. It resides [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-client.sh;hb=HEAD|here]] ([[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob_plain;f=server-examples/autodock/dock-client.sh;hb=HEAD|download]]) . 
- 
- === Step 4: Start BOINC clients ===
- 
-  * Start your own and address them to your project
-  * When this works, try persuading your peers to also run some work units
- 
- === Step 5: Analyse results ===
- 
- Again, this step was not conceptionally changed, except for a few file locations have been modified. This just slightly adapted version of ''docker'' 's "lower half" is kept [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-post.sh;hb=HEAD|here]].
- 
-  * it is basically a single script to execute - but from the right location
  
  == BOINCed variant of Raccoon ==