[Debian Wiki] Update of "BOINC/Server/Projects/AutoDock" by SteffenMoeller

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The "BOINC/Server/Projects/AutoDock" page has been changed by SteffenMoeller:
https://wiki.debian.org/BOINC/Server/Projects/AutoDock?action=diff&rev1=56&rev2=57

Comment:
partial rewrite of the filtering of results

  {{attachment:BOINC_Server_AutoDock_Overview.png}}
  
  In the following, we describe the yellow arrow of above figure, i.e. how to get from the boinc-server-autodock Debian package with the help of what is shipping with boinc-server-maker to a web site that invites users to contribute and to a repository of ligand evaluations that can be interpreted by Raccoon. All scripts described or referenced below (if not referenced directly) are available from the [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=summary|git repository]]. 
+ 
  == Preparation of BOINC side ==
  
  The AutoDock BOINC project first of all is a regular BOINC project. All tools one knows about how to set up BOINC projects are working completely the same. We prepared a script to set up the AutoDock project at a predefined location with no human intervention. As nice as it is, please take the extra time to mentally follow the [[BOINC/ServerGuide]]. This transports a bit - not too much - of an extra understanding on how BOINC works internally, which we consider to help you all in helping us to improve the workflow. The current implementation is working solely with AutoDock Vina. Support for the classical AutoDock 4.x was once described on [[BOINC/ServerGuide/AutoDockApp]] and has yet to be updated and incorporated into our scripts.
  
  The executable scripts all reside in /usr/share/boinc-server-autodock/bin. All BOINC-specific preparation is completed with the script "[[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/install.sh|install.sh]]" in that directory. Caveat: This first cleans the database, do not use it inadvertedly. Then, it invokes separate scripts to perform steps 2.2 and 2.3 as described below.
  
+ === Technical preparation ===
+ 
+ Below, we propose to keep ligands files in directories. Those ligand files are plenty - it may be millions. Classical file systems like 'ext3' will not handle those easily. Which alternative to chose is a long debate in the community. The file systems 'xfs', 'jfs' and 'ext4' should perform well. A problem remains with tools like 'ls' that attempts to read through all files. We suggest to reserve half a terabyte for the project, which will allow to keep several folders will ligands for input
+ and results alike.
+ 
- === Project-specific configuration ===
+ === Docking-specific configuration ===
  
  The script [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/install.sh|install.sh]] expects a set of environment variables to be defined. By default all the values are being retrieved from the script [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=share/autodockvina_set_config.sh|autodockvina_set_config.sh]].
  
@@ -100, +106 @@

  
  === Results filtering ===
  
- Having the simplest assimilator implementation, it requires additional effort to process the work results. The compounds names together with predicted binding affinities may be extracted from the output files with use of a tool [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/autodockvina_get_top_energies.sh|autodockvina_get_top_energies.sh]] provided by boinc-server-autodock package. This script, executed in the directory with output files or with appropriate input parameters, should output the ligands names with binding affinity values. This data may be the first of interest for the project owner, and the script may easily be extended to extract more detailed information about docking results from the output files and the database. From the social point of view, it can be interesting to get the list of top ligands together with the names of users whose computers found them, and to display them at the project website. 
+ The default-assimilator of the BOINC project places all returned work units in separate files.
+ This is nicely compatible with an automated processing by shell scripts - the alternative would be to fill a database while performing the assimilation. 
+ The script [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/boinc-server-autodock.git;a=blob;f=bin/autodockvina_get_top_energies.sh|autodockvina_get_top_energies.sh]] retrieves the compound names together with predicted binding affinities from the output files.
+ The script by default expects to be executed in the directory with output files.
+ It produces a table with ligands names and corresponding binding affinity values.
+ This data may be the first of interest for the project owner, and the script may easily be extended to extract more detailed information about docking results from the output files and the database.
+ To keep attracting users, it is suggested to routinely retrieve the list of top ligands together with the names of users whose computers found them, and to display this info at the project website.