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SOMA2 Modelling Environment README File
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Version 1.4 Aluminium (31 Jan 2012)
Overview
--------
SOMA2 is WWW browser operated modelling environment for computational
drug discovery and molecular modelling with workflow capabilities.
SOMA2 offers interfaces to scientific programs, which can be connected
as a workflow. The workflow is then automatically executed in the computing
environment and the results can be analysed within the SOMA2 environment.
SOMA2 supports use of scientific applications in remote computers as well as in
the local SOMA2 server. From version 1.4 SOMA2 supports also grid computing and
operations related to X509 certificate and proxy maintenance, bringing yet
larger computing scalability under one centralized system.
SOMA2 installation package contains only a few SOMA2 capsules (descriptions
that define the program interfaces and facilitates the automatic execution of
programs). These capsules use free and open source licensed Open Babel program
package that is distributed alongside with SOMA2. It is intended that installers
of SOMA2 will create the SOMA2 capsules for the scientific programs available
at their local sites. Almost any scientific application operated "traditionally"
from the command line can be attached to be used via SOMA2.
Documentation
-------------
The SOMA2 installation package contains only the SOMA2 user manual in html
format. It will be automatically installed to be used via the SOMA2 WWW
interface when the SOMA2 package is installed. The rest of the end-user
documentation (user manual, tutorials) as well as the technical documents
(installation, WWW interface, workflow manager, how to create SOMA2 capsules)
are available on SOMA2 WWW pages, see http://www.csc.fi/soma.
Contents of the Package
-----------------------
Brief overview of the installation package structure. The tools associated with
each of the SOMA2 modular components are also listed.
- capsules
SOMA2 capsules (scientific program descriptions)
Tools: XML, shell scripts
- grape
Workflow manager program Grape
Tools: Java
- somaweb
CGI program components of SOMA2 user interface
Tools: Perl
- somaweb-data
WWW data components of SOMA2 user interface
Tools: JavaScript, HTML, CSS
- somaweb-lib
Support libraries of SOMA2 user interface and SOMA2 toolkit
Tools: Perl
- toolkit
SOMA2 toolkit
Tools: Perl, shell scripts
- xsd
XML schema for SOMA2 program XML descriptions
- install.sh
SOMA2 installation script
- somake
SOMA2 build tool
- somake.properties
Main configuration file for SOMA2 installation
- third-party
Third-party libraries and components included in this package
Please refer the technical documentation for the details of the different
components.
Changes
-------
For changes and update history of SOMA2, see files "CHANGES" and "ChangeLog",
which are included in this installation package.
Installation
------------
Please edit file "somake.properties" to specify the installation locations
and other system specific issues. Download the third-party libraries and
components that are needed before the installation. See details in the
"Technical Requirements" and "Third-Party Components" below and the
detailed instructions in every download package.
Then execute installation script "install.sh" which will install the files.
Note that this may require "root" user privileges to the current system.
Make sure that all the installation locations have read and execution
permissions for all (or for dedicated users/groups). Note that directory
containing the CGI binaries and directory containing SOMA2 capsule log files
require special permissions. For detailed description of the installation,
see "SOMA2: Technical Requirements and Installation" document available on
SOMA2 WWW pages.
SOMA2 uses several third-party libraries and program components. Some of
them are included in this package, some are distributed as separate packages
and some of them have to obtained from the program vendor. A few of the
libraries must be installed before running install.sh script. For the details,
see chapters "Technical Requirements" and "Third-Party Components" below.
SOMA2 user interface is a CGI web application so it needs a WWW server to
operate. None of the WWW server related components are included in this package
and they should be installed before the actual SOMA2 installation process. See
"Technical Requirements" below.
Technical Requirements
----------------------
General technical requirements for SOMA2 installation are described below.
Installation locations of libraries refer to "somake.properties" configuration
file definitions. If not otherwise stated, the default installation location
of a library can be used.
Server:
- Linux operating system with standard GNU utilities (gsed, awk, etc.)
- Java JDK 1.5 or later (http://www.sun.com/java) with additional libraries
JGraphT Java library (http://jgrapht.sourceforge.net)
JGraphT 0.5.3 is included in SOMA2 installation package in
directory "third-party/jgrapht/"
Installed into: "${bindir}/grape/lib/"
Installed by SOMA2 installer
- Apache ant build tool (http://ant.apache.org)
- Perl 5.8 or later with additional libraries
Perl core modules
Supplied as part of Perl distribution
XML::Twig (http://www.xmltwig.org)
This library needs to be obtained from the software vendor and
installed manually, available also as CPAN module (http://www.cpan.org)
VOMS::Lite
This library needs to be obtained from the software vendor and
installed manually, available also as CPAN module (http://www.cpan.org)
Template Toolkit (http://www.template-toolkit.org)
This library needs to be obtained from the software vendor and
installed manually, available also as CPAN module (http://www.cpan.org)
- Passwordless SSH communication to all computing platforms running programs
connected to be used via SOMA2
Excluding "localhost" and grid
(in cases where SOMA2 and programs are run on the same platform or
applications are run in grid)
- Shared disk between all computing platforms and the server running SOMA2
User project files and the scripts executing the actual programs are
stored in the shared disk
Excluding "localhost" and grid
- The same user account must exist in all the computing platforms and
the server running SOMA2
Excluding "localhost" and grid
- Apache 2.x WWW server (http://httpd.apache.org)
User authentication (HTTP Basic, PAM, Cookie, Etc.)
SSL protocol for secure communication
Altered suEXEC module to enable CGI program execution as an authenticated user
Source code and instructions for altered suEXEC are
available from the SOMA2 WWW pages see:
http://www.csc.fi/english/pages/soma/downloads
Client:
- WWW browser
JavaScript support enabled
Java Plug-in installed
Cookie support enabled (if cookie authentication used)
- SOMA2 is tested to be compatible with the following browsers
Internet Explorer 8/9
Firefox 3 and later
Opera 11
Chrome 14 and later
Third-Party Components
----------------------
SOMA2 modelling environment makes use of several third-party applications.
The installation locations of the third-party components, their functions
in SOMA2 and how to obtain/install them are described in the following.
Installation locations refer to "somake.properties" configuration file definitions.
- Ext JS JavaScript library (http://www.extjs.com)
All tables, popups and trees within SOMA2 user interface
Ext JS 4.0.2a is included in SOMA2 installation package in directories
"third-party/ext/" and "third-party/ext_images/"
Installed into: "${webdatadir}/ext/" and
"${webdatadir}/images/"
Installed by SOMA2 installer
- Open Babel (http://openbabel.sourceforge.net)
Molecule file format conversions and property calculation
Slightly modified version of Open Babel 2.2.3 is available
as a separate installation package, see:
http://www.csc.fi/english/pages/soma/downloads
Installed into: "${toolkitdir}/openbabel2"
Open Babel needs to be compiled and installed manually, please
use the provided version or SOMA2 will not function correctly
- JDB (http://www.isi.edu/~johnh/SOFTWARE/JDB/index_old.html)
ASCII data filtering tools
JDB 1.14 is available as a separate installation package, see:
http://www.csc.fi/english/pages/soma/downloads
Installed into: "${toolkitdir}/jdb"
JDB needs to be configured and installed manually
- SOMA2 supports several tools for building and visualising molecular structures.
Options are to use either ChemAxon Marvin or JMol and JChemPaint together
Chemaxon Marvin Java applets (http://www.chemaxon.com)
Marvin applets are not included in SOMA2 installation package
Installed into: "${webdatadir}/marvin"
Marvin needs to be obtained from the software vendor and installed
manually
JMol applet (http://jmol.sourceforge.net)
JMol applet is not included in SOMA2 installation package
Installed into: "${webdatadir}/jmol"
JMol needs to be obtained from the software vendor and installed
manually
JChemPaint applet (http://jchempaint.sourceforge.net)
JChemPaint applet is not included in SOMA2 installation package
Installed into: "${webdatadir}/jchempaint"
JChemPaint needs to be obtained from the software vendor and
installed manually
- NorduGrid ARC (http://www.nordugrid.org/arc/)
Excluding non-grid systems
Middleware for grid computing
NorduGrid ARC needs to be obtained from the software vendor and
installed manually
SOMA2 Software License
----------------------
SOMA2 Software is Copyright (C) 2004-2011 CSC - IT Center for Science Ltd.
SOMA2 Software is distributed under the terms of GNU General Public License.
SOMA2 Software refers to everything contained in this distribution, except for
third-party libraries and components located in "third-party" directory. SOMA2
Software also excludes used third-party libraries and components which are not
contained in this distribution. All the third-party libraries and components
are distributed under their licenses and they are copyrighted by their authors.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
How to Contribute
-----------------
Please see up-to-date instructions of how to contribute to the
SOMA2 effort from the SOMA2 WWW pages, see http://www.csc.fi/soma.
Additional Information
----------------------
For more information, please visit the SOMA2 WWW pages
http://www.csc.fi/soma
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