Bug 2534:

  Added readme.txt, license.txt and thirdpartylicenses.txt to root of repository
  Added dependencies.csv and edited readme.txt to refer to it

svn path=/vcell/trunk/VCell/; revision=9470

dependencies.csv

@@ -0,0 +1,75 @@
+"Package Name","License(s)","Location in Repository","Function","Notes"
+"Apache Commons Math","Apache License v. 2.0","/VCell/apache_commons_math_2.2.jar",,
+"ARQ-2.8.1","Custom MIT style license ",,,
+"Bioformats_omexml_locicommon","Choice of GPL 2.0 or Commercial License – Cannot Release","/Vcell/bioformats_omexml_locicommon_brnch41.jar",,
+"COPASI","Artistic License 2.0 for non-commercial use, Restricted license for commercial use","/Vcell/copasi_build30.jar",,
+"GlgGraphLayoutNG","Custom Proprietary – we can distribute object code only.","/Vcell/GigGraphLayoutNG.jar",,
+"ICU-4J","BSD","/Vcell/ICU-4J.jar",,
+"IRI","Sun Microsystems Free License","/Vcell/iri-0.7.jar",,
+"JAI_codec","Sun Microsystems Free License","/Vcell/jai_codec.jar",,
+"JAI_core","Sun Microsystems Free License","/Vcell/jai_core.jar",,
+"JavaCC","BSD","/Vcell/javacc4.0.jar",,
+"Jdom","Custom Apache style license","/Vcell/jdom_1.0.jar",,
+"Jena","Custom MIT style license ","/Vcell/jena-2.6.2.jar",,
+"Jlink","Custom restrictive ","/Vcell/JLink.jar",,
+"js","Mozilla Public License 1.1","/Vcell/js.jar",,
+"jvisit","Custom BSD style license","/Vcell/jvisit.jar",,
+"libsblmj","LGPL 2.1 or later","/Vcell/libsbmlj.jar",,
+"log4j","Apache License v. 2.0","/Vcell/log4j-1.2.13.jar",,
+"Lucene-core","Apache License v. 2.0","/Vcell/apache_commons_math_2.2.jar",,
+"MiriamJavaLib","GPL – this dependency is being removed","/Vcell/MiriamJavaLib-standalone-20080421.jar",,
+"NetCDF","Custom MIT style license ","/Vcell/NetCDF2_2_20_VCell.jar",,
+"ojdbc5","Oracle Technology Network Development and Distribution License","/Vcell/ojdbc55.jar",,
+"oracle_classes12","Oracle Technology Network Development and Distribution License","/Vcell/oracle_classes12.jar",,
+"org.junit.source","Common Public License v. 1.0","/Vcell/org.junit.source_4.8.1.v4_8_1_v20100427-1100.jar",,
+"Script-api","part of Java","/Vcell/script-api.jar",,
+"Script-js","part of Java","/Vcell/script-js.jar",,
+"slf4j-api","X11 License – essentially same as MIT license","/Vcell/slf4j-api-1.5.6.jar",,
+"slf4j-log","X11 License","/Vcell/slf4j-log4j12-1.5.6.jar",,
+"sonic_Client","RESTRICTED LICENSE – We can't distribute any part of it","/Vcell/sonic_Client.jar",,
+"sonic_Crypto","RESTRICTED LICENSE – We can't distribute any part of it","/Vcell/sonic_Crypto.jar",,
+"sonic_Selector","RESTRICTED LICENSE – We can't distribute any part of it","/Vcell/sonic_Selector.jar",,
+"sonic_XA","RESTRICTED LICENSE – We can't distribute any part of it","/Vcell/sonic_XA.jar",,
+"Stax-api","Apache License v. 2.0","/Vcell/stax-api-1.0.1.jar",,
+"Wstx-asl","Choice of LGPL or Apache 2.0","/Vcell/wstx-asl-3.2.9.jar",,
+"xercesImpl","Apache License v. 2.0","/Vcell/xervesimpl-2.7.1.jar",,
+"Xml-apis","Apache License v. 2.0","/Vcell/xml-apis.jar",,
+"Acme","ACME Freeware license (Modified BSD)","/Vcell/thirdParty.jar",,
+"genlogic","Custom non-commercial license – potential problem","/Vcell/thirdParty.jar",,
+"Iowagie","Mozilla Public License 1.1","/Vcell/thirdParty.jar",,
+"Sonicsw","RESTRICTED LICENSE – We can't distribute any part of it","/Vcell/thirdParty.jar",,
+"RPI – graphdrawing","Public Domain","/Vcell/thirdParty.jar",,
+"Stanford-enalbert","Custom license – seems okay","/Vcell/thirdParty.jar",,
+"Flanagan-fmath","Custom, problematic terms – currently violated - probably needs replacing","/Vcell/thirdParty.jar",,
+"GIFUtils","Public Domain","/Vcell/thirdParty.jar",,
+"Jama","Public Domain","/Vcell/thirdParty.jar",,
+,,,,
+"NUMERICS PACKAGES:",,,,
+"BLAS (incl LINPACK)","BSD","Numerics",,
+"csfqp","RESTRICTED LICENSE","Numerics",,
+"GLUT","Free BSD style license","Numerics",,
+"Hy3S","GPL 2.0","Numerics",,
+"IDAWin","UCHC","Numerics",,
+"Ifortran","INTEL Library – not free.  ","Numerics",,
+"LibSBML","LGPL","Numerics",,
+"NetCDF","Custom MIT style license ","Numerics",,
+"PCGPack ","License status Pending – can't release for now","Numerics",,
+"Qhull","Custom free license","Numerics",,
+"Smoldyn","GPL 2.0 – use okay since it is a separate executable","Numerics",,
+"Sonic ","RESTRICTED LICENSE – We can't distribute any part of it","Numerics",,
+"Stochastic – Gibson Original","UCHC","Numerics",,
+"Stochastic – VcellStoch","UCHC","Numerics",,
+"Sundials","BSD","Numerics",,
+"TinyXML","Custom MIT style license ","Numerics",,
+"zip and unzip","Custom MIT style license ","Numerics",,
+"zlib","Custom MIT style license ","Numerics",,
+,,,,
+"Chombo","BSD",,,
+"Frontier","LGPL",,,
+,,,,
+,,,,
+"New in 5.0 Beta",,,,
+"JSCi","LGPL  2.1","/Vcell/vcellClientThirdParty.jar",,
+"wsdl4j","Common Public License v. 1.0","/Vcell/wsdl4j-1.5.1.jar",,
+"Apache Commons Discovery","Apache License v. 2.0","/Vcell/commons-discovery-0.2.jar",,
+"Apache Commons Logging","Apache License v. 2.0","/Vcell/commons-logging-1.0.4",,

install.txt

@@ -0,0 +1,123 @@
+install.txt
+
+=======================================================================
+=======================================================================
+=============== Standalone Installation ===============================
+=======================================================================
+=======================================================================
+
+
+VCell Client
+============
+
+create a vcell.properties from vcell.properties.standalone_template (e.g. edit to specify installation directory).
+
+run VCellClientTest
+
+usage: VCellClientTest ( (-local [userid password]) | (-open filename) ) -Dvcell.propertyfile="installdir/vcell.properties" -Xmx500M
+
+
+
+
+=======================================================================
+=======================================================================
+=============== Distributed Installation ==============================
+=======================================================================
+=======================================================================
+
+A Virtual Cell multi-user distributed application requires 
+- a JDBC compliant relational database (e.g. Oracle 11g - Oracle)
+- a JMS compliant message oriented middleware (MOM) (SonicMQ - Progress Software)
+- a PBS-like scheduling middleware (Torque, Maui, Rocks cluster)
+
+The VCell services consist of a
+
+1) VCell client application.
+2) Bootstrap service (authentication), VCell Connection - provides RPC and messaging services to the client.
+3) VCell Services (Simulation dispatcher, Database, Simulation Data, Simulation Data Exporter, Simulation launcher).
+4) Cluster Managment Console
+
+1) VCell Client
+===============
+cbit.vcell.client.test.VCellClientTest ( ((-local|host[:port]) [userid password]) | (-open filename) ) -Dvcell.propertyfile="installdir/vcell.properties" -Xmx500M
+
+2) VCell Bootstrap services
+===========================
+create a vcell.properties from vcell.properties.server_template (e.g. edit to specify installation directory).
+
+cbit.vcell.server.LocalVCellBootstrap host port messaging [logfile|-] -Dvcell.propertyfile="installdir/vcell.properties" -Xmx500M
+
+3) VCell Cluster services
+=========================
+create a vcell.properties from vcell.properties.server_template (e.g. edit to specify installation directory).
+
+cbit.vcell.messaging.server.SimulationWorker {-local|-pbs} serviceOrdinal memorySizeMB [logdir]
+cbit.vcell.messaging.server.DatabaseServer serviceOrdinal [logdir]
+cbit.vcell.messaging.server.SimDataServer serviceOrdinal [EXPORTONLY] [logdir]
+cbit.vcell.messaging.server.SimulationDispatcher serviceOrdinal [logdir]
+
+4) Server management console
+============================
+cbit.vcell.messaging.admin.ServerManageConsole
+
+
+=======================================================================
+=============== ORACLE DATABASE CONFIGURATION =========================
+=======================================================================
+
+Database creation commands (in sqlplus or other database client - as user "sys").
+
+oracle-sql> CREATE USER VCELL
+oracle-sql> PROFILE "DEFAULT"
+oracle-sql> IDENTIFIED BY "password" DEFAULT TABLESPACE "USERS"
+oracle-sql> TEMPORARY TABLESPACE "TEMP"
+oracle-sql> ACCOUNT UNLOCK;
+
+oracle-sql> GRANT UNLIMITED TABLESPACE TO VCELL;
+oracle-sql> GRANT "CONNECT" TO VCELL;
+oracle-sql> GRANT "RESOURCE" TO VCELL;
+oracle-sql> ALTER USER VCELL DEFAULT ROLE  ALL;
+oracle-sql> COMMIT;
+
+To create the VCell tables run SQLCreateAllTables either command-line with the proper classpath or via the following.
+
+java> cbit.vcell.modeldb.SQLCreateAllTables.main("oracle","database_host", "database_sid", "vcell", "vcell_database_password");
+
+in "vcell.properties" file:
+
+vcell.server.dbConnectURL = jdbc:oracle:thin:@database_host:1521:database_sid
+vcell.server.dbDriverName = oracle.jdbc.driver.OracleDriver
+vcell.server.dbUserid = vcell
+vcell.server.dbPassword = vcell_database_password
+
+
+=======================================================================
+=============== SONICMQ MESSAGING SERVER CONFIGURATION ================
+=======================================================================
+
+create queues: 
+
+fileChannel, simReq, dataReq, dbReq, simJob, workerEvent, lsfJobInfo
+
+create topics:
+
+serviceControl, daemonControl, clientStatus
+
+in "vcell.properties" file:
+
+vcell.jms.provider = SonicMQ
+vcell.jms.url = tcp://jms_host:2506
+vcell.jms.user = jms_user
+vcell.jms.password = jms_password
+vcell.jms.queue.fileChannel = fileChannel
+vcell.jms.queue.simReq = simReq
+vcell.jms.queue.dataReq = simDataReq
+vcell.jms.queue.dbReq = dbReq
+vcell.jms.queue.simJob = simJob
+vcell.jms.queue.workerEvent = workerEvent
+vcell.jms.queue.lsfJobInfo = lsfJobInfo
+vcell.jms.topic.serviceControl = serviceControl
+vcell.jms.topic.daemonControl = daemonControl
+vcell.jms.topic.clientStatus = clientStatus
+vcell.jms.workerPrefetchCount = 1
+vcell.jms.servicePrefetchCount = 1

license.txt

@@ -0,0 +1,9 @@
+All code in the Virtual Cell software written by the Richard D. Berlin Center for Cell Analysis and Modeling at the University of Connecticut Health Center is 
+
+Copyright (c) 1999-2011 University of Connecticut Health Center 
+
+and licensed under the MIT License (MIT):
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.