CONFIDENTIAL Systems Biology for Drug Discovery Meta Core

CONFIDENTIAL Systems Biology for Drug Discovery Meta. Core. TM (System requirements and installation) Copyright Gene. Go 2000 -2003

System Requirements - Server • CONFIDENTIAL Hardware: – Dual XEON 3. 2 or higher, XEON Dual Core 2. 2 or higher, Opteron 2. 2 or higher – 4 or more GB of memory – 250 GB SCSI/SAS HDD • 80 GB minimum for database • 20 GB minimum for application • • – RAID is recommended Operating system: – Red. Hat Enterprise Linux 4/5 (32 or 64 bit) – Su. SE 10 (32 or 64 bit) – Cent. OS 4/5 (32 or 64 bit) Software: – Oracle RDBMS 10. 2 – Oracle client with development libraries and database utilities (exp/imp) – Development packages (gcc, make, etc) – X Window base + libs + development packages (needed for some libraries) – Java JDK version 1. 5. 0 or higher – bzip 2 is required System settings – In order to use paper highlighting capabilities, Meta. Core server should have HTTP access to Pub. Med Oracle settings: – Dedicated server mode (not shared!) Copyright Gene. Go 2000 -2003

System Requirements - Client • • CONFIDENTIAL Hardware: – 2. 0 GHz processor or higher is recommended – 1 GB RAM or more Operating system: – Windows 2000/XP/Vista, Mac Software: – Internet Explorer 6 or higher, Safari 3. 0, Firefox 3. 0 or higher – Macromedia (Adobe) Flash plugin version 8 or higher – JRE 1. 5. 0 for Map. Editor and Meta. Search Software and OS settings: – Access to ports 8100 (or 80 if configured to use this port) on the Meta. Core server – Popup window blockers should be switched off – Active. X execution should be enabled for report generation Copyright Gene. Go 2000 -2003

CONFIDENTIAL Client/Server Architecture • • • Oracle server and Meta. Core software can be installed on the same or separate machine When using separate servers for Oracle and MC, Meta. Core should have an access to port 1521 of Oracle server Fast (Gig. E is recommended) network connection is required between MC and Oracle Internet tcp/80 tcp/1521 Meta. Core tcp/8100 tcp/8001 Oracle Client computer Copyright Gene. Go 2000 -2003

Installation • • • CONFIDENTIAL Install Oracle server and client, create Oracle instance for Meta. Core Install JDK on Meta. Core server Create “genego” user on the Meta. Core server - you should install everything under this user Unpack. tar. gz distribution Set ORACLE_HOME and JAVA_HOME Run “configure” script, specify installation prefix, Oracle connection parameters Run “make” If installation is successful, you can run MC by executing startup script If you want to run Meta. Core on standard http port, you should manually edit httpd. conf, located inside Meta. Core tree (just make sure it still runs under genego userid) and run startup script under the root account See instalation manual for details Copyright Gene. Go 2000 -2003

Updates CONFIDENTIAL • • • Unpack update outside Meta. Core installation tree Under “genego” user run “configure” script, specify installation prefix Run “make” • Update will also back up data and scripts in “backup” folder - don’t remove it Copyright Gene. Go 2000 -2003

Maintenance • • CONFIDENTIAL Backups: – Oracle backups - full or partial (only user data tables) data dump – Filesystem backups - several directories inside Meta. Core tree, containing original data files uploaded, jobs status + maps folder (if using Map. Editor) Temporary files: – You can set up cron job, deleting files which are week older in Meta. Core tmp directories – Automatic cleanup is performed during every MC update installation Monitoring: – Apache’s access_log and error_log are available for diagnostics and access statistics Firewall: – Meta. Core server: • Open TCP ports 8100 (or 80, depending on settings) for incoming connections • Allow outgoing HTTP connections to Pub. Med servers • Allow outgoing TCP connections to Oracle server’s port 1521 (if installed on separate machine) – Oracle server: • Open TCP port 1521 for incoming connections from Meta. Core server Copyright Gene. Go 2000 -2003