**Monthly Status Report for Systems & Application Support for National
Cancer Institute Center for Bioinformatics & Laboratory of Population
Genetics**

**Contract #: GS-35F-0562L Order #: 32528**

March 2007

[Desktop, Database Administration and Systems Support
4](#desktop-database-administration-and-systems-support)

[Key Accomplishments 4](#key-accomplishments)

[Outreach and Communications 18](#outreach-and-communications)

[Issues and Recommended Resolution
18](#issues-and-recommended-resolution)

[Conferences and Publications 18](#conferences-and-publications)

[caCORE 19](#cacore)

[Key Accomplishments 19](#key-accomplishments-1)

[Outreach and Communications 21](#outreach-and-communications-1)

[Issues and Recommended Resolution
21](#issues-and-recommended-resolution-1)

[Conferences and Publications 22](#conferences-and-publications-1)

[C3D 22](#c3d)

[Key Accomplishments 22](#key-accomplishments-2)

[Outreach and Communications 30](#outreach-and-communications-2)

[Issues and Recommended Resolution
30](#issues-and-recommended-resolution-2)

[Conferences and Publications 31](#conferences-and-publications-2)

[ATV 31](#atv)

[Key Accomplishments 31](#key-accomplishments-3)

[Outreach and Communications 31](#outreach-and-communications-3)

[Issues and Recommended Resolution
31](#issues-and-recommended-resolution-3)

[Conferences and Publications 31](#conferences-and-publications-3)

[caXchange 31](#caxchange)

[Key Accomplishments 31](#key-accomplishments-4)

[Outreach and Communications 32](#outreach-and-communications-4)

[Issues and Recommended Resolution
32](#issues-and-recommended-resolution-4)

[Conferences and Publications 32](#conferences-and-publications-4)

[CTMSi/C3PR/C3D Web Services 32](#ctmsic3prc3d-web-services)

[Key Accomplishments 32](#key-accomplishments-5)

[Outreach and Communications 32](#outreach-and-communications-5)

[Issues and Recommended Resolution
32](#issues-and-recommended-resolution-5)

[Conferences and Publications 32](#conferences-and-publications-5)

[caBIG Protocols 33](#cabig-protocols-1)

[Key Accomplishments 33](#key-accomplishments-6)

[Outreach and Communications 33](#outreach-and-communications-6)

[Issues and Recommended Resolution
33](#issues-and-recommended-resolution-6)

[Conferences and Publications 33](#conferences-and-publications-6)

[caArray 33](#caarray)

[Key Accomplishments 33](#key-accomplishments-7)

[Outreach and Communications 34](#outreach-and-communications-7)

[Issues and Recommended Resolution
34](#issues-and-recommended-resolution-7)

[Conferences and Publications 34](#conferences-and-publications-7)

[caBIG Support 34](#cabig-support)

[Key Accomplishments 34](#key-accomplishments-8)

[Outreach and Communications 35](#outreach-and-communications-8)

[Issues and Recommended Resolution
35](#issues-and-recommended-resolution-8)

[Conferences and Publications 35](#conferences-and-publications-8)

[caGRID 35](#cagrid)

[Key Accomplishments 35](#key-accomplishments-9)

[Outreach and Communications 35](#outreach-and-communications-9)

[Issues and Recommended Resolution
35](#issues-and-recommended-resolution-9)

[Conferences and Publications 35](#conferences-and-publications-9)

[caIntegrator 35](#caintegrator)

[Key Accomplishments 35](#key-accomplishments-10)

[Outreach and Communications 37](#outreach-and-communications-10)

[Issues and Recommended Resolution
37](#issues-and-recommended-resolution-10)

[Conferences and Publications 38](#conferences-and-publications-10)

[caMOD 38](#camod-1)

[Key Accomplishments 38](#key-accomplishments-11)

[Outreach and Communications 38](#outreach-and-communications-11)

[Issues and Recommended Resolution
38](#issues-and-recommended-resolution-11)

[Conferences and Publications 38](#conferences-and-publications-11)

[caNanoLab (formerly caLAB) 38](#cananolab-formerly-calab)

[Key Accomplishments 38](#key-accomplishments-12)

[Outreach and Communications 38](#outreach-and-communications-12)

[Issues and Recommended Resolution
38](#issues-and-recommended-resolution-12)

[Conferences and Publications 39](#conferences-and-publications-12)

[caTIES 39](#caties)

[Key Accomplishments 39](#key-accomplishments-13)

[Outreach and Communications 39](#outreach-and-communications-13)

[Issues and Recommended Resolution
39](#issues-and-recommended-resolution-13)

[Conferences and Publications 39](#conferences-and-publications-13)

[caTISSUE 39](#catissue)

[Key Accomplishments 39](#key-accomplishments-14)

[Outreach and Communications 39](#outreach-and-communications-14)

[Issues and Recommended Resolution
39](#issues-and-recommended-resolution-14)

[Conferences and Publications 40](#conferences-and-publications-14)

[DCP / DESK 40](#dcp-desk)

[Key Accomplishments 40](#key-accomplishments-15)

[Outreach and Communications 40](#outreach-and-communications-15)

[Issues and Recommended Resolution
40](#issues-and-recommended-resolution-15)

[Conferences and Publications 40](#conferences-and-publications-15)

[LPG Support 40](#lpg-support)

[Key Accomplishments 41](#key-accomplishments-16)

[Outreach and Communications 41](#outreach-and-communications-16)

[Issues and Recommended Resolution
41](#issues-and-recommended-resolution-16)

[Conferences and Publications 41](#conferences-and-publications-16)

[lpgLIMS 42](#lpglims)

[Key Accomplishments 42](#key-accomplishments-17)

[Outreach and Communications 42](#outreach-and-communications-17)

[Issues and Recommended Resolution
42](#issues-and-recommended-resolution-17)

[Conferences and Publications 42](#conferences-and-publications-17)

[Spores 42](#spores-1)

[Key Accomplishments 42](#key-accomplishments-18)

[Outreach and Communications 42](#outreach-and-communications-18)

[Issues and Recommended Resolution
42](#issues-and-recommended-resolution-18)

[Conferences and Publications 42](#conferences-and-publications-18)

[Application and Training Support Statistics
43](#application-and-training-support-statistics)

[Bioinformatics and Clinical Application Support Summary
43](#bioinformatics-and-clinical-application-support-summary)

#   {#section .unnumbered}

# Desktop, Database Administration and Systems Support

## Key Accomplishments

### Current

#### Account Maintenance

##### Managed user accounts and group memberships in NIH Active Directory, NCI E-Directory, NCICB OpenLDAP and Unix/Linux local password databases

##### Assisted users with expired passwords

##### Closed 233 NCICB Support Wizard Accounts Tickets

##### Set up Resource Accounts for individual developers to control and track access on QA Application servers

##### Maintained daily account synchronization between GForge project developers and CVS write access accounts

##### Created FTP and SFTP user accounts for TCGA test, analysis datasets downloads and analysis datasets management.

##### Created CPAS QA account and CPAS Role account

##### Beginning automation for the GForge to CVS account synchronization process

##### Removed Admin access on all GForge projects as well as CVS for terminated user

##### Created a SOP wiki as a guide for the creation of LDAP accounts

##### Added or modified accounts in OpenLDAP for CDS users

#### Desktop Support

##### LPG and NCICB desktop support ticket metrics met or exceeded NCI Network Center parameters

###### <http://dino.nci.nih.gov/support/coreservices/supportstats.html>

##### Closed 127 NIH Help Desk tickets

##### Corrected Daylight Savings change on various Win 2k pc\'s and servers

##### Installed Pointsec encryption software on LPG\\HC laptops

##### Installed Pointsec encryption software on NCICB\\6116 laptops

##### Placed hardware orders\\requests for 3 pc\'s and 4 laptops, and for memory for DBA Linux machines

##### Surplused 4 older monitors, 1 laptop and 1 pc

##### Temporarily moved some NCICB users in preparation for Stage 2 of move to East Jefferson

##### Worked on stage 2 of NCICB move to East Jefferson and any cleanup\\issues

##### Installed and set up new Linux box for Dr Hu

##### Worked with several remote users to get them the installer and license for Enterprise Architect

##### Configured and setup new windows box for Dr Finney

##### Worked on procuring new printers for 2115

##### Set up new desktops for contractor staff

#### Facilities Management

##### Coordinated maintenance for fire suppression system

##### Planning reorganization of Helgerman Court Server Room cabling

#### General Database Administration

##### Checked daily DB backups.

##### Installed Oracle patch 9.2.0.7 on cbiodev40 workstation to test implementation of this upgrade.

###### The upgrade from 9.2.0.6 to 9.2.0.7 is necessary due to Oracle desupporting 9.2.0.6 and therefore no longer providing security patches for that version.

###### Upgrade to version 9.2.0.7 in the DEV and QA environments is planned for the April maintenance window.Whatever was done

#### Patch Management

##### Patches are currently on hold until the upgrade to 9.2.0.7 is completed as patches for version 9.2.0.6 are no longer provided by Oracle.

#### Security Engineering

##### HHS Security Compliance

###### Modified the /etc/init.d/syslog on all Solaris servers to prevent syslogd from accepting messages from the network.

##### NCI Security

###### Delivered NIST 800-53 documentation for C3D. Several individual responses were required for each document.

###### Delivered NIST 800-53 documentation for DESK. Several individual responses were required for each document.

###### Delivered the 21 CFR 11 for C3D Document to the ISSO for response and approval. No response has been given yet.

###### Verified the use of Level 1-5 (L1-L5) distinction in the 800-53and updated documentation to reflect the change.

###### Collaborating with the Network Team to run a script that will fully integrate the HHS Minimum Security Configuration Standards for NCI. Continuing to update the master copy with the items that have been implemented during the April audit/data call.

###### Supported Information Systems Security Officer with data needed for the Office of Inspector General Audit

###### Assisted the Network Team with PIA creation 

##### Incident Reports:

###### WebGenome

####### Investigated webGenome report of malformed requests from developers by examining webGenome logs on Solaris server running Apache and JBoss

####### Documented log file aberrations and Internet Protocol (IP) source of aberrations

####### Traced back location of aberrant Internet Protocol (IP) address and found it internal to Health and Human Services (HHS)

####### Generated Investigation and Incident Report

###### Virtual Colonoscopy Breach

####### Extracted and delivered in hardcopy twenty (20) instances of full names and/or social security numbers and the corresponding patient files for the Virtual Colonoscopy breach to the NCI Imaging Group

####### Extracted and delivered in hardcopy forty six (46) instances of last names or partial names and the corresponding patient files for the Virtual Colonoscopy breach to the NCI Imaging Group

##### Disaster Recovery Testing

######  Continuing coordination of a full DRCP test and updating solutions (Documentation, DataGuard Status etc.). Documentation is now in place for a new test phase.

###### Meeting with the Systems Team and the Database Administration Team to coordinate NCIA Disaster Recovery Test simulating NCIA data loss

###### Documenting Disaster Recovery Test simulation Strategy

##### Privacy Impact Assessments

###### Delivered Privacy Impact Assessment (PIA) for The Cancer Genome Atlas (TCGA) to the Information Systems Security Officer (ISSO)

###### Assisted the Network Team with PIA creation

###### Updated the Point of Contact Information for the following NCICB applications per the Information Systems Security Officer\'s request for the existing Privacy Impact Assessments

####### NIH NCI Director\'s Challenge Toward a Molecular Classification of Cancer (caARRAY)

####### Cancer Data Standards Repository (caDSR) 

####### GForge

####### Nanotechnology Characterization Laboratory (formerly NCLFS, now NCL)

####### Quality Indicator Portal (QI Portal)

####### The Cancer Laboratory Information Management System (caLIMS)

####### Cancer Image (caIMAGE)

##### Apache Tomcat Vulnerability

###### Investigated Apache Tomcat JK Web Server Connector Stack Overflow Vulnerability for possible exposure

##### NCICB General Support System (GSS)

###### Concluded testing for the NCICB General Support System (GSS) Internal Security Test & Evaluation( ST&E)

###### Documented results of testing for the NCICB General Support System (GSS) Internal Security Test & Evaluation( ST&E)and generated recommendations for failures

##### NCIA C&A nearly completed (800-53, System Security Plan and Risk Assessment)

##### Patch Management:

###### Applied latest RHEL3 and RHEL4 system patched to NCICB Dev and QA Linux servers.

###### Applied Microsoft patches to all NCICB Windows Servers 

#### Server Hardware Support

##### Updated the Intel/AMD Server Inventory for NCICB

##### Built a Solaris 8 server named cbiogedp104 (previous was cbioapp201) for web-application server.

##### Rebuilt a Linux RHEL3 server, cbioatlas, and added two 146GB drives on this server.

##### Added two Gigabit Ethernet UTP cards in cbiodb2-d (SUN Fire v880) for migration.

##### Installed a cable management arm on cbiodb20 (SUN Fire v1280).

##### Contacted IBM regarding a hardware error with an IBM BladeServer, hc-nciacedara-2. They dispatched an on-site engineer who replaced the mainboard for the blade, and the problem has been resolved.

##### Built Windows 2003 server for NCIA Cedara project, HC-NCIACEDARA-2

##### Diagnose and implement several potential resolutions to reboot issues with cbiodb2-d

###### Placed support call with SUN, which eventually led to IO board replacement mentioned below.

###### Worked with SUN Field Engineer to repair IO fans in cbiodb2-d.

###### Worked with SUN Field Engineer to repair IO_board cbiodb2-d.nci.nih.gov

#### Server Room Migration

##### Re-created the MultiMigrate job for cbiodb10 to mirror the volumes to the EVA san at 6116.

##### Physically moved cbiodb20.nci.nih.gov from the 4th floor server room to 1st floor server room.

##### Physically moved cbiodb2-d.nci.nih.gov from the 4th floor server room to the first floor server room

##### Physically moved two SVM units from the 4th floor server room to the first floor server room

#### Storage Administration

##### Resolved performance issues, replaced failed hardware, recovered space on filesystems, continued monitoring and alerting for disk usage.

##### Migrated all of the NFS archivedg data to the loaner trays at HC.

##### Migrated NFS testdg to the loaner trays at HC.

##### Verified with the DBAs that the filesystem dbexport on cbiodb5 was no longer needed, and removed the filesystem, which was using the NFS Pool.

##### Removed the SVM volumes used by nfsb from both cluster servers

##### Added 500gb to /data10 on cbiodb530 for caArray.

##### Added 6gb to /nfsb/clinicaltrials, which was only 6gb to begin with.

##### Added 30gb to /backupfs on cbiodb10. This svm volume was also added to the Consistency Group on the SVM, since it is replicated to the 6116 svm domain.

##### Added 25gb to /nfsa/home.

##### Added 25gb to /nfsa/group.

##### Re-created the SVM MultiMirror jobs for backupfs on cbiodb5 and cbiodb10 to use the new EVA data at 6116.

##### Added 15g to /nfsb/ncicb.

##### File system cleanup script (logpurge.pl) deployed to active application servers and grid nodes to manage logs from Zope, JBoss, Tomcat

##### Replaced batteries in (4) Sun A1000 disk arrays

##### HC Storage Migration Phase 1 Project Plan

###### Completed STK SAN migration in 6116

####### Migrate cbiodb20 data from 4th floor SAN to 1st floor SAN

####### Migrate cbiodb2-d data from 4th floor SAN to 1st floor SAN

####### Clear SVM of old volumes, pools

####### Cleared all RAID sets on FLX240

####### Move FLC200 disk array to HC

####### Move FLX240 disk controller to HC

##### Execute multiple SAN audits against HC SAN using Brocade utility

##### Install updated version of Santricity on hcadmin3

##### FLX280 controller firmware upgrade

###### Coordinated firmware upgrade of FLX280 at Helgerman Court by Sun Engineer during maintenance, required to connect higher capacity drive shelves

###### Shut down all systems connected to HC SAN

###### Supported upgrade and integration of new shelves

###### Sun Engineer did not properly reapply settings after firmware upgrade, so SAN rapidly became unstable after maintenance

###### Worked for several hours during the maintenance weekend to get our storage back on line, including trouble shooting, working with our storage vendors and implementing a short term work around of disabling one controller on the FLX280

###### Later identified problem that Auto Volume Transfer (AVT) was re-enabled on controllers after firmware upgrade. Fixing this will require another SAN shutdown.

##### Disk array installation under FLX280

##### Prep FLA200 from 6116 for connection to FLX280 in HC

##### Deleted following HBAs from 6116 SVM

###### 21fd00051e03b35e (rhapsody)

###### 200000e069c00eb6 (jni)

###### 210000e08b05fd60 (qlogic)

###### 210000e08b051661 

##### Stale SVM volume issue on 6116 SVM resolved

##### Multiple mirror syncs and filesystem fsck\'s on cbiodb2-d to repair hardware issues

##### Add 500G to lpgws502:/data, expanding to 1.5TB 

#### Systems and Application Monitoring

##### Managed Sitescope monitors and license points

##### Sitescope monitoring of cbionfsa does not work when failed over to the other cluster node. The ssh key had to be the same between both cluster servers.

##### Updated sitescope monitor for cagrid QA and Prod, to add more monitor URL, with sequential monitoring for cagrid-browser

#### System and Network Administration

##### Closed 66 Support Wizard Systems and Performance Tickets

##### Installed primer3 on lpgws501, lpgws502 and ncicbstarfish, per request from Dr. Lee.

##### The SRL for home_rvg overflowed. Detached the rvg and resynced. After looking into this further discovered that all of the nfsa rvgs showed a status of paused due to network disconnection. When we fail the services over to cbiofs101, the rvgs are connected. Tried failing nfsb from cbiofs101 to cbiofs102 and that also becomes disconnected on that fs102. A case with Veritas has been opened.

##### The SRL for home_rvg overflowed again and had to be resynced.

##### Cluster Server Issues:

###### File Server cluster services hung several times. While working with Veritas to determine why the replication stopped working from cbiofs102 to lpgfs105, the cluster services hung and both nodes had to be rebooted. During one of the failovers of the nfsa services from cbiofs101 to cbiofs102, the cluster services hung when attempting to unmount /nfsa/lee_DataBase. Was unable to force a umount of the filesystem and therefore did a reboot of the server after moving all other services to the 2nd cluster node. Once cbiofs101 was rebooted, the nfsa services attempted to come up on cbiofs102 and hung the cluster services again. Ended up having to reboot this cluster node as well, after which the services came up, all on cbiofs101.

###### After all the cluster services were up, found that one volume, mgc, showed a status of Enabled/Needsync. The data within the volume appeared to be fine. Ran vxvol resync against the volume, which brought it back to Enabled/Active.

###### During March maintenance, backed out the latest Solaris recommended patches from cbiofs101, cbiofs102 and lpgfs105. We\'ll need to monitor the cluster services to see if we have any additional problems with it hanging.

###### After hours, had to fail over the nfsb services to fs102 to release the SVM volumes from which data was migrated, and then failed the services back to fs101. Also failed nfsd to fs102 and left them running on this node. An hour later, fs101 and all the NFS services running on this server were unresponsive and the system had to be rebooted. All NFS services were brought up on fs101 and left running on this server.

##### The root filesystem on lpgapp501 was filling up. The apache lpgws_rewrite.log was over 1gb in size so cleaned up the log file. This will no longer be a problem once the web applications are converted to apache2 during March maintenance.

##### Rewrote an FTP file synchronization script and moved that functionality from ncicbstarfish to the file server cluster. The script synchronizes files for public ftp access.

##### Added large file support to /nfac/caarraydata file system.

##### Added files to the public FTP server site.

##### Updated administration document for private/public IP and host/service naming information.

##### Installed Qmail software on cbiodb530 and cbiodb540 so that DBAs can get emails from the servers.

##### Sendmail troubleshooting / configuration on cbioapp101

##### Upgraded the Baseboard Management Controller firmware on all IBM BladeServers.

##### Upgraded the Management Module firmware for the IBM BladeCenter

##### Upgraded the IOS on the NCIA Cisco switch module located in the IBM BladeCenter

##### Troubleshot issue with Requisite Pro web site and created 3 requested Projects

##### Updated wiki with information on requisite pro server which includes basic info and instructions on how to create projects

##### Resolved cbioapp504 issues caused by auditd (known issue with RHEL), resolved by deleting audit.d logs

##### Per the request of App Support Manager, modified permissions on /nfsa/ftp/cacore/EVS/NCI_Metathesaurus/archive

##### Updated to jre1.5.0_10 on hcadmin2

##### Diagnose and resolve connectivity issues with nciavapacheprod5001 and nciavtomcatprod5001, bounce apache & tomcat

##### Multiple restarts of oracle http and reports services on nt-cbiohc-ocb to resolve connectivity issues

##### DST work

###### Verify correct time on approx. 30 hosts

###### Manually modifed time on a few Linux hosts that did not get DST patch

##### Multiple zope251 restarts on cbioapp102

##### Restart jboss402-app on cbioapp502 to resolve rembrandt issues

##### DNS changes for cbiodb20 & cbiodb2-d

#### Technology Stack

##### Created jdk1.5.0_10 32bit linux ncicb package

##### Created jdk1.5.0_10 64bit solaris ncicb package

##### Created jdk1.5.0_10 amd64 Linux ncicb package

##### Created jdk1.5.0_06 amd64 Linux ncicb package

##### Revised jboss binding port set generation script to simplify the process and to add new instances. 

##### Pre-configured and customized jboss-4.0.5.GA for new technology stack and created ncicb package

##### Updated port binding set configuration for Jboss binding manager for jboss405 instance

##### Verified Java JDK DST change patches on several servers

#### TestTrack Pro and CVS Support

##### Administered server configuration and project/repository access policy

##### Performed account, project group, and repository administration

##### Performed daily synchronization for GForge Project developer accounts with corresponding CVS repository accounts

##### Implementing automation of the GForge to CVS account synchronization process - In progress

##### Migrated caMod TestTrack Pro Bugs and Feature Requests to corresponding Trackers within GForge

##### Planning on SOP for inserting TestTrack Pro attachments to GForge trackers

##### Start of TestTrack Pro migration of Bug tracker to GForge tracker for Rembrandt

#### Tomcat/JBoss Deployments and Support

##### The following were deployed to Sandbox, Stage and/or Production tiers as requested by the development teams:

###### EVSUpdate

###### Downloadcenter

###### REMBRANDT v1.5

###### CGEMS

###### CSP

###### caMOD

###### SPORES

###### NCIA Portal

###### caBIG Protocols

###### caCORE 3.2

###### CDEBrowser 3.2

###### Curation Tool 3.2

###### UMLModelBrowser 3.2

##### Restarted tomcat on cbiogrid108 due to after hours page that the service was not working.

##### Work with developers to adjust Hibernate logging parameters for various applications on Stage & Prod - CSM, caCORE API, REMBRANDT & CGEMS.

##### Working on EVS Metaphrase trouble shooting for intermittent failures

##### Setup jboss404/ncicb-comm instance on solaris Dev and QA tiers

##### Setup jboss_deploy config files for sporesDB (spores.war) for Stage and Production

##### Restarted jboss404/ncicb-caint instance to refresh DB connections

##### Reconfigured QA ncicb-core UPT for CSM developers to clean up resource utilization

##### Contacted developers regarding the user lock out mechanism for UPT. Verified it was a known bug which is being addressed

##### Restarted MAGE-OM daemon on production to resolve connectivity issues with the DB

##### Setup startup script for both WebGenome RServe and analysis services on DEV tier (Analysis nodes) to handle startup upon reboot

##### Met with developers to setup a deployment script for the analysis server that would alleviate possible issues with the manual process.

##### Provided cdebrowser logs to developers for baseline comparison

##### Worked on REMBRANDT v1.5 release to Production

##### Restarted cbioapp101:jboss404-core instance due to \"out of memory\" (jvm) error

##### Troubleshoot cbioapp507 jboss404-caint instance java heap memory issue, after deployment of REMBRANDT. Increased min and max JAVA heap sizes to 2 GB.

##### Decommissioned (and archived) DTSRPC2_0 from Stage and Prod EVS Servers

##### Deployed NCIA portal to staging and production

##### Reconfigured tomcat (4.1.18) development environment for caBIG Protocols

##### Added Jboss 4.0.4 stack for caXchange CTOM API on DEV & QA servers.

##### Troubleshoot CGEMS Bulk Download issue (505 unable to change directory error), due to caftp-stage not having the mounted drives that hosted the files.

##### Evaluate the impact on the new tomcat vulnerability for mod_jk versions 1.2.19 and 1.2.20

#### Web/Application Server Maintenance

##### Closed 80 Support Wizard Deployment Tickets

##### Worked with LogicBlaze Fuse technical support on ssl and mod_jk configuration to make apache as the front-end for Fuse server.

##### Worked with LogicBlaze Fuse tech support on http binding module configuration issue.

##### Created CPAS QA environment using latest technology stack for Tomcat and JDK in preparation for upgrading stating and prod CPAS to v1.7

##### Deployed updates to the lpgws web application on lpgapp501 for LPG.

##### Migrated the web applications on lpgws501 to apache 2.2.3 during March maintenance.

##### Modified apache log rotation script to integrate caCORE 3.2 & caIntegrator applications into web usage statistics.

##### Modified apache log rotation script to perform self cleanup of fail safe files.

##### Installed and configure Logpurge on all caGRID QA servers

##### Identify issues post Logpurge installation, and provide help on Logpurge scripts improvement

##### Apache 223 upgrade completed on the 4-tier Linux web/app servers.

##### Apache 223 upgrade completed on the 4-tier caArray web/app servers.

#### Zope Updates and Support

##### Deployed the following to Stage and/or Production Tiers:

###### NCICB

###### EMICE

###### caIntegrator/Rembrandt

###### Presentations.zexp

###### ISPY (Plone)

###### CCCT (Plone)

##### Restarted production Zope251 on cbioapp102 and cbioapp104 after hours to resolve 23 different service availability issues.

##### Automated Zope251 container restarts through Sitescope for cbioapp101/102/104/105 to handle Zope unavailability issues.

##### Added new product PresentationManager for caBIG

##### Added new products GenericPloneSkin, Navigation, PrivateFolder, LDAPUserFolder for ISPY

##### Restarted caBIG production zope instance due to being unaccessible.

##### Created vhost conf files for tcga-analysis-dev.nci.nih.gov and edci-dev.nci.nih.gov/edci-ut apache URLs.

##### Requested DNS cname updates: http://edci-dev.nci.nih.gov, http://edci-ut.nci.nih.gov, http://tcga-analysis-dev.nci.nih.gov

##### Performed maintenance (zope pack) of all instances on all tiers (DEV, QA/UT, Stage, Prod)

##### Worked with developers on approval to archive, decommission old instances and sites on all tiers

##### Moved several application URLs from apache 1.3.33 to apache 2.2.3

##### Reviewed Tramline and Plonetramline (products that enhance ftp) for TCGA Plone site and provided feedback to developers.

##### Copied csp-secure (csp-files) data from dev to stage on the shared drive (cbionfsb) and wrote script to implement the process successfully.

#### Centra

##### App Support: Preparing for anticipated upgrade on 4/20/07; will schedule formal Breeze/Centra comparison as soon as upgrade is complete

##### App Support: Soliciting new quote for potential upcoming renewal.

#### SupportWizard

##### App Support: SupportWizard annual support contract expired in February. 

###### Worked with vendor to extend coverage and get new quote with reinstatement fee to cover time period until renewal. 

###### Prepared SOW, JFOC, and Purchase Request and collected relevant approval signatures for renewal to be processed by April 30, 2007.

#### VMWare ESX Server

##### Built a new VMWare VI3 Server, cbiovi3-402.nci.nih.gov. This server is located in the 6116/175 server room.

##### Migrated the following VMs from cbiovs404 to a new VI3 server, cbiovi3-401

###### cbiovdev5011 - EVS Development

###### cbiovqa5001 - EVS QA

###### cbiovqa5004 - EVS/caCORE QA

##### Migrated the following VM from cbiovs401 to a new VI3 server, cbiovi3-401

###### nt-cbiotrainst - LMS training test box

###### cbiovdev5004 - DB Services Tier Development

##### Updated all VI3 servers to current patch level

##### Updated all ESX 2 servers to current patch level

##### Allocated more memory to the following VMs

###### cbiovdev5020 - caBig Zope Dev

###### cbiovdev5031 - caBig Plone Dev

##### Increased the storage allocation to cbiovqa5003

##### Created online update depot for VI3 patches

##### Migrated the following failover VMs to cbiovi3-401

###### 6116-ncicbapps-4

###### nt-cbiohc-ocb

##### Created the following new VM\'s

###### cbiovwprofile-1 (optimizeit)

###### cbiovftppd5002

###### cbiovftppu5002

###### cbiovdev5044 (64 bit web app dev)

###### cbiovqa5013 (64 bit web app qa)

###### cbiovftpdev5002

##### Added additional VM drive onto cbiocaqa-1

##### moved cbiorp-1 image to cbiovs401

#### Linux FTP Server Migration

##### Began production pilot of SFTP server

###### Created users accounts for all 76 current SFTP users on the new LINUX SFTP server.

###### Added /etc/fstab mount entries and mounted all SFTP users' login directories.

###### Tested and verified that LINUX SFTP users' accounts are working from three different clients.

###### Created the cbioftps5000.nci.nih.gov virtual service on BigIP to support highly available SFTP service

###### Coordinated DNS entries for the host, the virtual service and server alias name.

###### Resolved access issues related to privileges on the SFTP server.

###### Cloned SFTP server cbiovftpps5001 to create cbiovftpps5002 for HA and load balancing behind BigIP

###### Added cbiovftpps5002 to BigIP SFTP pool

###### Registered cbiovftpps5002 in DNS

###### Resolved issues with SSHD on cbiovftpps5001 and cbiovftpps5002 and tested access to caftps.nci.nih.gov through the firewall 

###### Provided access authentication information to TCGA team for their tcgsdryrun user.

###### Creating/Modifying documentation for SFTP administration and SFTP user account creation

##### Migrated anonymous FTP sites to new Linux server, replacing cbioftp1

###### Added mounts to /etc/fstab on cbiovftppd5001 so it can fully replace cbioftp1.

###### Changed the BigIP pool for ncicbfalcon to use the new RedHat LINUX VSFTP server.

###### Had CNAME ftp1.nci.nih.gov modified to resolve to cbioftppd5000.nci.nih.gov.

###### Had host cbioftp1.nci.nih.gov changed to a CNAME in DNS resolving to cbioftppd5000.nci.nih.gov.

###### Had host ncicbfalcon.nci.nih.gov changed to a CNAME in DNS resolving to cbioftppd5000.nci.nih.gov

##### Working on migrating authenticated FTP sites/user accounts to new Linux server, replacing cbioftp2

###### Created NFS mounts on cbiovftppu5001.nci.nih.gov

###### Duplicated cbioftp2.nci.nih.gov authenticated user account caarrayftp2 on cbiovftppu.nci.nih.gov

###### Migrated LPG reviewer account from cbioftp1.nci.nih.gov to caftpu.nci.nih.gov

### Planned

##### Datbase Administration

###### Finish testing and troubleshooting PostgreSQL replication from the binary implementation.

##### Security

###### Generate Privacy Impact Assessment for EAGLE

###### Internal Security Test & Evaluation: Finalize NCICB General Support System (GSS) Internal Security Test & Evaluation (ST&E) document

##### WebApps

###### Working with NCICB Web(Zope/Plone) developers on approval to archive/decommission old Zope instances and legacy web sites on all tiers. Establish a standard process to do the same going forward.

###### Create an inventory of all websites hosted under various Zope/Plone stacks as a preliminary task to plan for future migration projects.

##### GForge

###### Create SOP for inserting TestTrack Pro attachments to GForge trackers.

###### Complete TestTrack Pro migration of Bug tracker to GForge tracker for Rembrandt.

##### Server Engineering

###### Build LexGrid 2.0 prototype server and work with EVS team on performance tuning and baselining

###### Begin work on Oracle Cluster Server Project

##### Storage

###### Complete 6116 STK SAN migration to EVA

###### Complete SAN firmware updates and disk array installation at HC

## Outreach and Communications

##### Attended weekly CBIIT Infrastructure meetings

##### Met with Systems COTR weekly

## Issues and Recommended Resolution

##### NCICB Web Team is deploying more web sites under the dynamic Zope/Plone architecture. Work is in progress to collaborate with the developers and to produce a meaningful SOP on various aspects surrounding this architecture. In particular, fail-over and web site recovery strategies need to be discussed for a more robust web architecture with high availability.

##### We need to discuss 3DNS project and more forward to enable automatic fail-over between NCICB sites

## Conferences and Publications

##### Two engineers attended FOSE 2007 at the Washington DC Convention Center 

# caCORE

## Key Accomplishments

### Current

#### General

##### App Support: Updated general caCORE staging and production content on the Download Center

##### Systems: Modified apache log rotations to integrate caCORE 3.2 applications into web usage statistics.

#### caAdapter

##### Training: Requested to participate in a user review for updated slides for the current training available for caAdapter. Updates will include in-depth model mapping functionality.

#### caDSR Tools

##### DBA: Refreshed SBR and SBREXT schemas in UMLSTG (cbiodb20) database with current SBR and SBREXT schema contents of CBPROD (cbiodb10) 

##### DBA: Deployed script (load_tool_options.sql) for data loading in SBREXT owned objects in UMLSTG (cbiodb20) for Sandbox refesh (CDE Curation Tool)

##### DBA: Deployed script (update_options_url.sql) for data loading in SBREXT owned objects in CBPROD (cbiodb10) for caDSR Sandbox

##### DBA: Deployed script (load_options_url.sql) for data loading in SBREXT owned objects in CBPROD (cbiodb10) for caDSR Freestyle Search

##### DBA: Updated schema SBR tables with edited version of script (update_ui_metadata_live.sql) with new URLS as they related to the Sandbox

##### DBA: Createad script for automated refresh.

##### Tier 2: Participating in future design meetings to represent the modeling perspective; first meeting was 3/30/07

##### Systems: Re-enabled the \"touch\" cron job to redeploy UMLModelbrowser on production/sandbox every night to refresh model views dynamically until the software bug is fixed.

##### Systems: Deployed CDECuration Tool to sandbox

##### Systems: Performed UML Modelbrowser (Sandbox) troubleshooting after DB refresh.

##### Systems: Sentinel Tool and FreeStyle tools -Investigate and resolve issues on sandbox and production after DB refresh

#### EVS 

##### DBA: At the request of developers, installed Oracle 10g client on cbioatlas server and configured for use by the meme user on this machine.

##### DBA: Move the metaphrase schema from the old cbioatlas database to metaphrase_atlas on EVSSTG.

##### DBA: Created script to automatically refresh the Metathesaurus schema from source to target database.

##### App Support: Modifying the NCICB Download Center to allow for the submission of NLM licensing agreements.

##### App Support: Updated EVS staging and production content on the Download Center

##### Systems: EVS Update deployed.

##### Systems: Developed scripts to support EVS database updates

#### LexGRID

##### At the request of the development team, investigated time differential of deploying LexGRID data in Staging versus Development environments.

###### Discovered that a single application server is used to load the data to the servers on both tiers.

###### This server is on the same LAN segment as the Staging database, but must cross the network to access the Development database.

#### caBIO 

##### DBA: Created a cmapload schema in CBTEST database for data loading pertaining to the caBIO refresh of data. 

##### Systems: Modified caCORE 3.2 application WAR file to minimize the hibernate SQL logging and redeployed on Stage, Prod and Sandbox servers after consulting with the caBIO developers

##### Systems: Switched the Production caCORe31/32 and Sandbox caCORE32 API to point to Stage caBIO DB to allow production DB refresh without major downtime to end users.

#### CSM

##### DBA: Migrated MySQL schema csmauthschema3_1 from CSMDEV instance to CSMQA instance.

#### SIW

##### App Support: Shanell Gray has written a draft SOP to describe the process involved in submitting a model for initial annotation (step 1 in a three step process). She is now reviewing the original submission packages sent by model owners and creating a tracker item for all new models 

##### Tier 2: 6 models at various stages in the process

##### Tier 2: Working with the Systems team to create an automated script for weekly refreshes of the sandbox environment.

##### Tier 2: Developing slide presentations on how to import and export models, how to use the SIW, and how to use the SIW to reuse existing metadata for two upcoming Developer Bootcamps.

##### Training: Assisting Tier 2 with a presentation for the upcoming Developer Bootcamps.

##### Systems: Updated apache SIW configuration

##### Systems: Deployed SIW 3.2 to production

### Planned

##### Training: Development of training for the SIW; this project is on hold pending further updates from Dianne Reeves on caCORE curriculum plans; Jenny Brush is heading up project and investigating potential for developer boot camp. Current caCORE courses are more general -- not hands-on as requested by VCDE group. 

##### Tier 2: Work on improving the GForge Site for SIW model submissions as time allows

##### Systems: Support various development and QA efforts before the caCORE 3.2.x point release.

##### Systems: Work with the caBIO development team to separate the caBIO JNDI DS entries into a separate file for more flexibility.

## Outreach and Communications

##### Representatives from our group participate in various caCORE related teleconferences

##### Representatives from our group participate in the Architecture, Documentation and Training, and Vocabulary and Common Data Elements caBIG Workspaces

##### Claire Wolfe has been asked to join the caDSR Future Design working group, which meets weekly to discuss design changes across the caDSR tools. 

##### Systems: Work with developers to adjust Hibernate logging parameters.

##### Systems: Assisted developers to monitor the number of DB connections used/available for the caBIO/caDSR apps.

##### Systems: Perform EVS Metaphrase trouble shooting for intermittent failures

##### Systems: Helped caDSR Development manager to identify the caCORE API application web statistics through web usage Portal.

##### Systems: Developing enhanced Deployment Instructions document to streamline deployment request process.

## Issues and Recommended Resolution

##### Systems: Sandbox refresh SOP needs to be refined. Various issues have surfaced post sandbox DB refreshes due to lack of proper documentation and clear information from the developers.

## Conferences and Publications

##### Claire Wolfe is working with the caBIG V/CDE reuse small group to come up with recommendations for semantic reuse. They are currently working on a white paper to present recommendations for improving the process/tools/training to enhance metadata reuse.

##### Claire Wolfe will be presented sessions on the SIW at two Developer Bootcamps in August: one for caBIG participants one April 18-19 and another for NCICB personnel on April 25-26.

##### Stephanie Whitley will attend and present a posted on FormBuilder at the ONS Congress conference from April 23 -- 27, 2007

# C3D

## Key Accomplishments

### Current

#### Work with Potential Adopters

  -------------- --------------------------------- ------------ ----------------
  **Name**       **Organization**                  **Status**   **Instructor**

  C3D Overview                                                  
  -- Military                                                   
  Cancer                                                        
  Institute                                                     

  03/01/07, 9:30                                                
  am                                                            

  Miguel Buddle  Military Cancer Institute         Complete     Kim Diercksen

  Dr. Jarred     Military Cancer Institute         Complete     Kim Diercksen
  Holmes                                                        

  Diane Papay    Military Cancer Institute         Complete     Kim Diercksen

  Jennifer       Military Cancer Institute         Complete     Kim Diercksen
  Pappas                                                        

  George Peoples Military Cancer Institute         Complete     Kim Diercksen

  Virginia Van   Military Cancer Institute         Complete     Kim Diercksen
  Horne                                                         

  C3D Overview                                                  
  -- University                                                 
  of Minnesota                                                  
  and University                                                
  of Nebraska                                                   

  03/14/07, 3 pm                                                

  Matt Beecher   University of Minnesota           Complete     Kim Diercksen

  Ken Cowan      University of Nebraska            Complete     Kim Diercksen

  Marsha Ketcham University of Nebraska            Complete     Kim Diercksen

  Julie Maloney  University of Nebraska            Complete     Kim Diercksen

  Oleg Shats     University of Nebraska            Complete     Kim Diercksen

  Simon Sherman  University of Nebraska            Complete     Kim Diercksen

  Jessica Tvrz   University of Nebraska            Complete     Kim Diercksen

  C3D Overview                                                  
  -- University                                                 
  of                                                            
  Pennsylvania                                                  

  03/15/07, 9 am                                                

  Wallace        University of Pennsylvania        Complete     Kim Diercksen
  Wormley                                                       

  William        University of Pennsylvania        No Show      Kim Diercksen
  Ihlenfeld                                                     
  -------------- --------------------------------- ------------ ----------------

#### Study Build Highlights

##### 02_C_0140 (Rembrandt): ON HOLD

##### 2003_0919: PRODUCTION

##### AE_0104_085: PRODUCTION

###### Data entry on hold pending results of NCI Efficacy Audit

##### AE -- Second study: PREBUILD

###### Evaluating the protocol document and forms submitted by Shira 

##### AZCC_0210: PRODUCTION 

###### Completed third round of UAT and changes

###### Discussed QA options for comparing production data entry to existing SPSS files after 30 patients are entered; explained verification and approval functionality in Oracle Clinical; created dataset reports through IReview

###### Study reviewed, approved, and activated

###### Alpha patient positions created

###### Continuing work on custom report needs

##### AZCC- Second Study: PREBUILD

###### Brought study to CCMG for approval based on concerns about non-compliance of forms. Dianne talked with Steve Rodney and, after talking through issues, he agreed to not use the three forms on which there were the most concerns: the FACT ES questionnaire, Exit Interview form, and Participant Contact form. While the study does not use our forms, it does make substantial reuse of CDEs. Only 20 CDEs will need to be created. These CDEs seem generic enough to allow reuse by other groups. Therefore, Dianne recommended that we proceed with the study as is.

###### Requested additional information from team: protocol specifications, schedule of visits, PI information, reporting requirements, validation and derivation procedure requirements, etc.

###### Demonstrated CDE Browser and explained the CDE GLIB migration process

###### Working on form annotation and CDE curation 

##### BREAST CANCER DATA MART: BUILD

###### Waiting on further specifications from Dr. Zujewski

###### Preparing to load tables into C3D

##### DC_0205: PRODUCTION

##### DUKE 500: PRODUCTION 

##### DUKE P1_CPT_BCNU_RD (CPT-11): PRODUCTION

##### ILOPROST_01279: PRODUCTION

##### ISPYCALGB150007: PRODUCTION

###### Communicated with Rachel to understand all change requests.

###### Met with Dianne Reeves on new CDEs and permissible values required based on change requests team submitted.

###### Finished post-production changes. 

###### Met with Subha on 3/29/07 to discuss current status and concerns; followed up with list of post-production changes made, source of change requests, and fields that need image links.

##### LOMBARDI_02452: PRODUCTION

##### LOMBARDI_03058: CLOSING

##### LOMBARDI_04251: PRODUCTION

###### Prepared CTMS data extractions on 3/09/07 and 3/23/07

###### Assisted in responding to Theradex query

##### MDACC SPOREs study (NCI protocol 6012): PREBUILD - ON HOLD

###### Still waiting on details; no updates

##### OHSU -- Second Study: PREBUILD

###### Awaiting details from Lara Fournier

##### UAMS_2004_59: UAT

###### The requested changes to CRFs and edit checks have been completed.

###### Mmbers of UAMS team are reviewing the changes to finalize the UAT document.

###### The request for Lab Loader changes has been sent to Christo Andonyadis. 

##### UCI_97_05: PRODUCTION

##### UCI_02_06: PRODUCTION

##### UCI_04_04: PRODUCTION

###### Assisted Andrea in answering questions from CDUS Webmaster

##### UPCC_07403: PRODUCTION

##### Skills Development Sessions for Adopters

+--------------------+----------------------+------------+------------+
| **Name**           | **Organization**     | **Status** | **In       |
|                    |                      |            | structor** |
+--------------------+----------------------+------------+------------+
| 2010: Setting Up a |                      |            |            |
| Study              |                      |            |            |
|                    |                      |            |            |
| Thursday, March    |                      |            |            |
| 15, 2007; 11 AM    |                      |            |            |
| Eastern Time       |                      |            |            |
+--------------------+----------------------+------------+------------+
| Davey, Sean        | Arizona              | Complete   | Joe Uhimov |
+--------------------+----------------------+------------+------------+
| Fournier, Lara     | OHSU                 | Complete   | Joe Uhimov |
+--------------------+----------------------+------------+------------+
| Hoschander, Shira  | AECOM                | Complete   | Joe Uhimov |
+--------------------+----------------------+------------+------------+
| Hwang, Andrea      | Chao                 | Complete   | Joe Uhimov |
+--------------------+----------------------+------------+------------+
| Li, Jieping        | Lombardi             | Complete   | Joe Uhimov |
+--------------------+----------------------+------------+------------+
| Walls, Troy        | Arkansas             | Complete   | Joe Uhimov |
+--------------------+----------------------+------------+------------+
| Zheng, Xin         | AECOM                | Complete   | Joe Uhimov |
+--------------------+----------------------+------------+------------+

#### Support for Local Adopters

##### Duke: 

###### Worked with Michael and Eric on their new Neurologic Exam form and Lesion Measurement Form.

###### Assisted Seth with new DVG subset.

###### Researched and created new Key template in OCDEV per Wilma's request, waiting on Joe's review and approval to create in OCPROD

###### Performed GLIB replication on 3/30

##### UPENN

###### Wallace Wormley appointed New Director of Biomedical Informatics for Abramson Cancer Center; held C3D Overview with him on March 15, 2007 to discuss Enterprise adoption options

#### Study Reviews

##### AZCC_0210 -- review complete; study activated

##### 07_C_0053 -- review complete; activation on hold pending obsolete questions decision

##### 07_C_0058 -- review complete; study activated

##### 07_C_0081-- review complete; study activated

##### 07_C_0097 -- review complete; study activated

##### 07_C_0101 -- review complete; activation on hold pending obsolete questions decision

##### 07_C_0106 -- review complete; activation on hold pending obsolete questions decision

#### I Review / J Review

##### No news from ICS regarding JReview version 9 

#### Patches and TARs

##### 6097268.994: RDC Activity List shows active discrepancies, but forms do not show those discrepancies even though they exist -- As of February 24, 2007, Oracle has recreated the problem. No further updates.

##### 5074948.993 DCI Visit Date Not Printing on Form: New patch -- 4.5.1.53 supersedes 4.5.1.43. Completed prepatch testing on 4.5.1.53. 

##### OPA Level Privileges in Production Mode vs. Test Mode: Waiting on Oracle fix for "Severe Loss of Service" Bug 5497129. Test privileges will be saved in table opa_level_privileges (production table) instead of opa_level_privilegest (test table) if the OC site security screen is opened after being in any test mode screen. Oracle plans to release a fix with the following patches: 4.5.1.21.1 for OC 4.5.1and 4.5.0.65.1 for OC 4.5.0. No ETA on patches yet. Current Status still: "Development to Q/A"

##### 6124825.993 -- Slowness in "Validate" and "Apply" mass changes: Oracle has published as a bug and committed to a fix by Summer 2007 

##### 6133475.993 -- Is it possible to display batch loaded data on a PDF form w/o having a message that the data was entered in Character mode? TAR was submitted on request from Christo as part of preparing for caBIG Annual Meeting. No resolution has been provided yet; responses are very slow. An enhancement request has been filed on behalf of NCI ER 5904126 ( BATCH LOADED DATA TO BE MARKED AS ENTERED IN PDF FOR CRFS CREATED IN PDF MODE)

##### 6214977.993: Not able to delete a validation procedure in Arkansas study. Oracle is investigating

##### SW ticket #22300: Under Investigation: User experiencing unusual problem with one particular CRF in C3D. For some reason data is not being saved in the Pharmakin Cycle 3 CRF for patient 11 in protocol 04 C 0121. Conducted a Centra session with the user because we are not able to reproduce this error; tested Oracle-provided a workaround which did not resolve the problem. It appeared that the user was able to enter and save data into the form successfully; however, the entered data disappeared when the user closed the form.

##### SW ticket #23417: User experiencing unusual problem. The eCRF appearance / icon on the RDC spreadsheet states that the form is blank, but it does have response data filled in DCMs. Thorough research underway.

##### Lab Loader Enhancement: -Uncovered an incorrect error message in the 'CDW Staged Labs' worksheet. Per Patrick Conrad, the OTHER LABS DCI is not accounted for in the DCI Book \"Dr. Linehan\'s CRF Pages Version E\". The error returned is not correct. His group will include a new error message for Missing Events in the DCI Book.

#### Other Projects

##### DBA: Created C3D users for OCPROD as requested by NCICB Application Support.

##### DBA: Resolved and troubleshoot Oracle Clinical database issues (i.e., kill hung sessions, reset user password, performance issues, functional issues etc.)

##### DBA: Setup clinical protocols for data loading from the Clinical Center.

##### DBA: To facilitate requests of Trainers, created a script to change passwords for groups of Training Accounts in OCTRN. Documented new procedure on the NCICB Wiki site.

##### DBA: Worked with OC_Study team to identify issue with C3DDCPAPIUSER account on OCTRN for the C3D Webservices deployment. Partial functionality was not available as the OC scripts were not run during initial account creation.

##### DBA: Met with Applications Support personnel to discuss and finalize response for C3D security documentation to be provided to Booz Allen.

##### DBA: At request of OC_Study, evaluated patch 4.5.1.53 for implementation into OCDEV and OCVAL environments. Responded to OC_Study that the 4.5.1.53 patch recommends (but does not require) addition patch of 4.5.1.49 to mitigate all known issues associated with the bug being patched. Awaiting decision from OC_Study regarding implementation of the patch.

##### 21 CFR Part 11 Compliance: Completed compliance assertion matrix requested by Bruce and Blaise and returned to them on 3/16/07

##### C3D STUDY BUILDING SKILLS DEVELOPMENT: Held first session with representatives from Albert Einstein, Arizona, Arkansas, Chao, Lombardi, and Oregon to begin instruction and mentoring on Easy Study Design

##### CABIG VS CCR TEMPLATE GAP ANALYSIS: Dianne Reeves and Liz Ness are presnted their analysis of differences between CCR and caBIG Templates. We are working on evaluating the changes and planning upgrade to caBIG template.

##### CANCER IMAGING PROGRAM: Tried to contact Lalitha Shankar and Antoinette Tan to see where things stand. Lalitha is out until April 2nd and Antoinette is out until June. 

##### CTEP Site Codes: Prepared proposal on how to proceed with CTEP Site Code implementation/transition

#### CTMS Interoperability Demo: 

##### Dynamic Linking: worked with Christo to investigate dynamic linking capabilities and to set up example in 04_C_0121 demo study in OCTRN

##### NEW LAB TEST NAMES: Continued work on analysis of database structure changes to support AE related New Lab Test names (TTP 2036). CDE loading team loaded 29 new lab tests into production. Manually created the new lab test questions in glib in OCDEV, created lab panel in OCDEV to start evaluate structure changes that are needed.

### Planned

##### ACTIVATION: Arkansas

##### caBIG TEMPLATE UPDATE: Planning to create new version of caBIG Template forms to better match enhancements provided in CCR Template

##### FLEX FIELDS: awaiting feedback from Christo and team

##### IREVIEW / JREVIEW: Still waiting on version 9.0

##### MedDRA 10.0: CTEP is converting from MedDRA 9.0 to MedDRA 10.0 on 7/1/07; planning for conversion / transition in C3D

##### NEW C3D ADOPTERS: Expecting decisions from MD Anderson, University of Nebraska, and University of Minnesota, along with first studies from CIP groups

##### SET UP OF ADOPTER GFORGE SITE: currently on hold due to other pressing priorities

#### Protocol Builder Support for March

  -------------------------- ----------- ----------- ----------- -----------
                             **Mar       **Mar       **Mar       **Mar
                             2007**      2006**      2005**      2004**

  Clinical Tickets           228         255         140         168

  Studies in Build           5           4           3           7

  Study Reviews              7           3           3           1

  Active Production RDC      616         491         399         243
  Users                                                          

  Live Active Production     130         96          64          33
  Studies\*                                                      
  -------------------------- ----------- ----------- ----------- -----------

\* Active studies into which data is currently being entered (does not
include any template, training, test, or non-active studies)

#### Study Activity to Date 

+-------------------+-----------+-------------+----------+-----------+
| **Active          | **        | **Cancer    | **\#     | **\#      |
| Studies**         | Project** | Center**    | Pa       | Re        |
|                   |           |             | tients** | sponses** |
+-------------------+-----------+-------------+----------+-----------+
| 02_C_0140         | Rembrandt | North       | 0        | 0         |
|                   |           | American    |          |           |
|                   |           | Brain Tumor |          |           |
|                   |           | Consortium  |          |           |
+-------------------+-----------+-------------+----------+-----------+
| 2003_0919         | SPOREs    | MD Anderson | 47       | 298,899   |
+-------------------+-----------+-------------+----------+-----------+
| AE_0104_085       | caBIG     | Albert      | 0        | 0         |
|                   |           | Einstein    |          |           |
+-------------------+-----------+-------------+----------+-----------+
| AZCC_0210         | caBIG     | Arizona     | 0        | 0         |
+-------------------+-----------+-------------+----------+-----------+
| DC_0205           | D         | H. Lee      | 478      | 80,558    |
|                   | irector's | Moffitt     |          |           |
|                   | Challenge | Dana Farber |          |           |
|                   |           |             |          |           |
|                   |           | Duke        |          |           |
|                   |           |             |          |           |
|                   |           | Memorial    |          |           |
|                   |           | Sloa        |          |           |
|                   |           | n-Kettering |          |           |
|                   |           |             |          |           |
|                   |           | U of        |          |           |
|                   |           | Michigan    |          |           |
+-------------------+-----------+-------------+----------+-----------+
| Iloprost          | SPOREs    | UCHSC       | 121      | 274,406   |
+-------------------+-----------+-------------+----------+-----------+
| ISPYCALGB150007   | caI       | Seattle     | 46       | 4,612     |
|                   | ntegrator | Cancer Care |          |           |
|                   |           | Alliance    |          |           |
|                   |           | (SCCA, U of |          |           |
|                   |           | Washington) |          |           |
|                   |           |             |          |           |
|                   |           | UTS         |          |           |
|                   |           | outhwestern |          |           |
|                   |           | Medical     |          |           |
|                   |           | Center      |          |           |
|                   |           | Harold      |          |           |
|                   |           | C.Simmons   |          |           |
|                   |           | CCC         |          |           |
|                   |           |             |          |           |
|                   |           | UCSF        |          |           |
|                   |           |             |          |           |
|                   |           | MSKCC       |          |           |
|                   |           |             |          |           |
|                   |           | UNC         |          |           |
|                   |           |             |          |           |
|                   |           | UPENN       |          |           |
|                   |           |             |          |           |
|                   |           | UAB-        |          |           |
|                   |           | Birmingham  |          |           |
|                   |           |             |          |           |
|                   |           | Gtown       |          |           |
|                   |           | Medical     |          |           |
|                   |           | Center      |          |           |
|                   |           |             |          |           |
|                   |           | U of        |          |           |
|                   |           | Chicago     |          |           |
|                   |           | Hospitals   |          |           |
+-------------------+-----------+-------------+----------+-----------+
| LOMBARDI_02452    | caBIG     | Gtwn /      | 35       | 404,332   |
|                   |           | Lombardi    |          |           |
+-------------------+-----------+-------------+----------+-----------+
| LOMBARDI_03058    | caBIG     | Gtwn /      | 17       | 265,895   |
|                   |           | Lombardi    |          |           |
+-------------------+-----------+-------------+----------+-----------+
| LOMBARDI_04251    | caBIG     | Gtwn /      | 13       | 100,113   |
|                   |           | Lombardi    |          |           |
+-------------------+-----------+-------------+----------+-----------+
| OHSU_288          | caBIG     | OHSU        | 0        | 0         |
+-------------------+-----------+-------------+----------+-----------+
| UCI_97_05         | caBIG     | UCI / Chao  | 136      | 38,381    |
+-------------------+-----------+-------------+----------+-----------+
| UCI_02_06         | caBIG     | UCI / Chao  | 181      | 313,254   |
+-------------------+-----------+-------------+----------+-----------+
| UCI_04_04         | caBIG     | UCI / Chao  | 1        | 3,573     |
+-------------------+-----------+-------------+----------+-----------+
| UPCC_07403        | caBIG     | UPENN       | 22       | 65292     |
+-------------------+-----------+-------------+----------+-----------+

#### Patches Applied / Investigated

+--------+------------+-----------------------+------------------------+
| **P    | *          | **Applied to**        | **Status**             |
| atch** | *Purpose** |                       |                        |
+--------+------------+-----------------------+------------------------+
| OC     | RDC Onsite | Beta was applied to   | Oracle has agreed to   |
| 4.5.2  |            | OCTRN in Aug 2006     | support our efforts of |
|        |            | This must be          | un-installing in OCTRN |
|        |            | uninstalled with      | the previously         |
|        |            | support from Stephen  | installed              |
|        |            | Clover from Oracle    | pre-production version |
|        |            | UK.                   | of RDC OnSite 4.5.2    |
|        |            |                       | and subsequently       |
|        |            | Install production    | re-installing the      |
|        |            | release on OCTRN.     | production version. We |
|        |            |                       | are in the process of  |
|        |            | OCVAL                 | developing a           |
|        |            |                       | comprehensive project  |
|        |            | OCDEV                 | plan for this and the  |
|        |            |                       | other pending patches. |
|        |            | OCPROD                |                        |
+--------+------------+-----------------------+------------------------+
| OC     | Addresses  | Not Applicable        | Obsolete               |
| 4.     | several    |                       |                        |
| 5.1.43 | issues,    |                       | Superseded by 4.5.1.53 |
|        | including  |                       |                        |
|        | the DCI    |                       |                        |
|        | Visit Date |                       |                        |
|        | (TAR       |                       |                        |
|        | 507        |                       |                        |
|        | 4948.993), |                       |                        |
|        | Internet   |                       |                        |
|        | Explorer   |                       |                        |
|        | 7.0 and    |                       |                        |
|        | Adobe 8.0  |                       |                        |
|        | concerns   |                       |                        |
+--------+------------+-----------------------+------------------------+
| OC     | Addresses  | Recommended by Oracle | Prepatch testing       |
| 4.     | some Adobe | for application in    | underway               |
| 5.1.49 | issues     | conjunction with      |                        |
|        |            | 4.5.1.53              |                        |
+--------+------------+-----------------------+------------------------+
| OC     | Addresses  | 1\) OCVAL             | ###### Pre-            |
| 4.     | several    |                       | patch testing underway |
| 5.1.53 | issues,    | 2\) OCDEV             |                        |
|        | including  |                       | Received confirmation  |
|        | the DCI    | 3\) Targeting April   | and instructions from  |
|        | Visit Date | maintenance window    | Oracle that we can     |
|        | (TAR       | for installation on   | install OC 4.5.1.53    |
|        | 507        | Production            | before OC 4.5.2 and    |
|        | 4948.993), |                       | prevent PDF users from |
|        | Internet   | 4\) OCTRN -- after    | having to reinstall    |
|        | Explorer   | 4.5.2 fix is complete | the plug-in more than  |
|        | 7.0, and   | on that instance      | one time               |
|        | Adobe 8.0  |                       |                        |
|        | concerns   |                       |                        |
+--------+------------+-----------------------+------------------------+

## Outreach and Communications

##### Led caBIG™ C3D CCMG biweekly meetings on 3/13/07 and 3/27/07

##### Participated in CCR C3D CCMG on 3/14/07 and 3/28/07

##### Held meeting with John Speakman and Christo Andonyadis to get a better understanding of CTMS Interoperability plans and needs and to request involvement in planning; set meeting to be a monthly recurrence to keep discussions flowing

##### Representatives from our group participate in:

###### caBIG™ Clinical Trials Management Systems Workspace and its Special Interest Groups

###### Oracle Clinical User Group (OCUG) Focus Groups: Administration & Configuration Management, Data Interchange Standards, Data Management, Dosing, Randomization and Unblinding Group (DRUG), Global Library Management, Laboratory Data Handling, RDC, System Integration, System Validation, Training, Validation & Derivation Procedures 

##### Tasneem Shahmalak was appointed Co-Chair for the Oracle Clinical Lab Data Handling Focus Group.

##### Attended bi-weekly OCUG Administration and Technical Configuration teleconferences.

##### Attended meeting with OC_Study group to discuss implementation of Oracle Clinical patches 4.5.1.53 and 4.5.1.49 on OCDEV, OCVAL, and OCPROD environments. Also discussed uninstalling 4.5.2 beta version from OCTRN and reinstalling official release 4.5.2 to this environment.

## Issues and Recommended Resolution

##### Staffing 

###### Joe Barry resigned from his position. His last day in the office was March 16, 2007.

###### Kanchi Krishnamurthy is returning from maternity leave on April 2, 2007.

###### Sirisha Yerredu is transitioning over to the TerpSys team on April 2, 2007.

###### We are continuing to recruit more Oracle Clinical programmers.

##### IReview/JReview -- Various problems causing instability; working with vendor; beta patch currently under testing

## Conferences and Publications

##### Developing poster on C3D standards for the Oncology Nurses' Society annual meeting scheduled for April 23 -- 27, 2007 in Las Vegas

##### Planning for SPORES meeting scheduled for July 7 -- 10, 200 in Baltimore

# ATV

## Key Accomplishments

### Current

##### DBA: Worked with Systems Team and developers to troubleshoot ADT Data Load process on CCCPROD database - copied ADT schema over to cbiodev40 machine to test process without affecting other databases.

##### Systems: ATV performance DB load issue - Testing and troubleshooting tasks performed in coordination with DBA and ATV project lead.

##### Systems: Daily load is currently disabled on production for ATV.

## Outreach and Communications

##### Coordinated teleconference with Systems Team members and developers to discuss strategy for testing ADT Data Load process.

##### Worked to facilitate transition from NCICB to CC. Provided configuration and other example files to help with a local deployment.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# caXchange

## Key Accomplishments

### Current

##### Systems: Met with Development team on reviewing the DEV environment and deployment procedure.

##### Systems: Coordinate and completed QA environment installation and configuration.

##### Systems: Created NCICB CA signed client certificates to test mutual authentication.

##### Systems: Created caXchange CTOM QA instance.

### Planned

##### Systems: Support staging deployment for caXchange with Lombardi as a pilot.

## Outreach and Communications

##### Systems: Met with the caXchange Team to discuss deployment and setup issues

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# CTMSi/C3PR/C3D Web Services

## Key Accomplishments

### Current

##### DBA: Created the caxchqa in CCCQA on cbiodb30.

##### DBA: Create user C3PR_LOMB in CCCQA (cbiodb30).

##### App Support: Updated C3PR staging and production content on the Download Center

##### Systems: Created & signed client certificates using NCICB CA to test mutual authentication.

##### Systems: Provide assistance for CTMSi development efforts and DEMOs

##### Systems: Worked with CTMSidevelopment team to evaluate system reset strategy, and wrote script to implement the process successfully.

### Planned

##### Systems: Support CTMSi QA environment for their demos.

## Outreach and Communications

##### Systems: Coordinated a meeting with C3DWS project lead and Lombardi to discuss mutual authentication for their local C3PR installation with NCICB C3D servers.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# caBIG Protocols

## Key Accomplishments

### Current

##### Systems: Modified database connection source in the caBIG Protocols application and re-deployed the application.

##### Systems: Re-established caBIG Protocols development environment.

## Outreach and Communications

##### None at this time.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# caArray

## Key Accomplishments

### Current

##### DBA: Assist the QA and development teams with identifying data loading performance problems in the QA tier - determined database statistics need to be updated during the data loading process.

##### Tier 2: Working with Dev team to determine details about feature requests and additions to the caArray platform, specifically the User Management Section

##### Tier 2: Assisting the Development team with the troubleshooting of bug and the identification of workarounds

##### Tier 2: Continuing to work with NCICB team members to update ownership of experiments for people that no longer are involved

##### Tier 2: Working with University of Pittsburgh to deploy a local version of the application.

##### Tier 2: Working with OSUMC to deploy a local version of the application.

##### Systems: Completed - FTP server config for large Zip files

##### Systems: Enabled File system support for largefiles on NFS shares used by caArray

##### Systems: Coordinate tasks related to Web server URL configuration

##### Systems: Provided details about NCICB Certification authority for SSL enabled sites signed by internal CA.

##### Systems: Moved several application URLs from apache 1.333 to apache 2.2.3

##### Systems: SVN Access control adminstration, based on GForge accounts and roles

##### Systems: Shutdown old Jboss-4.x instances on caArray servers.

### Planned

##### Tier 2: Continued support of version 1.4 and 1.5 development and deployment efforts; Expecting 1.5 in shortly

##### Training: Will begin the updating of training materials after the release of caArray 1.5. The application is expected to have major GUI changes in this release

##### Systems: Complete TCGA-caARRAY instance installation and configuration

## Outreach and Communications

##### Attended weekly caArray status meetings

##### App Support / Training: Acting as a liaison between the caArray team and adopters to assist with any problems they are having in fulfilling their contractual requirements

##### Systems: Developing enhanced Deployment Instructions document in collaboration with caARRAY and other teams to streamline deployment request process.

## Issues and Recommended Resolution

##### Systems: We are planning to address duplication of data sets across multiple file systems and in database to reduce storage requirements.

##### Systems: Several FTP sites have been in use over the years for the caArray project. A list has been generated and work in progress to determine the scope and perform clean-up.

## Conferences and Publications

##### None at this time.

### 

# caBIG Support

## Key Accomplishments

### Current

##### Systems: caBIG Zope and Plone sites deployed.

##### Systems: Provided compressed archive of contact list product to developers

##### Systems: Added new product PresentationManager for caBIG

##### Systems: Restarted caBIG production zope instance due to being unaccessible

##### Systems: Performed maintenance (zope pack) of all instances on all tiers (DEV, QA/UT, Stage, Prod)

##### Systems: Assisted developer in installation of Postgres SQL database on Linux.

### Planned

##### Systems: Working with developers on approval to archive, decommission old instances and sites on all tiers

## Outreach and Communications

##### None at this time.

## Issues and Recommended Resolution

##### Systems: Met with developers on their utilization of UT to determine their current usage and what we would like to do as far as separating the roles that it plays to another dev server and stage server for user testing.

## Conferences and Publications

##### None at this time.

# 

# caGRID

## Key Accomplishments

### Current

##### Systems: Install tomcat with globus environment for caNanolab caGrid service on DEV and QA

##### Systems: Installed and configure Logpurge on all caGRID QA servers

### Planned

##### Systems: Installed and configure Logpurge on all caGRID PROD servers

## Outreach and Communications

##### Participating in caGRID Adopter teleconferences

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

### 

# caIntegrator

## Key Accomplishments

### Current

#### General

##### Systems: Completed caIntegrator Zope deployments for staging and production

##### Systems: Moved several application URLs from apache 1.333 to apache 2.2.3

##### Systems: Restarted jboss404/ncicb-caint instance to refresh DB connections after a DB update on stage and prod

##### Systems: Setup startup script for analysis server on DEV tier for startup on reboot

##### Systems: Met with developers to setup a deployment script for the analysis server that would alleviate possible issues with the manual process.

##### Systems: Provide assistance during load testing on production for Rembrandt and CGEMS. Compiled data after analysing the jvmstat report to gather memory usage before and after testing.

##### Systems: Working on setting up optimizeIt for caIntegrator performance analysis

##### Systems: Setting up New Jboss instance for JMS service on QA and DEV

#### Rembrandt/I-Spy Portal

##### DBA: Increased number of allowable database processes to 500 in Rembrandt QA database which is necessary for stress/load testing of application.

##### DBA: Performed Rembrandt staging and production database deployments to fix an application bug.

##### Clinical: Enhancing and maintaining ISPY study build in C3D

##### Training: Working with Subha and Rachel (UCSF) to schedule training and facilitate data entry in C3D

##### Systems: Completed Rembrandt URL updates to accomodate new site layout.

##### Systems: Restarted Rembrandt on stage to resolve application issue due to load testing.

##### Systems: Worked on Rembrandt v1.5 release to Production

##### Systems: Troubleshoot cbioapp507 jboss404-caint instance java heap memory issue, after deployment of Rembrandt

#### CGEMS

##### DBA: Performed CGEMS staging database deployment.

##### DBA: Performed CGEMS staging and production deployments, refreshing snp_analysis_finding_fact table in the process.

##### DBA: Refreshed CGEMS qa database using data from the development database.

#### CSP

##### DBA: Created and loaded the CSP staging schema in the RBTSTG database.

##### DBA: Performed CPS production deployment, created and loaded cspprod schema in RBTPROD.

##### App Support: Was requested by the government sponsor to train several NHGRI staff on the use of CSM for the handling of user provisioning

##### Systems: Provide the problem analysis and solving assistance on issues for authentication through NIH siteminder server for both NIH network account and eRA account for CSP.

##### Systems: Staging initial deployment and environment setup for CSP

##### Systems: Completed setup of various components necessary for CSP deployment on stage/Prod. Worked with NIH SSO and eRA team to enable siteminder support and access to eRA commons DB for CSP. Completed setup of UPT for CSP on Stage/Prod.

##### CGEMS

##### Systems: Deployment of CGEMS v1.1 completed on stage and production.

##### Training Courses: In Development

  ---------------------------- ------------------------------------------
  Course                       Percent Complete

  CGEMS Overview               75 %
  ---------------------------- ------------------------------------------

#### WebGenome

##### DBA: Created user WEBGPROD in RBTPROD (cbiodb10). Used SQLLDR to load data into two tables, cytological_map and cytoband. Deployed script Create_table_oracle.sql.

#### EAGLE

##### DBA: Created an eagledev schema in RBTDEV for Eagle development use. 

### Planned

##### Training: Set up meeting with caIntegrator government sponsor and training government sponsor to discuss training options for all caIntegrator applications

##### Systems: Determine the performance gains by separating the JMS service to a separate JBoss container for caIntegrator apps.

##### Systems: Setup Load Balancing for existing caIntegrator apps on stage as a proof of concept

##### Systems: Provision DEV and QA VM instances for EAGLE/TARGET project using a RED HAT ES4 64-bit platform.

## Outreach and Communications

##### Representatives from our group participate in various caIntegrator related teleconferences and meetings

##### Systems Team organized meetings to discuss various efforts related to caIntegrator performance improvements.

## Issues and Recommended Resolution

##### Systems: Work with the developers to generate baseline performance data under various load conditions. This will assist in determining the number of Jboss containers needed to support various caIntegrator apps across all tiers.

##### Systems: Migration to RED HAT ES 4 platform will allow Jboss instances to be configured with larger JVM heap sizes. 

## Conferences and Publications

##### Don Swan will be presenting a poster, providing Booth coverage, and conducting demos at the American Association of Cancer Research is scheduled for April 14 -- 18, 2007 in Los Angeles

# caMOD

## Key Accomplishments

### Current

##### At request of developers, performed data refresh of CAMOD from production database to staging database.

##### Refreshed schema CAMODDEV21 in CADEV (cbiodb2-d) with data from CAMODPROD on CAMOD (cbiodb10).

##### Refreshed caMOD qa database using data from caMOD production.

## Outreach and Communications

App Support: Attended monthly CCG meeting

## Issues and Recommended Resolution

No Activity

## Conferences and Publications

No Activity

# caNanoLab (formerly caLAB)

## Key Accomplishments

### Current

##### Systems: Install tomcat with globus environment for caNanolab caGrid service on DEV and QA

## Outreach and Communications

##### None at this time.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# caTIES

## Key Accomplishments

### Current

##### App Support: Integrating De-ID in a local installation of caTIES

##### App Support: Completed caTIES work instructions.

## Outreach and Communications

##### Attending developer's meetings for caTIES

##### Participating in the Tissue Banks and Pathology Tools adopter support meetings

##### Participate in the Tissue Banks and Pathology Tools caBIG Workspace

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# caTISSUE

## Key Accomplishments

### Current

##### App Support: Completed caTISSUE CAE and caTISSUE CORE work instructions.

##### Working with Ari Kahn and Subhashree Madhavan on deploying a modifiable version of caTISSUE Core on NCI servers. Currently filling in the Architectural Review Checklist (ARC)

## Outreach and Communications

##### Attending developer's meetings for caTISSUE CORE and caTISSUE CAE

##### Participating in the Tissue Banks and Pathology Tools support meetings

##### Participate in the Tissue Banks and Pathology Tools caBIG Workspace

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# DCP / DESK

## Key Accomplishments

### Current

##### DBA: Provided weekly refreshes of the REGULATORY schema in DCPDEV, DCPQA and DCPPROD as requested.

##### DBA: Performed quarterly Clinical and Preclinical data migration.

##### DBA: Create new DESK user accounts.

##### DBA: Worked with Westat personnel to investigate and resolve a Discoverer issue on DESK. The issue was that the summary values on reports were not being calculated. Metalink Note 290870.1 provided the path to resolution, which was to modify a configuration file on the system.

##### DBA: As per developer request, performed several application deployments into DCPQA environment.

##### DBA: As per developer request and DESK deployment schedule, implemented Quarterly Release on DCPPROD environment. 

##### App Support: Assisted with the quarterly DESK / DCP CR release

##### App Support: Updated work instructions for the continued handling of password resets

##### App Support: Upon request of the NCICB government lead assisted DESK Oracle Clinical help desk with the resolution of OC issue.

### Planned

## Outreach and Communications

##### Attended weekly DCP DESK technical meetings and monthly CCG meeting.

##### Met with Security Team personnel to provide security related information regarding the DESK system.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# LPG Support

## Key Accomplishments

### Current

##### DBA: At request of government personnel, upgraded the MySQL PROTDEV database instance on cbiows501 server from 4.1.19 to 5.0.27.

##### DBA: Systems Team personnel provided additional server space on lpgapp501 sufficient to run nightly backups of Genome Browser database. Configured and tested automated backups for this database.

##### Systems: Deployed updates to the lpgws web application on lpgapp501 for Bob Clifford.

##### Systems: Coordinated with DBA team to get a nightly backup of the Genome Browser mysql data on lpgapp501. The /cgwb_backup filesystem was created to hold the exports.

##### Systems: Restarted mysql twice after hours on lpgapp501 due to sitescope alerts that the cgwb web application was down. DBA\'s are investigating the cause of mysql not running - appears to be related to the process in place for backing up mysql data.

##### Systems: Installed primer3 on lpgws501, lpgws502 and ncicbstarfish, per request from Dr. Lee.

##### Systems: The root filesystem on lpgapp501 was filling up. The apache lpgws_rewrite.log was over 1gb in size, so cleaned up the log file. This will no longer be a problem once the web applications are converted to apache2 during March maintenance.

##### Systems: Investigated system hang on lpgws501. Some processes were making heavy use of a network mounted file-system which cause the system\'s network to hang. Rebooted lpgws501 to resolve the issue.

##### Systems: Investigated problems with hung file-system mounts on lpgapp501 and lpgws502. Needed to bounce the NFS services on lpgws502 to resolve the issue.

##### Systems: Investigated issues with running R on ncicbstarfish. These issues were directly related to the NFS file server problems on lpgws502 and the R problems were resolved when the NFS mounts had been restored.

### Planned

##### Systems: Integration of significant amounts of additional storage to hold LPG trace files and other scientific data

## Outreach and Communications

##### Systems: Meet with LPG leads

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# lpgLIMS

## Key Accomplishments

### Current

##### App Support: Assisted Johns Hopkins complete a local install of lpgLIMS

### Planned

##### App Support: Update the caLIMS work instructions to take into consideration the change to lpgLIMS

##### App Support: Assisting the government sponsor with the creation of installation instructions.

## Outreach and Communications

##### None at this time.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# Spores

## Key Accomplishments

### Current

##### Systems: Troubleshooted sporesdb availability on stage and production

##### Systems: Updated File system to NFS share on DEV

##### Systems: Staging deployment review and evaluation.

##### Systems: CSM, and UPT 3.2 upgrade and reconfiguration for SPORES

## Outreach and Communications

##### None at this time.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time. 

# Application and Training Support Statistics

## Bioinformatics and Clinical Application Support Summary

  ---------------------------------- --------- --------- --------- ----------
  **Application/Tool**               **March   **March   **March   **March\
                                     2004**    2005**    2006**    2007**

  BIOgopher                          0         0         0         0

  C3D/Oracle Clinical - caBIG        0         0         18        17

  C3D/Oracle Clinical - CCR          162       115       138       189

  C3D/Oracle Clinical - NCICB        5         16        93        22

  C3D/Oracle Clinical - SPOREs       1         9         6         1

  C3PR                               0         0         1         3

  caAdapter                          0         0         0         0

  caArray                            0         56        50        38

  caBIG                              0         0         0         0

  caBIG - Information                0         3         5         0

  caBIG Forums                       0         25        0         0

  caBIG Protocols                    0         0         1         1

  caBIO                              13        4         11        7

  caCORE SDK                         0         3         11        7

  caDSR - CDE Browser                6         2         9         6

  caDSR - CDE Curation Tool          0         0         11        13

  caDSR - Compliance Review Response 0         0         0         0
  Tool                                                             

  caDSR - Compliance Review Tool     2         0         1         0

  caDSR - CRF Loader                 1         0         0         0

  caDSR - Freestyle                  0         0         0         0

  caDSR - Sentinel Tool              0         0         5         1

  caDSR - UML Model Browser          0         0         9         6

  caDSR Administration Tool          2         3         2         0

  caDSR Suite                        6         7         14        15

  caFramework                        0         1         0         0

  caGRID                             0         0         51        14

  caIMAGE                            0         0         1         0

  caIntegrator - Analysis Servers    0         0         0         3

  caIntegrator - CGEMS               0         0         0         26

  caIntegrator - CSP                 0         0         0         10

  caIntegrator - ISPY                0         0         7         8

  caIntegrator - Rembrandt           0         0         7         39

  caIntegrator - WebGenome           0         0         0         13

  caIntegrator - WGI                 0         0         0         0

  caLAB                              0         0         0         5

  caLIMS                             4         13        8         3

  caMassClass                        0         0         0         0

  caMatch                            0         0         2         0

  caMOD                              2         0         17        18

  caTIES                             0         0         0         4

  caTISSUE CAE                       0         0         0         0

  caTISSUE Core                      0         0         0         3

  caWorkbench                        0         1         0         0

  CDS                                0         0         0         29

  Centra eMeeting                    4         4         1         1

  CGAP                               0         0         0         0

  CMAP                               0         0         0         1

  CSM                                0         0         3         2

  CVS - caBIG                        0         19        38        2

  CVS - HL7                          0         0         0         0

  CVS - NCICB                        0         1         13        12

  DESK                               29        25        13        29

  Enterprise Architect               0         2         0         0

  Enterprise Vocabulary Services     3         0         14        10
  (EVS)                                                            

  Firebird                           0         5         1         36

  Gene Expression Data Portal (GEDP) 2         2         0         0

  GForge                             0         0         25        33

  LMS/Training Partner               0         0         0         1

  MGC                                3         1         1         0

  NCI Metathesaurus                  0         0         0         0

  NCI Thesaurus                      0         4         1         4

  NCIA                               0         0         10        18

  NCICB & related Web sites          14        21        76        133

  Not an NCICB Application Issue     7         21        17        31

  SAFE                               0         0         0         7

  SIW                                0         0         17        9

  TestTrack Pro                      4         33        9         3

  Total                              270       396       717       833
  ---------------------------------- --------- --------- --------- ----------

#### Ticket Volume by Month

![](media/image1.wmf){width="8.245833333333334in" height="5.6375in"}

#### Training Attendance Summary

  ------------ ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ------------
  **Training                                                                                                                                                                                                                    
  Classes Held                                                                                                                                                                                                                  
  / Attendee                                                                                                                                                                                                                    
  #s**                                                                                                                                                                                                                          

  **October                                                                                                                                                                                                                     
  2005 --                                                                                                                                                                                                                       
  March 2007**                                                                                                                                                                                                                  

  **Course**   ** **      **Oct**    **Nov**    **Dec**    **Jan**    **Feb**    **Mar**    **Apr**    **May**    **June**   **July**   **Aug**    **Sept**   **Oct**    **Nov**    **Dec**    **Jan**    **Feb**    **Mar**    **Course**

                          **2005**   **2005**   **2005**   **2006**   **2006**   **2006**   **2006**   **2006**   **2006**   **2006**   **2006**   **2006**   **2006**   **2006**   **2006**   **2007**   **2007**   **2007**   **Totals**

  C3D / RDC    Classes    3          3          2          1          1          0          0          1          1          2          1          1          0          1          1          2          2          4          25
  Hands-On                                                                                                                                                                                                                      

               Trainees   9          7          2          6          4          0          0          6          9          4          2          1          0          4          2          5          8          4          71

  caArray      Classes    3          3          3          3          2          1          1          0          3          1          0          0          0          0          1          2          1          3          26

               Trainees   3          3          5          3          2          1          1          0          6          3          0          0          0          0          1          2          1          3          34

  CDS Web      Classes    0          0          0          0          0          0          0          0          0          0          0          0          0          0          0          2          0          2          4

               Trainees   0          0          0          0          0          0          0          0          0          0          0          0          0          0          0          5          0          3          8

  EVS          Classes    1          0          0          0          1          0          0          1          0          0          0          1          0          1          0          0          1          0          6

               Trainees   26         0          0          0          11         0          0          14         0          0          0          11         0          9          0          0          3          0          74

  FIREBIRD     Classes    0          0          0          0          0          0          0          0          0          0          0          0          0          0          0          4          4          1          9

  OP           Trainees   0          0          0          0          0          0          0          0          0          0          0          0          0          0          0          13         6          3          22

  Using Form   Classes    0          0          0          0          0          0          0          0          1          0          1          0          1          0          1          0          1          0          4
  Builder                                                                                                                                                                                                                       

               Trainees   0          0          0          0          0          0          0          0          11         0          12         0          4          0          5          0          2          0          34

  Monthly      Classes    7          6          5          4          4          1          1          2          5          3          2          2          1          2          0          10         9          10          
  Totals                                                                                                                                                                                                                        

               Trainees   38         10         7          9          17         1          1          20         26         7          14         12         4          13         6          25         20         13          
  ------------ ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ------------

#### Training Details for March 2007

  ----------------- --------------------------------- ------------ ----------- ---------------- ---------------
  **Name**          **Organization**                  **Status**               **Instructor**   

  **caArray                                                                                     
  Application                                                                                   
  Demonstration**                                                                               

  3/05/2007, 2:00                                                                               
  PM -- 4:00 PM                                                                                 

  Dhaval, Rakesh    University of Pittsburgh Medical               Completed                    Swan, Don
                    Center-Cancer Institute                                                     

  **1000: LMS Web                                                                               
  Self-Service                                                                                  
  Overview**                                                                                    

  3/06/2007, 2:00                                                                               
  PM - 2:30 PM                                                                                  

  Fee, Craig        TerpSys                                        Completed                    Pearce, Calla

  Kirby, Justin     TerpSys                                        Completed                    Pearce, Calla

  White, John       TerpSys                                        Completed                    Pearce, Calla

  Yurasko, Erica    TerpSys                                        Completed                    Pearce, Calla

  **Intro to RDC**                                                                              

  3/09/2007, 9:00                                                                               
  AM                                                                                            

  Rabban, Joseph    University of California at San                Completed                    Whitley,
                    Francisco Cancer Center                                                     Stephanie

  **CDS Training**                                                                              

  3/13/2007, 9:00                                                                               
  AM                                                                                            

  Pach, Deborah     Rush University Medical Center                 Completed                    Whitley,
                                                                                                Stephanie

  Licciardi, Nancy  Rush University Medical Center                 Completed                    Whitley,
                                                                                                Stephanie

  **CDS Training**                                                                              

  3/15/2007, 9:00                                                                               
  AM                                                                                            

  Kahlil, Menawar   Johns Hopkins University --                    Class                        Whitley,
                    Sidney Kimmel Cancer Center                    Cancelled                    Stephanie

  **Intro to RDC**                                                                              

  3/15/2007, 9:00                                                                               
  AM                                                                                            

  Chhieng, David    University of Alabama at                       Completed                    Whitley,
                    Birmingham Cancer Center                                                    Stephanie

  **caArray                                                                                     
  Application                                                                                   
  Overview**                                                                                    

  3/15/2007, 3:00                                                                               
  PM -- 5:00 PM                                                                                 

  Goswami, Samridhi SCI Group                                      Completed                    Swan, Don

  **FIREBIRD                                                                                    
  Operation Pilot**                                                                             

  3/20/2007, 11:00                                                                              
  AM -1 2:30 PM                                                                                 

  Ferrell, Lee      Quintiles                                      Completed                    Buck, Heather

  White, John       TerpSys                                        Completed                    Buck, Heather

  Gendleman, Brent  5AM Solutions                                  Completed                    Buck, Heather

  **Intro to RDC**                                                                              

  3/26/2007, 9:00                                                                               
  AM                                                                                            

  Hearn, Gordon     University of Alabama at                       Completed                    Whitley,
                    Birmingham Cancer Center                                                    Stephanie

  **CDS Training**                                                                              

  3/27/2007, 9:00                                                                               
  AM                                                                                            

  Kahlil, Menawar   Johns Hopkins University --                    Completed                    Whitley,
                    Sidney Kimmel Cancer Center                                                 Stephanie

  **Intro to RDC**                                                                              

  3/15/2007, 9:00                                                                               
  AM                                                                                            

  Leung, Eleanor    Duke University, Comprehensive                 Completed                    Whitley,
                    Cancer Center                                                               Stephanie

  **caArray                                                                                     
  Application                                                                                   
  Demonstration**                                                                               

  3/30/2007, 1:00                                                                               
  PM -- 2:00 PM                                                                                 

  Salcido, Joanne   ABC2                                           Completed                    Swan, Don
  ----------------- --------------------------------- ------------ ----------- ---------------- ---------------

#### Training Courses in Development

  ----------------------- -----------------------------------------------
  **Course**              **Percent Complete**

  caIntegrator: CGEMS     75%

  FIREBIRD Overview       1% \-- On hold per project manager
  ----------------------- -----------------------------------------------

#### Training Courses Requested

  ----------------------- -----------------------------------------------
  **Course**              **Applicable Comments**

  caIntegrator: Rembrandt Update for newly released version

  caIntegrator: ISPY      Creation will take place after CGEMS is
                          completed

  CDS AR (Analysis and    Prioritize with other CDS requested courses and
  Reporting)              begin after CDS: Web

  CDS PA (Protocol        Prioritize with other CDS requested courses and
  Abstraction)            begin after CDS: Web

  CDS SL (Smart Loader)   Prioritize with other CDS requested courses and
                          begin after CDS: Web

  FIREBIRD                Currently investigating what needs to be
                          created for the production release.
  ----------------------- -----------------------------------------------

**Monthly Status Report for NCICB Informatics Application Support**

**Contract #: GS-35F-0562L Order #: 263-FQ-516786**

**March 2007**

[NCIA (National Cancer Imaging Archive) Support
50](#ncia-national-cancer-imaging-archive-support)

[Key Accomplishments 50](#key-accomplishments-19)

[Outreach and Communications 51](#outreach-and-communications-19)

[Issues and Recommended Resolution
51](#issues-and-recommended-resolution-19)

[Conferences and Publications 51](#conferences-and-publications-19)

[Learning Management System Support
51](#learning-management-system-support)

[Key Accomplishments 51](#key-accomplishments-20)

[Outreach and Communications 52](#outreach-and-communications-20)

[Issues and Recommended Resolution
52](#issues-and-recommended-resolution-20)

[Conferences and Publications 52](#conferences-and-publications-20)

[GFORGE Support 53](#gforge-support)

[Key Accomplishments 53](#key-accomplishments-21)

[Outreach and Communications 53](#outreach-and-communications-21)

[Issues and Recommended Resolution
53](#issues-and-recommended-resolution-21)

[Conferences and Publications 53](#conferences-and-publications-21)

[Firebird 54](#firebird)

[Key Accomplishments 54](#key-accomplishments-22)

[Outreach and Communications 54](#outreach-and-communications-22)

[Issues and Recommended Resolution
54](#issues-and-recommended-resolution-22)

[Conferences and Publications 54](#conferences-and-publications-22)

[CDS 55](#cds)

[Key Accomplishments 55](#key-accomplishments-23)

[Outreach and Communications 55](#outreach-and-communications-23)

[Issues and Recommended Resolution
55](#issues-and-recommended-resolution-23)

[Conferences and Publications 55](#conferences-and-publications-23)

#   {#section-4 .unnumbered}

# NCIA (National Cancer Imaging Archive) Support

## Key Accomplishments

### Current

##### DBA: Performed NCIA production data cleanup database deployment. 

##### App Support: NCIA SupportWizard Ticket count was eighteen (18) for the month.

##### Tier 2: Continuing to support MDACC and MSKCC with the submission of their IDRI data.

##### Tier 2: Submitted LIDC to NCIA

##### Tier 2: Continuing to support MDACC RIDER submissions

##### Systems: Cleaned up the error.log for the apache mirc application under /app on nciavapache5001, which was at 100% full.

##### Systems: Virtual Colonoscopy Breach

##### Extracted and delivered in hardcopy twenty (20) instances of full names and/or social security numbers and the corresponding patient files for the Virtual Colonoscopy breach to the NCI Imaging Group

##### Extracted and delivered in hardcopy forty six (46) instances of last names or partial names and the corresponding patient files for the Virtual Colonoscopy breach to the NCI Imaging Group

##### Systems: NCIA Disaster Recovery Testing

##### Meeting with the Systems Team and the Database Administration Team to coordinate NCIA Disaster Recovery Test simulating NCIA data loss

##### Systems: Deployed the NCIA portal application to staging

##### Systems: Deployed the NCIA portal application to production

##### Systems: Deployed the Cedara image visualization application to development and worked with the development team to ensure the server was configured properly.

### Planned

##### Tier 2: Prepare for the submission of RTOG data

##### Tier 2: Prepare for the submission of Amgen data

##### Tier 2: Prepare for the submission of ISPY data

##### Tier 2: Prepare for the submission of MSKCC RIDER data

##### Systems: Order additional storage for NCIA

##### Systems: Provide support for Cedara image visualization application

## Outreach and Communications

##### App Support: Participate in weekly NCIA Technical Team meetings

##### App Support: Participate in data submission strategy meetings

##### Coordinated NCIA disaster recovery/failover meeting.

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### Justin Kirby will be attending the In vivo Imaging caBIG face-to-face meeting schedule for April 12 -- 13, 2007

# Learning Management System Support

## Key Accomplishments

### Current

##### Instructor / User Support

###### Instructed trainers on how to access the Training Partner Instructor Remote Desktop. 

###### We are assessing use of this computer to allow Instructors access to the core application without having to install Oracle client software on their desktops/laptops and for Administrators.

##### Licenses

###### Sent Leslie information on license pricing to get her input into a ballpark number we should purchase and am waiting for a response. Tentatively prepared the paperwork for 250 additional licenses.

###### Completed JFOC and begun working on an SOW for the license purchase.

###### Began taking access away from online users who have not been active in 6 months; as we assign more new licenses I will move that time limit to 3 months as we discussed at the beginning of the project.

##### New Courses

###### Loaded caTISSUE course into the LMS

###### Working with caLIMS team to get updated training materials into the LMS

###### Working with Firebird trainer on the possibility of using the LMS for Firebird training, both live and computer-based

##### New Users

###### Demonstrated the LMS for the Center for Cancer Research; they are considering using the LMS to track CCR RDC training

##### Reports

###### Continuing work on developing internal and course-specific reports; planning to attend Reports training in May

###### Created a report to find count of users working toward roles.

##### System Upgrades and Enhancements

###### Creating Change Management SOPs for Training Partner Upgrades, Web site changes, and Administrative Module changes.

###### Drafting a formal post-maintenance testing plan

###### Continuing work with Training Partner to identify and test alternatives for non-AICC-compliant and non-SCORM-compliant training materials; have tested some suggestions and referred further questions as a result

##### Training 

###### Presented LMS training to Justin Kirby, Erica Yurasko, John White, and Craig Fee

###### Registered Calla Pearce for Training Partner Reports Training and Knowledge Expo 2007 Users Conference, May 7-11, 2007

##### Web Site Updates

###### Made several minor changes to the LMS website requested by Jenny Tucker and Leslie Derr

###### Working on additing a public forum for course requests - contacted Training Partner for support on best practices for implementation

###### Working with caBIG Website team to change the caTISSUE Core landing page to have the training section point to the LMS for training on caTISSUE Core.

## Outreach and Communications

##### Participating in caBIG™ Documentation and Training Workspace Calls

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### Calla Pearce will be attending Reports Training and the Training Partner Knowledge Expo 2007 User Conference in Victoria, British Columbia, May 7-11, 2007

# GFORGE Support

## Key Accomplishments

### Current

##### DBA: Refreshed Gforge staging database using data from a dump file provided by developer.

##### DBA: Created and loaded a temporary Gforge qa database with data from production.

##### DBA: Refreshed temporary Gforge qa database with data from production.

##### App Support: Processed thirty-three (33) GForge SupportWizard tickets

##### Systems: Migrated caMOD TestTrack Pro Bugs and Feature Requests to GForge

##### Systems: Preparing migration of Rembrandt TestTrack Pro Bugs to GForge

##### Systems: Fixed mailing list problem for HTrack GForge mail list

##### Systems: Re-pointed lpglims URL to GForge project as requested

##### Systems: Planning stages for LDAP backend of account administration

##### Systems: Update current account synchronization methods

##### Systems: Generate PKI / SSH instructions for public key authentication.

### Planned

##### Tier 2: Work on improving the Gforge Site for SIW model submissions as time allows

##### Systems: LDAP deployment planned for GForge/SVN/CVS LDAP integration

##### Systems: Create SOP for inserting TestTrack Pro attachments to GForge trackers.

##### Systems: Complete TestTrack Pro migration of Bug tracker to GForge tracker for Rembrandt.

## Outreach and Communications

##### Gforge Tiger Team : On hold by Frank Hartel until further notice

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# Firebird

## Key Accomplishments

### Current

##### App Support: Processed forty-three (43) FIREBIRD / SAFE SupportWizard Tickets

##### App Support: Completed the SAFE Token work instructions

##### Systems: Log files provided to developers to assist with troubleshooting Firebird issue.

##### Training Courses: In Development

  ---------------------------- ------------------------------------------
  Course                       Percent Complete

  FIREBIRD Overview            1% \-- On hold per project manager
  ---------------------------- ------------------------------------------

### Planned

##### Training: Training: Government Sponsor requested assistance in the creation of a FIREBIRD project ZOPE page.

##### Training: Researching what training modules will be needed for a production release. Development of training modules (currently on hold per project manager) directed at: 

###### Sponsor Registration Specialists

###### Investigator Community 

###### FDA Data Entry Operators

## Outreach and Communications

##### App Support / Training: Participate in weekly FIREBIRD meetings: FIREBIRD Core call, FIREBIRD Key call, and the FIREBIRD Investigator Support call

## Issues and Recommended Resolution

##### None at this time.

## Conferences and Publications

##### None at this time.

# CDS

## Key Accomplishments

### Current

##### App Support: Processed twenty-nine (29) CDS SupportWizard Tickets

##### App Support: Started a pilot to have CDS ticket routed though NCICB Application Support

##### Systems: Changed CNAME entries for cdsweb, cdspa and cdsar URLs to point to new development server

##### Systems: Assist with the various LDAP creation requests for CDS projects.

### Planned

##### App Support: Officially have all support requests for CDS routed to NCICB Application Support. Planned date to have all links point to NCICB Application Support is April 10, 2007.

##### Training: Development of training modules: 

###### CDS: AR (Analysis and Reporting)

###### CDS: PA (Protocol Abstraction)

###### CDS: SL (Smart Loader)

## Outreach and Communications

##### Representatives from our group participated in various CDS related teleconferences and meetings

## Issues and Recommended Resolution

##### Training: At the request of the government sponsor and the needs of the project we are giving the training while we are in the process of creating the training material. Due to this, the actual production of a training presentation will be elongated. Since we will be actively giving training our plan is to continue incorporate lessons learned from these trainings into the final training.

## Conferences and Publications

##### None at this time.