Thursday, January 24, 2008


Email from NCI:

We’ve received the annotated xmi file mapped and
verified by the EVS team. Please download file
from the files page on the GForge UML Model website (
The annotated xmi file is contained within that zip file. You now need to
proceed methodically through the annotated file and check mark the “Model Owner
Verified” box for all classes and attributes whose mappings you approve
of. If you agree with everything then save out the file as
Approved_CDC_v0_1_rv1.xmi and send me that file along with the new EAP file
(import the approved xmi into EA and save out). I will then set up your
model to be loaded to Sandbox. If you don’t agree with a concept mapping
then you can speak directly with Nicole Thomas ( on the EVS team
to make any changes. Make sure you send her the XMI file you’re working on
(check marks, new VDs, edits, etc.) if you do want to change something after
talking to her.

As I said, if you agree with the concepts, we can proceed directly to
loading. Please feel free to contact me if you have any questions or

  • Ran file through Semantic Integrator Software
  • Created approved file
  • SCI Group on site to install caBig node

Tuesday, January 22, 2008

NCPHI and Centers of Excellence Leadership Dinner

  • Kick off dinner for Wednesday's off-site retreat to discuss the public health research grid
  • At retreat discussed setting up grid nodes at each CoE then placing existing computational and/or data services on the grid to be consumed by other participants on the grid, then demo in 6 months.


  • Lab administrators installed MySQL on Redhat server VM
  • Vernicia Reese (BearingPoint) created tables based on Tom Savel's super minimum dataset using baseline UML then populated the tables with test data

Tuesday, January 15, 2008


  • Ran CDCv3.xmi file through Semantic Integration Workbench
  • Submitted FirstPass_CDCv3.xmi (SIW output file) to John White for completion of semantic integration process
  • FirstPass document accepted and will not be reviewed. This is the last step before semantic integration. John wrote,

That’s how it should look. I’ll set up the files for submission to the EVS team. They will verify and map appropriate concepts to your classes and attributes. When they are finished they will send me the annotated file. I’ll check it for errors and then post for you to download. You will then review the annotations and, if you approve, check mark the classes and attributes using the “Model Owner Verified” check box. I’ll keep you posted when we are ready for the next step. Feel free to contact me if you have any questions or concerns.

John W. White
Bioinformatics Application Analyst
NCICB Application Support
Contractor, TerpSys

NCICB Application Support
Local: 301-443-3540


Monday, January 14, 2008

Daily Lab / POC Activities

  • Successfully connected using VNC to Dallas grid node
  • Successfully downloaded grid software stack to Tarrant County grid node
To do
  • Test NCPHI node GridFTP
  • Test Dallas node GridFTP
  • Attempt NCPHI - Dallas GridFTP
  • Write up instructions to install grid node
  • Setup & test webex on Tarrant County grid node

Monday, January 7, 2008

Daily Lab / POC Activities

  • Loaded SUSE on home grid node (for testing purposes)
  • Next step: load globus software

Grid Publication

Submitted grid article to the Journal of the American Medical Informatics Association. They are now reviewing the paper.

Friday, January 4, 2008

Daily Lab / POC Activities


  • Created domain name and associated A records:,, and
  • Created host and client public and private keys and emailed public keys to HealthGrid to be signed
  • Tested VNC connectivity to host
  • Began shipping process with CDC personnel
  • Uploaded software stack to site for future installations

Thursday, January 3, 2008

Extramural Certificate Process

There are two certificates--one host certificate and one client certificate. They are created using the following commands:

$GLOBUS_LOCATION/bin/grid-cert-request -host `hostname`

** In the first command you can see why uniquely identifiable domain names are required for each server (-host ‘hostname’).

Each of these commands creates two files--one private key and one public key. Of course, the private key remains on the server.

The public keys are emailed to The HealthGrid folks (actually, we are working directly with one person) sign the keys then send the certificates back so that we may begin using the grid services.

Daily Lab / POC Activities

  • Received the following email from NCI

I’ve reviewed your model submission package and found that we will need one additional item. It is your FirstPass xmi file. Can you take the xmi file you sent and run it through the Semantic Connector using the SIW? When finished, it will prepend “FirstPass” to your xmi file. You can then either delete erroneous concepts mapped to your class/attributes using the “Review Annotated XMI file” in the SIW or leave it as it is and send to me. On another note, I noticed in your submission document you want to use 0.1 as a version number but your files have the version as 3.0. Should we say 3.0.1 or 1.0 maybe? The loading team recommends using 1.0 rather than 0.1. For now, I am going to name your files as listed below to follow naming protocol when I submit your package (let me know otherwise about the version number):



FirstPass_ CDC_v3_0_1_rv1.xmi

Submission_Form_ CDC_v3_0_1_rv1.doc

The revision number is for your and my benefit so we know what file we’re working with if edits need to be made down the road. So, go ahead and run the Semantic Connector and send me that file and I will continue from there. Please feel free to contact me if you have any questions or concerns.

  • Conference call to discuss status and establish a two hour block of time to review grid node setup. Minor technical issue with installation of SUSE on Tarrant County server. SUSE must be installed prior to grid setup session.
  • Shared IP addresses at each four nodes for network administration at each site
  • Firewall changes made for NCPHI Lab network
  • Dallas grid node built. Need domain name, if available, otherwise we'll have to use another methodology to create certificates. Certificates remain to be created

Medicus Installation

As the globus user (works better as root), make sure $GLOBUS_LOCATION is set, and run:

$GLOBUS_LOCATION/sbin/gpt-build globus_simple_ca_ae084d2a_setup-0.19.tar.gz

You will get a scary-looking message from gpt-postinstall saying that the installation didn't complete. All that means is that there's another step that you need to run as root.

As root, make sure $GLOBUS_LOCATION is set, and run:

$GLOBUS_LOCATION/setup/globus_simple_ca_ae084d2a_setup/setup-gsi -default

You should do this on each host on which you have Globus installed. At that point, you'll be able to create a host certificate request for each host by running the following as root on each host:

$GLOBUS_LOCATION/bin/grid-cert-request -host `hostname`

You can create a user certificate request by running the following as yourself:


Then you can follow the directions about mailing the certificate requests to the CA.

Wednesday, January 2, 2008

Daily Lab / POC Activities


  • Received the following email from

I’ve received your model submission files and am currently reviewing
them. I will be your main point of contact as we proceed through the
process of having your model loaded to the caDSR. At any time, please feel
free to contact me if you have any questions or concerns. I look forward
to working with you. I’ll be in touch as soon as I can after completing my


  • Installed all C Compiler libraries on Dallas County grid node server
  • Completed Globus install
  • Tomorrow: Medicus installation and cert requests
Installation Process

  • Confirm all C Compilers and supporting libraries installed
  • Confirm Java JDK version:
  • Confirm Ant version: 1.6.5
  • Confirm Full Toolkit Source Download version: 4.0.5
  • Confirm path: $PATH=./:/home/globus/java_card_kit-2_2_2/bin:/usr/local/apache-ant-1.6.5/bin:/usr/java/jdk1.5.0_14/bin:/home/globus/bin:/home/globus/bin/sbin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/opt/kde3/bin:/opt/cross/bin
  • Confirm environment variables:
    export GLOBUS_LOCATION=/usr/local/globus-4.0.5
    export LD_LIBRARY_PATH=/usr/lib:usr/local/lib:/usr/i586-suse-linux/lib:/lib
    export ANT_HOME=/usr/local/apache-ant-1.6.5
    export GLOBUS_LOCATION=/usr/local/globus-4.0.5
    export JAVA_HOME=/usr/java/jdk1.5.0_14
  • Change directory to gt4.0.5-all-source-installer (as su) then run the following:
    • ./configure
    • make
    • make install

  • Medicus installation
  • Certificate request
  • GridFTP Test