Changes between Initial Version and Version 58 of Using I2B2

01/21/14 11:18:40 (4 years ago)



  • Using I2B2

    v1 v58  
     3Our [[HERON]] data repository is based on [ I2B2]:
     5  i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners !HealthCare         System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origins
     7See [[I2B2Community]] regarding mailing lists, conferences, upstream collaboration etc.
     11 * [ Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)][[BR]]Shawn N Murphy, Griffin  Weber, Michael  Mendis, Vivian  Gainer, Henry C  Chueh, Susanne  Churchill, Isaac Kohane[[BR]]JAMIA2010;17:124-130 doi:10.1136/jamia.2009.000893
     13Corresponding presentation:
     14  * [ How to i2b2] (from AMIA March 2010 Summit among [ i2b2 events])
     17== i2b2 at KUMC ==
     19In addition to the main installation, we have other dev/test installs. See [[GroupOnly/Operations]] for details.
     22== i2b2 installation ==
     23In addition to the [ AUG e-mail repository], there is also [!forum/i2b2-install-help i2b2-install-help Google Group] which may be a helpful reference.
     25source:i2b2-backend-deploy automates the installation of the i2b2 cells that we use:
     27 1. PM Cell
     28 1. Ontology Cell
     29 1. CRC aka Data Repository Cell
     30 1. Workplace Cell
     32The [ HERON i2b2 hive (back end) deployment] generated documentation should help some, though it's not a complete substitute for reading the code.
     34**See #756, #1087 for status.**
     36See HeronLoad#heron_init for the way we created our schemas and such; it runs the SQL scripts from i2b2 to create datamarts etc.
     38For database password management, see also the `configure_i2b2_datasources` task under HeronLoad#release .
     40=== Apache, JBoss, and i2b2 ===
     42The parts look something like this:
     47digraph server_setup {
     49subgraph clusterDeploy {
     50 graph [label="app server"];
     52 apache -> mod_php  [label="/i2webclient/index.php"];
     53 mod_php -> libcurl;
     54 libcurl -> jboss_8080 [label="http://localhost:8080/i2b2/rest/..."];
     55 jboss_8080 -> "i2b2.war" [label="/i2b2/"];
     64=== History ===
     66attachment:Doc_for_i2b2_1.4_Install.doc is Arvinder's documentation on the original installation at KUMC in early 2010, along with attachment:Design_document_i2b2.doc (system architecture). It was a significant learning process regarding many dependencies:
     68   a. Java JDK: [ JDK RPM Installation for Linux (64-bit)] from Oracle (formerly Sun)
     69   a. JBoss 4.2.2 GA: [ i2b2 1.4 core docs]
     70     * [ Using mod_jk 1.2.x with JBoss/Tomcat bundle and Apache2] in the JBoss community wiki
     71   a. Apache Ant: directory layout from [ Installing Ant]
     72   a. Apache Axis2 1.1: i2b2 core docs and [ Apache Axis2 Installation Guide]
     73   a. Oracle 10g: ''source(s) not yet tracked down''
     74   a. Apache Web Server: [ How to install Apache on SuSE Linux] by richard laffers
     75     * note InformationResources#ApacheSecurityChecklist
     76   a. php: [ How to install PHP on SuSE Linux] by richard laffers
     77     * note `--with-curl` config option
     79attachment:Creating_a_Project_in_i2b2.doc has been partially automated; see `create_i2b2_project()` in source:i2b2-backend-deploy/
     82== Starting i2b2 application ==
     84''Now that #134 and #394 have been addressed...''
     86The normal `/etc/init.d/jboss start` mechanism starts jboss, and hence
     87the i2b2 hive, at boot time. To stop, use the conventional `/etc/init.d/jboss stop`.
     88The ssh tunnels necessary to connect i2b2 to the database start automatically
     89at boot as well.
     93== How do i2b2 Projects relate to the Enterprise Repository? ==
     94In [ How to i2b2] (from AMIA March 2010 Summit among [ i2b2 events]):
     96 * on slide 8, we see research cohorts in "project silos"
     97 * in slide 20 "Upload data through i2b2 Workbench" @@@
     98 * slide 9 has a nice figure:
     102There is some discussion of this in the the 2010 i2b2 paper.
     107> > > "Murphy, Shawn N." <SNMURPHY@PARTNERS.ORG> 7/8/2010 5:25 PM >>>[[BR]]        Hi Keith,[[BR]]        [[BR]]        Indeed, the current design is for each project to have its own data schema.[[BR]]        This is so we can cleanly manage user permissions and data ownership when[[BR]]        derived data is created for a project.  This can be facilitated with a package[[BR]]        of sql scripts that can create the new schema and move the data from an existing[[BR]]        schema for specific patient sets and data types.  They are under the source_code[[BR]]        section of the [ software page]        , in a package named[[BR]]        [[BR]]        Thanks,[[BR]]        Shawn.
     109== i2b2 and R ==
     111See [blog:2012/02/heron-bowcreek HERON Bow Creek Release brings Cancer Survival Analysis, R integration ] Feb 2012
     113based on:
     115 * Segagni D, Ferrazzi F, Larizza C, Tibollo V, Napolitano C, Priori SG, Bellazzi R.  [ R Engine Cell: integrating R into the i2b2 software infrastructure].  J Am Med Inform Assoc. 2011 Jan 24. [Epub ahead of print]