Changes between Initial Version and Version 58 of Using I2B2


Ignore:
Timestamp:
01/21/14 11:18:40 (4 years ago)
Author:
ngraham
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • Using I2B2

    v1 v58  
     1[[PageOutline]]
     2
     3Our [[HERON]] data repository is based on [https://www.i2b2.org/index.html I2B2]:
     4
     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
     6
     7See [[I2B2Community]] regarding mailing lists, conferences, upstream collaboration etc.
     8
     9Cite:
     10
     11 * [http://jamia.bmj.com/content/17/2/124.full 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
     12
     13Corresponding presentation:
     14  * [http://www.i2b2.org/events/slides/i2b2_AMIA_Tutorial_20100310.pdf How to i2b2] (from AMIA March 2010 Summit among [https://www.i2b2.org/events/index.html i2b2 events])
     15
     16
     17== i2b2 at KUMC ==
     18
     19In addition to the main https://heron.kumc.edu/ installation, we have other dev/test installs. See [[GroupOnly/Operations]] for details.
     20
     21
     22== i2b2 installation ==
     23In addition to the [https://community.i2b2.org/wiki/display/community/AUG+E-mail+Repository AUG e-mail repository], there is also [https://groups.google.com/forum/#!forum/i2b2-install-help i2b2-install-help Google Group] which may be a helpful reference.
     24
     25source:i2b2-backend-deploy automates the installation of the i2b2 cells that we use:
     26
     27 1. PM Cell
     28 1. Ontology Cell
     29 1. CRC aka Data Repository Cell
     30 1. Workplace Cell
     31
     32The [http://informatics.kumc.edu/devdoc/i2b2-backend-deploy/ HERON i2b2 hive (back end) deployment] generated documentation should help some, though it's not a complete substitute for reading the code.
     33
     34**See #756, #1087 for status.**
     35
     36See HeronLoad#heron_init for the way we created our schemas and such; it runs the SQL scripts from i2b2 to create datamarts etc.
     37
     38For database password management, see also the `configure_i2b2_datasources` task under HeronLoad#release .
     39
     40=== Apache, JBoss, and i2b2 ===
     41
     42The parts look something like this:
     43
     44{{{
     45#!graphviz
     46
     47digraph server_setup {
     48
     49subgraph clusterDeploy {
     50 graph [label="app server"];
     51
     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/"];
     56
     57}
     58
     59}
     60
     61}}}
     62
     63
     64=== History ===
     65
     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:
     67
     68   a. Java JDK: [http://www.oracle.com/technetwork/java/javase/install-linux-64-rpm-138254.html JDK RPM Installation for Linux (64-bit)] from Oracle (formerly Sun)
     69   a. JBoss 4.2.2 GA: [https://www.i2b2.org/software/projects/hivecore/i2b2core-doc-14.zip i2b2 1.4 core docs]
     70     * [http://community.jboss.org/wiki/usingmodjk12withjboss Using mod_jk 1.2.x with JBoss/Tomcat bundle and Apache2] in the JBoss community wiki
     71   a. Apache Ant: directory layout from [http://ant.apache.org/manual/install.html Installing Ant]
     72   a. Apache Axis2 1.1: i2b2 core docs and [http://ws.apache.org/axis2/1_1/installationguide.html Apache Axis2 Installation Guide]
     73   a. Oracle 10g: ''source(s) not yet tracked down''
     74   a. Apache Web Server: [http://laffers.net/howtos/howto-install-apache How to install Apache on SuSE Linux] by richard laffers
     75     * note InformationResources#ApacheSecurityChecklist
     76   a. php: [http://laffers.net/howtos/howto-install-php How to install PHP on SuSE Linux] by richard laffers
     77     * note `--with-curl` config option
     78
     79attachment:Creating_a_Project_in_i2b2.doc has been partially automated; see `create_i2b2_project()` in source:i2b2-backend-deploy/i2b2db.py
     80
     81
     82== Starting i2b2 application ==
     83
     84''Now that #134 and #394 have been addressed...''
     85
     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.
     90
     91
     92
     93== How do i2b2 Projects relate to the Enterprise Repository? ==
     94In [http://www.i2b2.org/events/slides/i2b2_AMIA_Tutorial_20100310.pdf How to i2b2] (from AMIA March 2010 Summit among [https://www.i2b2.org/events/index.html i2b2 events]):
     95
     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:
     99
     100[[Image(Screenshot.png)]]
     101
     102There is some discussion of this in the the 2010 i2b2 paper.
     103
     104
     105In members@i2b2aug.org:
     106
     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 [https://www.i2b2.org/software/index.html software page]        , in a package named i2b2DerivedDataMarts-src-14.zip[[BR]]        [[BR]]        Thanks,[[BR]]        Shawn.
     108
     109== i2b2 and R ==
     110
     111See [blog:2012/02/heron-bowcreek HERON Bow Creek Release brings Cancer Survival Analysis, R integration ] Feb 2012
     112
     113based on:
     114
     115 * Segagni D, Ferrazzi F, Larizza C, Tibollo V, Napolitano C, Priori SG, Bellazzi R.  [http://www.orbitproject.org/resource/r-engine-cell-integrating-r-i2b2-software-infrastructure R Engine Cell: integrating R into the i2b2 software infrastructure].  J Am Med Inform Assoc. 2011 Jan 24. [Epub ahead of print]