The MIMIC II Clinical Database Demo is an easy-to-use disk image that includes data from 4000 (of over 32,000) patients in the MIMIC II Clinical Database. Since all of the required software, including the operating system, is pre-installed and configured, it is an ideal way to begin exploring MIMIC II on a spare PC or Intel Mac with an absolute minimum of setup time.
No living patients are included in the demo subset (although many of these patients lived for up to several years following their ICU admissions documented in this data set). Although these data are exempt from HIPAA requirements for protecting health information of living individuals, the data have been very carefully de-identified, and we have removed free-text notes and reports as a further measure to reduce the possibility of disclosing information that might be used to identify these patients.
The disk image includes Ubuntu 10.04 (see the note below), PostgreSQL 8.4.8, pgadmin3 1.10.2, and MIMIC II v2.6 with data for 4000 patients. The entire contents of the disk image may be copied and redistributed freely, and all of the software included in it is open-source.
For the full database, including notes and reports for the 4000 patients in the demo, as well as full records for more than 28,000 additional patients, please apply for access to the MIMIC II Clinical Database project. Access is free, but it requires a data use agreement (DUA) to protect patient privacy.
The disk image mimic2_livecd.iso can be copied to a bootable 4GB or larger USB flash drive or a DVD.
Note that the virtual disk is encrypted, and you will need to enter the passphrase 2CIMIM_2v6 when booting the VM.
Use any PC that can boot from a USB flash drive and has at least:
The method for copying mimic2_livecd.iso to your USB flash drive depends on your operating system. This tutorial describes methods for doing so on Linux, Mac OS X, and Windows; a Google search on "creating bootable usb" will find many more. If you use a Mac, we recommend making a bootable DVD, since the bootable USB flash drive may not work.
Use any PC or Intel-based Mac that can boot from a DVD and has at least:
You can create a bootable DVD by downloading mimic2_livecd.iso and writing it to a blank DVD using any software for creating bootable DVDs. Ubuntu’s Burning ISO HOWTO describes how to do this on Windows, Mac OS X, and (of course) Ubuntu itself.
PowerPC-based Macs are incompatible with the demo image.
After booting the demo, log in as user mimic2 and password 2CIMIM_2v6 (note that case is significant in both the user name and the password).
If you are using a bootable USB or DVD, do not remove it during your session since it will be in constant use.
Graphical user interface: Double-click the elephant icon on the desktop to launch pgadmin3.
Command-line interface: Open a terminal window. Type
psql -d MIMIC2
and press Enter to start the PostgreSQL interactive terminal. To exit, type
and press Enter.
You can find MIMIC II SQL examples in the MIMIC II cookbook on the desktop. If you haven’t used PostgreSQL previously, read the pgadmin3 tutorial or the pgsql tutorial on-line; both tutorials include introductions to SQL. For additional information on PostgreSQL, visit http://www.postgresql.org/docs/.
With a network connection, you can save your work on cloud services such as Google Docs or Dropbox. You can also connect from any other networked computer to the PostgreSQL server on the PC that is running the MIMIC II Clinical Database Demo.
Exit from pgadmin3 or psql before shutting down the demo.
You can find the power button in the upper right-hand corner of the desktop. Alternatively, if you are using a terminal window, you can simply run either of these commands:
The USB/DVD version of the demo offers a method of installing itself on your PC, which will significantly improve performance and may simplify updating MIMIC II if you decide to apply for access to the remainder of the database. This is entirely optional, and the normal operation of the demo does not alter (or even read) the contents of your PC's disk drives.
If you decide to install the software on your PC, however, you will have the option of re-partitioning or erasing your disk drives. In this case please be certain that you have readable off-line backups of any files you may need in the future. (To access the self-installer, choose System -> Administration -> Install RELEASE.) You should also perform an update of Ubuntu as soon as possible after installing it on your PC, since the demo disk image contains Ubuntu 10.04, which has known vulnerability problems in its kernel. For more information on the issue see Ubuntu Security Notice USN-1253-1.
To install the demo database on your machine follow these steps:
create database mimic2; use mimic2; source mimic2dead.sql
If you have questions or suggestions about the MIMIC II Clinical Database Demo, please write to firstname.lastname@example.org.
Name Last modified Size Description
Parent Directory - MD5SUMS 04-Oct-2012 20:27 412 MIMICIICookBook_v1.pdf 08-Jul-2013 09:33 239K SHA1SUMS 04-Oct-2012 20:28 476 SHA256SUMS 04-Oct-2012 20:29 668 import.sh 23-Aug-2011 15:51 5.8K mimic2_flatfiles.tar.gz 29-Aug-2011 17:40 442M mimic2_livecd.iso 05-Sep-2013 11:22 2.3G mimic2_livecd_README.pdf 26-Aug-2011 15:12 85K mimic2dead.sql.gz 18-Sep-2014 14:39 454M