from PhysioNet, the research resource for complex physiologic signals


MIMIC II Clinical Database - Demo

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 deidentified, 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.

Requirements

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.

For use from a bootable USB flash drive:

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.

For use from a bootable DVD:

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.

Login

After booting the demo, login 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.

Access to the MIMIC II Clinical Database Demo

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
    \q
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.

Shutdown

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:

    sudo shutdown
or
    sudo poweroff

Installing the MIMIC II Clinical Database Demo software on your PC

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 repartitioning 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.

Installing into MySQL from MySQL dump

To install the demo database on your machine follow these steps:

  1. Download the MySQL mimic2dead.sql.qz file and unzipp it (on Windows, you can use 7zip to unzip the file).
  2. Start MySQL and run the following commands:
    create database mimic2;
    use mimic2;
    source mimic2dead.sql
    

Support

If you have questions or suggestions about the MIMIC II Clinical Database Demo, please write to mimic-support@physionet.org.

Icon  Name                     Last modified      Size  Description
[DIR] 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
Send feedback about this page to PhysioNet
Your comments and suggestions are welcome. We encourage you to use our feedback form to comment on this page. If you would like to receive a reply, please send your comments by email to webmaster@physionet.org.

Updated Friday, 16 December 2011 at 01:34 EST

NIBIB/NIH/NIGMS National Institute for Biomedical Imaging and Bioengineering National Institutes of Health National Institute of General Medical Sciences