<!DOCTYPE article PUBLIC "-//OASIS//DTD DocBook V4.1//EN">
<article>
<articleinfo>
<title>Linux Medicine-HOWTO</title>
<author>
<firstname>Gerardo</firstname>
<surname>Arnaez</surname>
<affiliation>
<address>
<email>garnaez_((AT))_yahoo.com</email>
</address>
</affiliation>
</author>
<author>
<firstname>Werner</firstname>
<surname>Heuser</surname>
<affiliation>
<address>
<email>wehe_((AT))_mobilix.org</email>
</address>
</affiliation>
</author>
<revhistory>
<revision>
<revnumber>2.0.2</revnumber>
<date>2002-03-02</date>
<authorinitials>gea</authorinitials>
<revremark>Starting to add more to the How-To section of FreePM. The installation section will need testing by others. Added Slicer info under a new section</revremark>
</revision>
<revision>
<revnumber>2.0.1</revnumber>
<date>2002-02-19</date>
<authorinitials>gea</authorinitials>
<revremark>
Minor changes, Changed license to GPL. Some more reorganization. Which to say I have deleted out a ton of comments that I put that were useless. More pimping of Debian-med.
</revremark>
</revision>
<revision>
<revnumber>2.0</revnumber>
<date>2002-02-05</date>
<authorinitials>gea</authorinitials>
<revremark>
Major changes. Conversion from linuxdoc to DocBook format. Have basically edited out nutrition sections and most of the German section for now until I can get help again the German section. Have switched focus of the article to Medical informatics and applications, less to research applications
which should probably be a different article. Will most likely put these things
I will not maintain at the end, so someone else has some where to begin.
Whew. Tired from DocBook Conversion.
</revremark>
</revision>
<revision>
<revnumber>1.4.3</revnumber>
<date>2002-02-5</date>
<authorinitials>gea</authorinitials>
<revremark> Doing minor checks of links. no big change yet</revremark>
</revision>
<revision>
<revnumber>1.4.2</revnumber>
<date>2002-02-05</date>
<authorinitials>gea</authorinitials>
<revremark>I have started to make structural changes to the documents. Changes Community to the fore-front. renamed Medical Application to Medical Record Application to make it more usable. I have not decide to change the version number as i have just moved links around and I am trying to structure the document a little bit better.</revremark>
</revision>
<revision>
<revnumber>1.4.1</revnumber>
<date>2002-02-05</date>
<authorinitials>gea</authorinitials>
<revremark>Gerardo Arnaez took over maintaining this document. Some new additions, some info on when last update. Links to sqlclinic.net and eors.org added.</revremark>
</revision>
<revision>
<revnumber>1.4</revnumber>
<date>Unknown</date>
<authorinitials>wh</authorinitials>
<revremark>XXX, minor changes </revremark>
</revision>
<revision>
<revnumber>1.3</revnumber>
<date>2001-03-01</date>
<authorinitials>wh</authorinitials>
<revremark>added links to gnutrition, Java SmokingMeter and HL7lib - Health Level 7 Library, some other links updated, Japanese translation proposed </revremark>
</revision>
<revision>
<revnumber>1.2</revnumber>
<date>2000-11-04</date>
<authorinitials>wh</authorinitials>
<revremark> Links to Nut, Free Practice Management, LittleFish,
GNUMed, REALTIQ, VISIdent, weight, OIO, CTSim, myPACS, BlazeLIMS, XNBC and PhysioNet added, new document URL, minor changes</revremark>
</revision>
<revision>
<revnumber>1.1</revnumber>
<date>2000-04-20</date>
<authorinitials>wh</authorinitials>
<revremark>links to Res Medicinae, QDS, sixpack and LinuxMedNews added, minor changes </revremark>
</revision>
<revision><revnumber>1.0</revnumber><date>2000-01-27</date><authorinitials>wh</authorinitials><revremark> LinuDent added, preface and disclaimer added,
minor changes, first official release</revremark></revision>
<revision>
<revnumber>0.2</revnumber>
<date>2000-01-26</date>
<authorinitials>wh</authorinitials>
<revremark> URLs checked, minor changes, second draft</revremark>
</revision>
<revision>
<revnumber>0.1</revnumber>
<date>1999-11-17</date>
<authorinitials>wh</authorinitials>
<revremark>first draft</revremark>
</revision>
<!-- Additional (*earlier*) revision histories go here -->
</revhistory>
<abstract>
<indexterm>
<primary>Abstract</primary>
</indexterm>
<para>Some pointers to Linux software (mostly GPLed) for the medical sciences (medical applications, Medline and other bibliography tools, applications for veterinarian medicine and others). UPDATE: I intend this HOWTO to be more and more geared to Medical applications and less to the others.
</para>
</abstract>
</articleinfo>
<!-- END TITLE STUFF HERE -->
<sect1 id = "preface">
<title>Preface</title>
<indexterm>
<primary>Preface</primary>
</indexterm>
<para>Life is the first gift, love is the second, and understanding is the third. -- <ulink url="http://www.capecod.net/˜tmpiercy/"> Marge Piercy</ulink>
<sect2 id="About">
<title>About the Document</title>
<para> This document is part of the <ulink url="http://www.linuxdoc.org">LINUX DOCUMENTATION PROJECT - LDP</ulink>.
</para>
<para> A Japanese translation is proposed by Shouhei Nagaoka, see the <ulink url="http://www.linux.or.jp/JF/"> Linux JF (Japanese FAQ) Project</ulink>.
<!-- Japanese section of Non-English Linux Info in <http://www.linuxdoc.org/links/nenglish.html of
http://www.linuxdoc.org/ -->
</para>
<para> <emphasis>This document isn't ready yet.</emphasis> If you like to write a chapter or even a smaller part by yourself, please feel free to contact me. Also your suggestions, recommendations and criticisms are welcome.
</para>
<para>
Note: Werner Heuser, no longer maintains this LDP.
</para>
</sect2>
<sect2 id="authors">
<title>About the Author(s)</title>
<para>
Gerardo Arnaez: I am an internal medicine doctor. I am extremely concerned with the state of medical informatics.</para>
<para>
Werner Heuser: Working as a system administrator in the computer departments of two German hospitals I get inspired to search for medical applications created with Linux software. Besides this HOWTO I have written the <ulink url="http://mobilix.org/howtos.html"> Linux-Mobile-Guide</ulink>, <ulink url="http://mobilix.org/howtos.html"> Linux-Infrared-HOWTO</ulink> and the <ulink url="http://mobilix.org/eco_linux.html"> Linux-Ecology-HOWTO</ulink>.
</para>
</sect2>
<sect2 id="copyright">
<title>Copyright, Disclaimer and Trademarks</title>
<para>NOTE: This license has changed to <ulink url="http://www.fsf.org/licenses/gpl.html">GPL license</ulink>.</para>
This is free documentation. It is distributed in the hope that it will be useful, but without any warranty. The information in this document is correct to the best of my knowledge, but there's a always a chance I've made some mistakes, so don't follow everything too blindly, especially if it seems wrong. Nothing here should have a detrimental effect on your computer, but just in case I take no responsibility for any damages incurred from the use of the information contained herein.</para>
<para>
Though I hope trademarks will be superfluous sometimes (you may see what I mean at <ulink url="http://www.opensource.org/osd.html">Open Source Definition</ulink> : If certain words are trademarks, the context should make it clear to whom they belong. For example <emphasis>MS Windows NT</emphasis> implies that <emphasis>Windows NT</emphasis> belongs to Microsoft (MS). Mac is a trademark by Apple Computer. All trademarks belong to their respective owners.
</para>
</sect2>
<sect2>
<title>Request For Comments</title>
<para>If you have any comments, suggestions, new information, please tell me: <garnaez_((AT))_yahoo.com>
</para>
</sect2>
</sect1>
<!-- END PREFACE -->
<sect1 id='debianmed'>
<title>Debian-Med
</title>
<sect2>
<title>DEBIAN-MED HOMEPAGE</title>
<para>A better place to look for medical information is <ulink url=" http://auric.debian.org/~tille/debian-med/">Debian-Med</ulink> which is already better organized than this page. You should look here first, then come here, as I think the focus of this How-To will eventually be a How-to install working applications that I think is useful and actually useful.
</para>
</sect1>
<sect1 id="community">
<title>Community</title>
<sect2>
<title>News</title>
<sect3>
<title>LinuxMedNews</title>
<para> <ulink url="http://www.LinuxMedNews.org/"> LinuxMedNews</ulink> is a site designed to facilitate, amplify and begin the process of fundamentally changing medical education and practice into a more effective, fair and humane enterprise using modern technologies. The site uses Zope and a slashdot clone Squishdot to accomplish these goals. It is not intended to be doctor-centric, it is intended to be an interesting/fun forum and resource for anyone who has an interest in health care and open source.
</para>
</sect3>
<sect3>
<title>The Spirit Project</title>
<para><ulink url="http://www.euspirit.org">The Spirit Project</ulink> is a multilingual source of opensource software that makes this document just pale in comparison. Well designed, too big for me go over in detail, but seems to be another good source for software development and group news.
</para>
</sect3>
</sect2>
<sect2>
<title>Organizations</title>
<sect3>
<title>American Medical Informatics Association</title>
<para><ulink url="http://www.amia.org">AMIA</ulink> is a association that is quite a resource for the informatics community. Unfortunately, they require a subscription to join, but I have found that some mailing-lists will add you. I have found the cs-wg mailing list the most interesting, with some of the best discussion going around. The discussion are extremely good and informative.
</para>
</sect3>
</sect2>
<sect2>
<title> Mailing Lists</title>
<sect3>
<title>OpenHealth</title>
<para><ulink url="http://www.openhealth.com/">OpenHealth</ulink> is a another community that I have found has a good mailing list discussion. You can join the mailing list by going <ulink url="http://www.openhealth.com/en/healthcare.html"> Here</ulink>. It also contains a <ulink url="http://www.openhealth.com/en/healthlinks.html"> Link</ulink> to a list of other opensource works.
</para>
</sect3>
<sect3>
<title>Open Source Health Care Alliance</title>
<para>
<ulink url="http://www.oshca.org/"> Open Source Health Care Alliance (OSHCA)</ulink> is a collaborative forum to promote and facilitate open source software in human and veterinary health care.
</para>
</sect3>
</sect2>
<sect2>
<title>IRC</title>
<sect3>
<title>IRC #openmed</title>
<para>An IRC channel, <emphasis>#openmed</emphasis>, has been set up on irc.openprojects.net. To learn more about IRC, click <ulink url="http://www.irc.net"> Here</ulink>. To learn more about Openprojects.net, click <ulink url="http://www.openprojects.net"> Here</ulink>.
</para>
</sect3>
</sect2>
</sect1>
<!-- MEDICAL RECORD APPLICATIONS -->
<sect1 id="record">
<title>Medical Record Applications</title>
<sect2>
<title>Debian Med</title>
<para>The linux distribution by Debian is a well known and highly respected one. The developers are all volunteers and dedicated. Recently, it was announced that Debian would start making a Debian Med Package. This is very very good news, because one of the things Debian is known for is its "APT-GET" interface. This allows applications to be installed with the simple command of "apt-get install [application]". For example, if I wanted to install the OIO record system, I would simply type in 'apt-get install oio' and the apt-get program would not only install the OIO software, but would also install any software that OIO is Dependant on to run, such as the postgres database and Zope software and would configure it so that you could immediately start using it.</para>
<para>If you think I sound enthusiastic about this project, I am, because it simply would be perfect for the rest of the projects that are being developed in that would ease installment.</para>
<para>I urge to visit the Debian Med Homepage, by clicking <ulink url="http://auric.debian.org/~tille/debian-med/">HERE</ulink>
</para>
</sect2>
<sect2>
<title>VISTA (DHCP)</title>
<para> <ulink url="http://www.hardhats.org"> VISTA</ulink> is a huge, VA hospital funded project, electron medical records system. I used this system, when I was a resident, in the Va hospital, and it simply was the best system (that I had used). I'm actually surprised that not more people know about this. I am not sure about the license, but the software and documentation is available under the Freedom of Information Act, but you need to send <ulink url="http://hardhats.org/foia.html"> REQUESTS</ulink> to get access to the software on CD. They are currently starting to host more and more of the code on-line, though.
</para>
<sect3>
<title>Last Update:</title>
<para> Constantly
</para>
</sect3>
</sect2>
<sect2>
<title>SQL Clinic</title>
<para>
<ulink url="http://www.sqlclinic.net"> SQL clinic</ulink> is an impressive application that was developed for mental health workers, sponsored by their local hospital. What is most impressive is the amount of documentation. However it is unclear how useful the application would be for other non mental-health professionals.
</para>
<para>
<blockquote>
<attribution>Thomas Good writes</attribution>
<para>
To address the point about its utility outside the mental health sector: we are doing a spin-off called (believe it or not) SQL Cafe. Why? The local Indian restaurant (www.tasteofindia.org - I do their web pages) has hired us to design a custom database that tracks vendors, customers, uses a cgi based on-line menu (to replace the html version, so modifications don't require html skills) and so on.
</para>
<para>
Seriously, one other thing about SQL Clinic is that it was designed to be reverse engineered and used for other purposes. It's all based on Lincoln Stein's CGI.pm module (a terrific tool) and the incredible horsepower of Postgres. So I suspect, once Ingo and I get it a bit more streamlined, that SQL Clinic may have greater utility as an example of how to access postgres via Perl than as a mere clinical application. At least that is our goal.
</para>
</blockquote>
</para>
<sect3>
<title>Last Update:</title>
<para>Feb 2, 20002
</para>
</sect3>
</sect2>
<sect2>
<title>Electronic Obstetrical Record System</title>
<para>
<ulink url="http://www.eors.org"> EORS</ulink> is a quite a well-developed medical management system used by the developers themselves in their OB practice. The layout is somewhat Star Trek-ish, but quite useful and well developed.
</para>
<sect3>
<title>Last Update:</title>
<para>Unclear
</para>
</sect3>
</sect2>
<sect2>
<title>Freemed</title>
<para> <ulink url="http://www.freemed.org/"> Freemed</ulink> is a medical management software package that runs in a web browser window. It currently uses Apache, an SQL back-end (usually MySQL, but there's an SQL Abstraction for this), and PHP, and is non-browser specific. It aims to duplicate all of the functionality of programs such as The Medical Manager, while remaining free to the community.
</para>
<sect3>
<title>Last Update</title>
<para>Unclear. July 9, 2001 ?
</para>
</sect3>
</sect2>
<sect2>
<title>Freemed-YiRC</title>
<para> <ulink url="http://freemed-yirc.familyandyouth.org/"> Freemed-YiRC</ulink> is a PHP package based on Freemed for use with Youth in Residential Care (YiRC) agencies. Its aim is to be a complete package to replace legacy non-free apps which aren't customizable. Since it's PHP-based, all that is needed for the client is a good Web browser with extensive table support. It can use both Postgres and MySQL databases.
</para>
<sect3>
<title>Last Update:</title>
<para>02/04/2002
</para>
</sect3>
</sect2>
<sect2>
<title>GNUMed</title>
<para> <ulink url="http://www.gnumed.net"> GNUMed</ulink> is a GNU's project to develop a comprehensive medical management solution.
</para>
<sect3>
<title>Last update:</title>
<para>2000-11-22
</para>
</sect3>
</sect2>
<sect2>
<title>GNotary</title>
<para> <ulink url="http://gnumed.net/gnotary/"> GNOTARY</ulink> is a client that provide the ability to notarize digital documents using a server to prove that digital documents have not been tampered with after their initial creation date. This is a very important piece of software.
</para>
<para>The author provides a GNotary server to provide the actually notarization on a separate system.</para>
<sect3>
<title>Last Update:</title>
<para>2001-06-24</para>
</sect3>
</sect2>
<sect2>
<title>Res Medicinae</title>
<para> <ulink url="http://sourceforge.net/projects/resmedicinae/"> Res Medicinae</ulink> is supposed to be a comprising software solution for use in Medicine which combines intuitive ease of use with the advantages of the Java platform. It uses latest technology adhering to common standards for medical software and will such be open to many other medical systems.is the attempt to overcome high pricing in the realm of medical information systems and to provide users with a stable, platform independent, extensive system using latest technology and being open to many other medical systems.
</para>
<sect3>
<title>Last Update:
</title>
<para> 2002-02-05
</para>
</sect3>
</sect2>
<sect2>
<title>The LittleFish Health Project
</title>
<para> The <ulink url="http://www.littlefish.com.au/lfproject/intro/lfhome.htm"> LittleFish</ulink> project is a user friendly patient information and recall system on an open source basis for the use by any community health organization. The project will follow the GEHR or Good Electronic Health Record standards. This Site has a lot of useful information about the what is involved in trying to design the project.
</para>
</sect2>
<!-- <sect2>Last Update:
<p>2000-04-01, I am currently trying to contact the maintainer
-->
<sect2>
<title>Free Practice Management - FreePM</title>
<para><ulink url="http://www.freepm.org"> FreePM</ulink> is an open source project to create a provider designed patient centered electronic medical record and practice management application. This is probably one of the most developed projects out there, seems already quite usable in its Demo. More significantly, they offer services to help actually run their software in a real office, but all the code is opensource and they seem committed to this philosophy.
</para>
<para>
I have successfully installed this and gotten it to run. Please look for further info in chapter 7.
</para>
<para> Read a review of it <ulink url="http://www.linuxmednews.com/linuxmednews/993731309/index_html"> HERE</ulink>.
</para>
</sect2>
<!--
<sect2>Last Update:
<p>Unclear, possibly Nov, 2001.
-->
<sect2>
<title>Open Infrastructure for Outcomes
</title>
<para> <ulink url="http://www.TxOutcome.org/"> OIO</ulink> is a Web-based information system for treatment outcome management. It is in production at the Harbor/UCLA Medical Center for clinical outcomes management and research data. Forms created with OIO and hosted on any OIO server can be downloaded as XML files. Once downloaded from the "Forms library" and imported into an OIO server, the necessary database tables are automatically recreated and the imported forms become immediately available to the users of that OIO server.
</para>
<para>Note: This application is already in quite useful, but lacks 'already-made' forms for use. But these can be quickly designed within the application's interface quickly. Another to really try!
</para>
</sect2>
<!--
<sect2>Last Update:
<p>
-->
<sect2>
<title>myPACS
</title>
<para><ulink url="http://sol.cc.u-szeged.hu/~kszabo/myPACS.html"> MyPACS</ulink> is a Web-based medical image management system. It is written in PHP 3.x and uses MySQL for the relational database back-end. It features searching capabilities, uploading of images and patient data from a Web browser into shared and private image repositories, and thumbnail creation and image conversion using ImageMagick. Currently MyPACS is not compatible with the DICOM standard.
</para>
<!--
<sect2>Last Update:
<p>
-->
</sect2>
<sect2>
<title>LIMS - Laboratory Information Management Systems</title>
<para>The LIMS ASTM Standard (E1578 Standard Guide for Laboratory Information Management Systems) can be found in ASTM`s Annual Book of Standards Volume 14.01 Healthcare Informatics; Computerized Systems and Chemical and Material Information. There is a small terminology section in this standard that covers 25 terms that relate to LIMS. The purpose of the standard guide is to educate new LIMS users on the purpose and functions and the process of procuring a LIMS.
</para>
<para> There is one other additional LIMS related standard in this book. This E2066 Standard Guide for Validation of Laboratory Information Management Systems. The BlazeLIMS Server by <ulink url="http://www.blazesystems.com/"> Blaze Systems Corporation LIMS</ulink> is now supported on Linux.
</para>
<!--
<sect2>Last Update
<p>
-->
</sect2>
<sect2>
<title>Meditux</title>
<para><ulink url="http://meditux.sourceforge.net/"> Meditux</ulink> is Java-servlet based software that provides a Web interface to MySQL or potentially any relational database engine which is JDBC capable. It was developed to support an Intranet site in a medical intensive care unit where it was used to collect clinical and research data.
</para>
<!--
<sect2>Last Update:
<p>
-->
</sect2>
<sect2>
<title>MEGA and Mumps Compiler</title>
<para>Mumps Compiler is a compiler for a subset of the Mumps language, a language used mainly in health care. It is compatible with most operating systems with a standard C compiler. License: GPL <ulink url="http://home.clara.net/finch/"> OMEGA</ulink> is an Open Source implementation of the M-Technology (MUMPS) programming language. It is extend-able, and currently embedded with MySQL; it is ideal as a trigger/validation front-end to SQL. License: free for non-commercial use.
</para>
</sect2>
</sect1>
<sect1 id="informatics">
<title>Medical informatics</title>
<sect2>
<title>What is it?</title>
<para>My extremely brief answer would be it is the study of how medical data is recorded, stored, retrieved, displayed and exchanged. One of the big problems facing medicine is how to transfer medical data from one system to another.
</para>
<para>Another answer comes from the AMIA.ORG site:</para>
<para> Medical informatics has to do with all aspects of understanding and promoting the effective organization, analysis, management, and use of information in health care. While the field of medical informatics shares the general scope of these interests with some other health care specialties and disciplines, medical informatics has developed its own areas of emphasis and approaches that have set it apart from other disciplines and specialties. For one, a common thread through medical informatics has been the emphasis on technology as an integral tool to help organize, analyze, manage, and use information. In addition, as professionals involved at the intersection of information and technology and health care, those in medical informatics have historically tended to be engaged in the research, development, and evaluation side of things, and in studying and teaching the theoretical and methodological underpinnings of data applications in health care. However, today medical informatics also counts among its profession many whose activities are focused on dimensions that include the administration and everyday collection and use of information in health care. For an account of some of the definitions that describe the field in more formal and scientific terms, click here.
</para>
</blockquote>
</para>
</sect2>
<sect2>
<title>Good Electronic Health Record - GEHR</title>
<para> The <ulink url="http://www.gehr.org/"> Good Electronic Health Record (GEHR)</ulink> , a major part of the work of the openEHR Foundation, is an evolving electronic health record architecture designed to be comprehensive, portable and medico-legally robust. It has been developed from the <ulink url="http://www.chime.ucl.ac.uk/HealthI/GEHR/"> Good European Health Record project</ulink> requirements statement and object model- the most comprehensive requirements documents ever developed for the electronic health record. This website is a public resource for documents and resources that have been used to build implementations of this record.
</para>
</sect2>
<sect2>
<title>HL7lib - Health Level 7 Library
</title>
<para> <ulink url="http://hl7lib.sourceforge.net"> HL7lib Health Level 7 Library</ulink> is a project that will provide a free, correct implementation of Health Level 7 functions. Health Level 7 is commonly used in large hospitals to send patient information among computer systems from different vendors. Since there is no reference implementation of HL7 many of these vendor systems vary widely in their interpretation of HL7.
</para>
</sect2>
</sect1>
<sect1 id="pda">
<title>PDA</title>
<sect2>
<title>Palm Pilots</title>
<para>An increasing role in data collection for instance in hospitals, will be played by hand-held computers (HPCs) or Personal Digital Assistants (PDAs). More commonly known as PALMs. Linux offers way to exchange these data to servers, for instance via the IrDA port. See <ulink url="http://mobilix.org/howtos.html"> Infrared-HOWTO</ulink> for details. A survey of non-Linux applications for the Palm device you may find at <ulink url="http://palmtops.about.com/compute/palmtops/msub14.htm"> PalmPilot Medical - Palmtops PDAs HPCs Palm - Net Links</ulink>.
</para>
</sect2>
<sect2>
<title>Linux Devices</title>
<para>For more info, on say Sharp Zaurus SL-5000D, look <ulink url="http://www.linuxdevices.com/index.html">Here</ulink>.
</para>
<para>This section will grow as I am getting touch with a doctor who is actively developing OB-GYNE applications to use on it
</para>
</sect2>
</sect1>
<!--
HOW TO INSTALL ACTUALL MEDICAL RECORDS -->
<sect1>
<title>Installing a Medical Record Application (not ready yet)
</title>
<sect2>
<title>Point of this section
</title>
<para>
This section is actually going to be the <emphasis>HOW-TO</emphasis> of this HOW-TO document. I intend to include instructions or refer
to instruction on installing what available systems that
are readily usable at this point.
</para>
</sect2>
<sect2>
<title>My Assumptions About You</title>
<para>I will try to be pretty cook book about how to install these applications, which means that if I can, i will always tell you what to type (at least what to type that works for me). The problem is that this assumes that you know what a shell window is and can switch directories with-in, which actually assumes a fair level of technical sophistication since most of us have gotten used to Microsoft based Windows systems. Which is to say that a lot of us only have interacted with a computer using a Graphics User Interface (Gui's), and that these installation require that you be familiar with Command Line Interfaces (CLI) like a terminal window or a shell.
</para>
<para>If you don't know what I am talking about then I recommend you ask someone (me possibly) about what shell windows are, and probably what a UNIX-based Operating system looks like, especially without a GUI.
</para>
</sect2>
<sect2>
<title>OIO
</title>
<sect3>
<title>What is it?</title>
<para>
The OIO system starts a higher level of abstraction
- starting with modeling "forms". The forms are then
used to model/build progress notes etc. The OIO system
makes use of a relational database back-end (PostgreSQL) - 1) making the data/metadata/presentation separation more distinct, 2) making integration with other system (e.g. legacy systems, GNUMed, SQL Clinic etc) easier, 3) making query construction/extension easier (via SQL).
</para>
<para>If you search the OpenHealth mailing list archives, you will see extensive discussion regarding this in the context of GEHR and OIO. GEHR uses the same approach but calls this intermediate level of abstraction "archetypes". The advantage of the OIO/GEHR approach is that the metadata components can be plug-and-play - meaning that the system can be easily extended/customized AND portable medical records become easier to implement.
</para>
</sect3>
</sect2>
<sect2>
<title>FreePM</title>
<sect3>
<title>Introduction to FreePM</title>
<para>
This is the second application that I see that I think is actually useful for the medical office. (One of my main concerns, as I will be using it exactly for that.)
</para>
</sect3>
<sect3>
<title>Where to to get it</title>
<para>You can get the entire package which include everything you need like Zope products and even python from <ulink url="http://www.freepm.org:8080/freepm_download/fpm_downloads">Here</ulink> and choosing FreePM-1.0b6-FULL-linux2-x86.tar.gz. This will include all the documentation.
</para>
</sect3>
<sect3>
<title>Basic Installation of FreePM</title>
<para>Given that Tim Cook has put together everything you need to get a fully running FreePM application, I will first deal with installing the application as if you downloaded the full 14MB gzipped file. However, since Zope can be installed separately, and you may have other Zope applications going on, I will also discuss how to install the FreePM Zope product separately from installing Zope.
</para>
<sect4>
<title>Using the 14MB FreePM download</title>
<para>Once you have downloaded the 14 MB package, be sure to also download the extensions_for_1.0b6.tar.gz. At this point, it really doesn't matter what directory you have download the gzipped tar files into, but to play it clean and safe, I would download them or move them into their own directory. Then go ahead and <userinput> gunzip FreePM-1.0b6-FULL-linux2-x86.tar.gz </userinput> to unzip the file and then <userinput>tar xvf FreePM-1.0b6-FULL-linux2-x86.tar.gz</userinput>
</para>
<para>Once the tar file has finished unpacking, you should see a new directory called FreePM-1.0b6-FULL-linux2-x86. To make things easier I would change the name of this directory to 'FreePM' like so <userinput>mv FreePM-1.0b6-FULL-linux2-x86 FreePM</userinput>
<para>Move the extensions_for_1.0b6.tar.gz to the newly created FreePM directory and look for the 'Extension' directory and go ahead and move it there and unpack using the <userinput>tar xvf</userinput>
</para>
</sect4>
<sect4>
<title>Installing the Zope server</title>
<para>Tim Cook was smart and kind of enough to write an install script to install the Zope. Once you are in the FreePM directory (remember, the one that you created when you untar-ed the 14MB file), you run the script by tying <userinput>./install</userinput>
</para>
<caution><para>DON'T FORGET TO WRITE YOUR ADMIN and PASSWORD that you will at this point otherwise you will need to re-install the Zope server and determine you new password for admin</para></caution>
</sect4>
<sect4>
<title>Running the Zope Server</title>
<para>Tim Cook also wrote two scripts to start the server and stop the server. Be sure you our in the FreePM directory. You will know this if you see the files 'start' and 'stop' in there. It is also the same directory where you ran the <userinput>./install</userinput>. To start the Zope server, type <userinput>./start</userinput>. However you might want to type <userinput>./start&</userinput> to make it a background process which will free up your terminal window. This will also allow you to stop the Zope Server by typing <userinput>./stop</userinput> instead of hitting the CRTL-C key combination, a rather blunt way of stopping the Zope server and not an aestheically pleasing way of stopping the zope process.
</para>
</sect4>
<sect4>
<title>Installing the FreePM zope products </title>
<para>The key thing before I talk about installing the zope products is that, the first user, Admin, can only add other users and can not by itself actaully magane any products. You first need to add a new user and make the user a manager before you can do anything else.
</para>
<para>
To log into the running Zope server, you need to open a browser, type in http://127.0.0.1:8080 or depending on how new the Zope server is http://127.0.0.1:9673. If you look at the output during the install it will tell you what to what port to connect. <caution><para>Note: Using the old port 8080 would conflict, which is why Zope changed the port connection.</para></caution> At this point you should the zope introductory page, if not, make sure you have the correct port.
</para>
<para>Go ahead and click on the link that says Zope management interface or enter http:127.0.0.1:8080/manage and you should the zope management screen. You know you are in the correct section if you see a root folder at the top of the Left Frame. To make sure we are on the same page, go ahead and click on the Root Folder icon in the right Frame.</para>
<para>You then should see the list of contents of the Root Folder on the Right Frame.</para>
<para>Look for and click on the <emphasis>acl_users</emphasis> folder. select add new user, fill in the required fields. You leave the domain field blank. And then besure sure to select role. In this case, click on <emphasis>manager</emphasis> for this user.</para>
<para>I am having problems sucessfully loggin out completely using zope, so when you intend to switch users, be sure to completely close all broswer windows.</para>
<para>Once you added a new user that has the role of manager, log back in. THat is to say, Close all browers and open up a new browers and go the the zope management screen. You should be asked for a login at this point. Go ahead and enter in you new user login and password.</para>
<para>Once you are logged in as an user (not the admin user), go ahead and click on the Root Folder on the top of the left frame. Scrool to the bottom of the Right Frame and you should see the Import/Export button. You see a new screen. In the Field Import File Name, enter FreePMProduct.zexp and then hit the import button. You should see a new scree nindicating success</para>
<para>The next step, is to again hit on the Root Folder Icon at the TOP LEFT FRAME. Again hit the Import/Export button, but this time, you want to import FreePM.zexp. Then hit the Import button. <caution><para>Note that it will take some time to import the FreePM.zexp Zope product as it is quite large and you may get a brower error. I almost lost hair doing this stage because I coulnd tfigure out what was going wrong. In fact nothing was going wrong, it just took some time to import this large (32MB) zope prodcut. If you want to make sure something is acutally going on, I recommend using the <userinput>top</userinput> unix command, which will show you that python is actively still working to import FreePM.zexp.</para> </caution></para>
</sect4>
<sect4>
<title>Running FreePM </title>
<para>To actually get to the FreePM, you need to open a browser and go to http://127.0.0.1:8080/FreePM</para>
<para>You should see the introductor screen of FreePM. However, so far I can only add patients but can not edit any sensitive information. This section will need a lot of work</para>
</sect4>
</sect3>
</sect2>
</sect1>
<sect1 id = "Imaging">
<title>Imaging Applications</title>
<sect2>
<title>Slicer</title>
<para>The Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical data built on top of <ulink url="http://publib.ketware.com.vtk">VTK</ulink> (http://public.kitware.com/vtk). Slicer can read industry standard CT and MR image volume file formats, including DICOM. Slicer can be used to create complex 3D models, script and render animations, and make measurements. Additional modules can be added to Slicer using C++ and Tcl.
</para>
<caution><para>Please Note: Slicer is a research tool only, and should not be relied upon for any clinical applications.</para></caution>
<para>Development of the Slicer is an ongoing collaboration between the MIT Artificial Intelligence Lab and the Surgical Planning Lab at Brigham & Women's Hospital, an affiliate of Harvard Medical School. Slicer has an active developer community and is being used for research at many institutions around the world. Valid email address and contact information required for download. See http://www.slicer.org for more information.</para>
<para>Slicer is available in source code form and can be compiled for Solaris, Linux, or Windows. Precompiled binaries are available for some platforms.
</para>
</sect2>
</sect1>
<sect1 id="thought">
<title>My thoughts</title>
<sect2>
<title>Too Many Projects</title>
<para>Having spend some time on looking at the available software, I can only say that currently, we simply have an abundance of development, but little progress. I keep seeing multiple projects trying to achieve the same thing, but the resources are spread too think and so they fail. I wonder if there were some way to concentrate the various developers onto one project. The questions remain as to what main ideas should be focused on. Obviously the first one should be a Medical records application. That is a coherent, portable, way to contain, process, and use all the medical data that is generate by a patient.</para>
<para>The second focus should be on software for a workign clinic. This seems to be much harder since it would involve the billling seciton. However this would also include things like scheduling and multitude of forms that a clinic uses in day to day use.
</para>
<para>THe third focus (one I know little about) would be in the more specialized applications like Imagaing, which seems to already have quite a bit of working software, but is inherently hard to make because not everyone has access to CT scanners and such.
</para>
</sect2>
<sect2>
<title>I am biased</title>
<para>The other thing I want to point out is that this is not an un-biased LDP, I may stress something more than others because I think the foundation is better or that I have seen it actually work, so if you feel something is not right, please feel free to let me know.
</para>
<sect3>
<title>Debian as Standard linux distribution</title>
<para>I realize that urging people to consider debian as the standard linux system when it comes to medical applications is probably like arguing about religions. But.. :) The point is that our audience is not Linux gurus who only use slack or can configure applications from source tar balls. Debian provides an extremely sophisticated and easy to use installation process that is ideal for people who want to get a system running.
</para>
</sect3>
</sect2>
</sect1>
<sect1 id="credits">
<title>Credits</title>
<itemizedlist>
<listitem>
<para>Gref Fergusion. For putting up with my constant questions.
<para><ulink url="http://ls7-www.cs.uni-dortmund.de/~wawro"> Martin Wawro LS7, Department of Computer Science, UniDO</ulink> <wawro@ls7.cs.uni-dortmund.de>
</para>
</listitem>
</itemizedlist>
</sect1>
</article>
<!--
TO LIST:
1. Incoporate debian-med stuff: The web page is at
http://auric.debian.org/~tille/debian-med/
Much better than this document
2. WRITE HOW SECTION ON FREEPM
3. WRITE HOW TO SECTION ON TXOUTCOME.ORG. The Obvious thing is that this thing really speeds up the production and maintanance of forms. Esp it seems to be able to track what forms for home with what answers and thenyou can print it out.
