Monthly Archives: January 2002

UK fails to exploit open source

Both Vnunet and the Register have articles here and here respectively about the UK’s National Computing Centre which reports that the UK is under utilizing open source software: ‘…Michael Gough, chief executive of the NCC, said: “The UK would benefit greatly from the establishment of a stable alternative to the use of proprietary software, both in terms of business innovation and competitiveness, and in support of the UK software industry.” The Register article says that they are advocating a ‘…National Library of Open Source software and compliance tests, to independently evaluate open source products for reliability and interoperability…’

Web Card Enables Medical Records

The Oklahoman has a story about a company that has a wallet-sized CD-ROM which will hold your medical data: ‘…Using technology that allows information to be stored on credit-card-size compact discs, Martin developed the Medical Web Card, which can hold volumes of medical details — even X-rays — and is easily viewed by any computer with a CD- ROM drive…The first updated card is free. Subsequent cards cost $14.95…’ This is also the first story in the newly created ‘Hardware’ subject heading.

Debian-Med Distribution Project Announced

Andreas Tille is announcing a medicine oriented Debian distribution project called ‘Debian-Med’ which ‘…will have two main components: Support for general practice and laboratory research. The general idea is adopted from the Debian Junior project. So we provide a set of packages which have dependencies from Debian packages which help solve certain tasks.

At first glance I have the following packages in my mind:

For General Practiciants:

– GnuMed
http://www.gnumed.org/
There will be ITPs for GnuMed and its tools soon from myself.
GnuMed will be a major part of Debian-Med and I will have focus
my own packaging work on this project.

– FreePM
http://www.freepm.org/
FreePM is an open source physicans office management & electronic
medical record application.
This is a Zope based project and there are reference implementations.
I think it would be worth packaging for Debian.

– Open Infrastructure for Outcomes
http://www.txoutcome.org/
Open Infrastructure for Outcomes (OIO) system facilitates the creation
of flexible and portable patient/research records. It aims to achieve
the “Holy Grail” of data portablity as elegantly described by
John G. Faughnan.
Another Zope based project.

– FreeMed
http://www.freemed.org (seems to be temporarily offline??)
Similiar to FreePM but PHP/MySQL based.
I personally prefer GnuMed because it uses PostgreSQL and has
a clear Client/Server structure but perhaps FreeMed yould be
turned into a nice web client to GnuMed.

Microbiology (if there are Debian packages I just name the package URL)

– ncbi-tools6 – NCBI libraries for biology applications http://packages.debian.org/unstable/libs/ncbi-tools6.html
(actively maintained by Aaron M. Ucko)

– seaview – A multiple sequence alignment editor
http://packages.debian.org/unstable/misc/seaview.html
(orphaned)

– clustalw – A multiple sequence alignment program
http://packages.debian.org/unstable/science/clustalw.html
(maintained by myself)

– phylip – A package of programs for inferring phylogenies.
http://packages.debian.org/unstable/misc/phylip.html
(maintained by myself)

– treetool – An interactive tool for displaying trees
http://packages.debian.org/unstable/science/treetool.html
(orphaned)

– molphy – Program Package for MOLecular PHYlogenetics
http://www.ism.ac.jp/software/ismlib/softother.e.html
(my package is in incoming)

– fastdnaml – A tool for construction of phylogenetic trees of DNA sequences
http://packages.debian.org/unstable/science/fastdnaml.html
(maintained by myself)

– njplot – A tree drawing program
http://packages.debian.org/unstable/science/njplot.html
(orphaned)

– readseq – Conversion between sequence formats
http://packages.debian.org/unstable/science/readseq.html
(maintained by myself)

– tree-puzzle – Reconstruction of phylogenetic trees by maximum likelihood
http://packages.debian.org/unstable/science/tree-puzzle.html
(maintained by myself)

– ARB
http://www.arb-home.de/
Integrated package for data handling and analysis.
I have preliminary packages of the recent Beta available. There
are several issues to sort out (especially concerning licenses of
Arb itself and the tools used by Arb).

Documentation and Research

– BioMail
http://www.biomail.org/
Nice if you are seeking for relevant literature.
Once there was an ITP for this program by another Debian developer. I
builded preliminary packages and suggested some changes upstream to
speed up packaging process. The maintainer who wanted to package it
seemed to lost interest and so just feel free to take over my
preliminary work which needs some cleaning and some discussion with
upstream.

– Medicine-HOWTO
http://mobilix.org/Medicine-HOWTO.html

Todo-List:

– Project page at debian.org

– Mailing list

– Logo? (Perhaps some skilled painter could take the idea of the GnuMed
logo and replace the GNU by the Debian swirl – just an idea)

– Packages …

– Documentation (including translation)

Further Links:

https://www.linuxmednews.com/projects/

http://www.openhealth.com/en/healthlinks.html

http://www.omp.de.vu (German)

I’m looking foreward for comments, suggestions and most importantly – help!

Kind regards

Andreas.

Computer system risk to confidential data

The potential problem stems from Windows XP and Internet Explorer 5.5, (and above) containing a means of automatically informing Microsoft when there is a system crash.

A possible risk to confidential data when using Microsoft Software has been identified by the Health Informatics Committee of The British Computer Society (BCS). Facilities in some Microsoft products can pose a serious risk to the confidentiality of patient data held on NHS computer systems. However, the problem could also affect any organisation which handles confidential data such as Government departments, the judiciary, police etc.

The potential problem stems from Windows XP and Internet Explorer 5.5, (and above) containing a means of automatically informing Microsoft when there is a system crash. When this facility is activated various pieces of information, including the computer file being worked on, is sent to Microsoft to enable them to analyse what went wrong. If this file contains confidential data, such as patient data in the case of the system being used by the health service, then that data is sent to Microsoft.

Consequently, BCS HIC is warning all healthcare, and other, users of confidential data, to be aware of this problem. The potential problem in the healthcare system may grow as many NHS computer systems are now using these MS products and the new arrangement between the NHS and Microsoft will expand usage. Such users are often also connected to the Internet via NHS net and this could mean that health service workers who are unaware of the problem could inadvertently send the information.

BCS HIC advises that all heath workers should be aware that if they are presented with a box suggesting they send information to Microsoft they click the “Don’t send”. Whilst those responsible for managing health IT systems should go to http://www.ciac.org/ciac/bulletins/m-005.shtml where there is a downloadable file enabling them to complete a Registry fix.

It is important that the Registry fix is only carried out by experienced IT support staff.

More information on the BCS can be found at www.bcs.org or by calling 01793 417417.

(More information on the data confidentiality problem is available from Dr Glyn Hayes, Chair Health Informatics Committee BCS, and President Primary Health Care Specialist Group, BCS on 01905 454705 or e mail glyn@conline.demon.co.uk.)