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.)

BBC: NHS warned on computer spending

Two more articles in continuing coverage of the UK’s National Health Service (NHS) computerization effort: One article from the BBC states: ‘…Recent reports from the National Audit Office “graphically illustrated” the need for improved information about equipment, bed management and hospital acquired infections, said the Tory MP [David Davis]. “Time and again, we have seen poor design, poor implementation and weak cost control,” he said. Link courtesy of Richard Shilling. The second article in Computer Weekly is an editorial about open source and the dangers of NHS cozying up to Microsoft: ‘…The Government will be taking a huge risk – should it be unsatisfied with the projects, will it be easy to move to another supplier? And how much would such a move cost? Microsoft’s track record on producing technology that can be easily integrated with that of its competitors raises an ominous spectre here… Link courtesy of Dave Scott.

Information Week: Get Well, Fast

Information Week has an article about the implications of having and not having healthcare information technology in the face of a bio-terrorism attack: ‘…Information-sharing among government health agencies and across health-care organizations still depends mostly on the phone, fax, and mail. That raises concerns about whether the health-care industry has the kind of collaboration tools needed to spot a biological threat quickly enough to contain it.

“This crisis is a wake-up call for the health-care industry to leverage IT for support and integration of care,” says Martin Lustick, Kaiser Permanente’s VP and associate medical director for operations… This link courtesy of Wayne Wilson.

BJHC: Open-source software for the NHS

Dr Adrian Midgley, Dr Douglas Carnall and Colin Smith have an article (abstract only, subscription required) in the British Journal of Healthcare Computing: ‘ Proprietary software places purchasers at their suppliers’ mercy for support and customisation; lock-in is the rule. Open-source software ensures that code is freely available for anyone to download and use. Software businesses that tailor and service the software for organisations can still be profitable but will free users from supplier lock-in. Several NHS organisations are already deploying open-source software with considerable satisfaction. Open-source development methods have yet to be widely used in the healthcare domain, but there are many lessons for the developers of applications. Thanks to Dave Scott for this link.

Information Technology and Child and Adolescent Psychiatry: Ethical Issues

Medscape (registration required) has an article on the ethical issues of Informatics in child and adolescent Psychiatry here: ‘…Principal among ethical issues concerning children and adolescents are those of their vulnerability and need for protection by either parents, guardians, or agencies; the complexity involved in transitioning from childhood to adolescence; and the problems innate to divorce and joint guardianship. Principal among ethical issues concerning psychiatric patients are those of confidentiality, the right to quality information, and the right to be informed of how information about patients may be used…

MSJ: Third Wave unravels mysteries of disease through DNA research

The Milwaukee Journal Sentinel has a report on a particularly interesting Biotech company, Third Wave: ‘…Third Wave is one of dozens of companies searching for the holy grail of genetic research, to reach a point that by examining a person’s genetic profile, doctors can predict a predisposition to disease or an adverse reaction to a particular drug.

In the dawning era of so-called personalized medicine, drugs and treatments will be specifically tailored to the individual…’

Sidebar
Skip to toolbar