# Diff of /trunk/community/papers/11_med-floss_luxemburg/paper-text.tex

revision 5594 by tille, Fri Dec 10 12:34:43 2010 UTC revision 5595 by naoliv, Fri Dec 10 13:36:32 2010 UTC
# Line 5  Line 5
5    free medical software into the focus of users. Those may be IT    free medical software into the focus of users. Those may be IT
6    service providers for smaller clinics, the doctors themselves,    service providers for smaller clinics, the doctors themselves,
7    researchers in pre-clinical environments or just skilled enthusiasts    researchers in pre-clinical environments or just skilled enthusiasts
8    with an ambition to apply their talents the biomedical domain.  At    with an ambition to apply their talents to the biomedical domain.  At
9    that time, the communities in computational biology, medical imaging    that time, the communities in computational biology, medical imaging
11    Software solutions. Debian as a Linux distribution provided a solid    Software solutions. Debian as a Linux distribution provided a solid
# Line 32  Line 32
32    different domains of applications.  Today, Blend task pages complement    different domains of applications.  Today, Blend task pages complement
33    canonical Debian package listings with additional information    canonical Debian package listings with additional information
34    (e.g. scientific references) and also cover software products    (e.g. scientific references) and also cover software products
35    which are relevant for a given domain, but not yet integrated into    that are relevant for a given domain, but not yet integrated into
36    Debian.  A growing community with continuously improving maintenance    Debian.  A growing community with continuously improving maintenance
37    procedures ease direct contributions to Debian, thus preventing unnecessary    procedures eases direct contributions to Debian, thus preventing unnecessary
38    fractioning of the open-source community, and allow for supporting customised    fractioning of the open-source community, and allow for supporting customised
39    versions of Debian, such as \DebianMed, within the Debian ecosystem.    versions of Debian, such as \DebianMed, within the Debian ecosystem.
40    % the others are inactive enough to not mention them here    % the others are inactive enough to not mention them here
# Line 71  increasing specialisation of software. Line 71  increasing specialisation of software.
71  With a smaller number of potential contributors, one needs to help  With a smaller number of potential contributors, one needs to help
72  the community as much as possible to develop itself and to develop  the community as much as possible to develop itself and to develop
73  a tight relationship with its users. Debian as a Linux distribution already  a tight relationship with its users. Debian as a Linux distribution already
74  help distributing software in a readily usable form. Moreover, modularisation aspects of Debian packaging do not only reduce the complexity of packaging individual software, by allowing to  helps distributing software in a readily usable form. Moreover, modularisation aspects of Debian packaging do not only reduce the complexity of packaging individual software: by allowing to
75  depend on other packages, it also eases maintenance of the  depend on other packages, it also eases maintenance of the
76  complete system. For example, due to modularisation updates and fixes in core libraries, most  complete system. For example, due to modularisation, updates and fixes in core libraries
77  of the time, make end-user software upgrades unnecessary. Performing binary builds  make end-user software upgrades unnecessary most of the time. Performing binary builds
78  for more supported hardware platforms than any other operating system and extensive quality  for more supported hardware platforms than any other operating system and extensive quality
79  assurance guarantee robust performance of deployed Debian systems.  assurance guarantee robust performance of deployed Debian systems.
80  \DebianMed complements the Debian infrastructure with a communication platform  \DebianMed complements the Debian infrastructure with a communication platform
# Line 118  programmers that tackle unresolved probl Line 118  programmers that tackle unresolved probl
118  software they are using.  software they are using.
119  This type of user is extremely valuable to a project, because they can  This type of user is extremely valuable to a project, because they can
120  implement and contribute any modification they need by themselves without having to rely  implement and contribute any modification they need by themselves without having to rely
121  on a projects manpower.  on a project's manpower.
122  %For the  %For the
123  %larger challenges there may be many different driving forces coming  %larger challenges there may be many different driving forces coming
124  %together. \marginpar{explain?}  %together. \marginpar{explain?}
# Line 135  Software solutions. Line 135  Software solutions.
135
136  There are many ties between adjacent fields of science and also software  There are many ties between adjacent fields of science and also software
137  developers and users outside of biological research benefit from \DebianMed's  developers and users outside of biological research benefit from \DebianMed's
138  and similar efforts. Mutual interest in neuroimaging software led the  and similar efforts. Mutual interest in neuroimaging software led to the
139  NeuroDebian project \cite{neurodebian} join forces with \DebianMed to improve  NeuroDebian project \cite{neurodebian} joining forces with \DebianMed to improve
140  the coverage of medical imaging software in Debian.  Even if some important  the coverage of medical imaging software in Debian.  Even if some important
141  packages like the Bio Image Suite \cite{bioimagesuite:2008} are not yet  packages like the Bio Image Suite \cite{bioimagesuite:2008} are not yet
142  packaged for Debian, there is already an extensive coverage of viewers, data  packaged for Debian, there is already an extensive coverage of viewers, data
# Line 161  drugs database (FDA, CA, FR, ZA) as a st Line 161  drugs database (FDA, CA, FR, ZA) as a st
161  connection with other medical health record applications (like for  connection with other medical health record applications (like for
162  instance GNUmed).  instance GNUmed).
163
164  An even larger task, managing a hospital is also tackled by several  The even larger task of managing a hospital is also tackled by several
165  projects and the most famous is OpenVista\cite{openvista:2008}. As an  projects, of which the most famous is OpenVista\cite{openvista:2008}. As an
166  enterprise grade health care information system it is rather  enterprise grade health care information system it is rather
167  complex and needs a dedicated maintenance team beyond \DebianMed,  complex and needs a dedicated maintenance team beyond \DebianMed,
168  with a strong technical background and familiarity with the peculiarities of  with a strong technical background and familiarity with the peculiarities of
# Line 172  packaging.  This has started in August 2 Line 172  packaging.  This has started in August 2
172  we will see OpenVista in Debian at some point in the future.  we will see OpenVista in Debian at some point in the future.
173
174  Another application for hospital management is  Another application for hospital management is
175  OpenMRS\cite{openmrs:2010} which is in preparation of being included  OpenMRS\cite{openmrs:2010}, which is in preparation of being included
176  into Debian and chances are good that this will be finished in the  into Debian and chances are good that this will be finished in the
177  beginning of 2011.  beginning of 2011.
178
179
180  \section{Principles of Free Software Distribution}  \section{Principles of Free Software distribution}
181  % To me this section is more a description of core properties of Debian than  % To me this section is more a description of core properties of Debian than
182  % about principles of Free software distribution. If my impression is wrong  % about principles of Free software distribution. If my impression is wrong
183  % then many other distributions should be mentioned here as well.  % then many other distributions should be mentioned here as well.
# Line 196  offer Debian packages. Line 196  offer Debian packages.
197  %has to decide, if this public source may be trusted.  %has to decide, if this public source may be trusted.
198
199  To make free Software development work, it requires a critical mass of  To make Free Software development work, it requires a critical mass of
200  supporters. Development without feedback prior to the submission of  supporters. Development without feedback prior to the submission of
201  the final product is disadvantageous.  The development of programs is  the final product is disadvantageous.  The development of programs is
202  not the main concern of a regular Linux Distribution.  However, with  not the main concern of a regular Linux distribution.  However, with
203  the focus on Free Software and smooth local compilation, Debian  the focus on Free Software and smooth local compilation, Debian
204  considerably eases the contribution of comments and concise feedback  considerably eases the contribution of comments and concise feedback
205  of the technically skilled early adopters. Debian helps to bring  of the technically skilled early adopters. Debian helps to bring
# Line 220  Policy and the Debian Free Software Guid Line 220  Policy and the Debian Free Software Guid
220  Free or not free: Debian has a collection of criteria, referred  Free or not free: Debian has a collection of criteria, referred
221  to as the  to as the
222  \printurl{www.debian.org/social_contract\#guidelines}{Debian  \printurl{www.debian.org/social_contract\#guidelines}{Debian
223    Free Software Guidelines (DFSG)}, that allow to free and open-source    Free Software Guidelines (DFSG)}, that allow to distinguish free and open source
224  software from other categories of software.  software from other categories of software.
225  The most notable of these rules is that a software license must permit  The most notable of these rules is that a software license must permit
226  modifications and that those modifications are allowed to be redistributed,  modifications and that those modifications are allowed to be redistributed,
227  while granting the recipient the same rights. Moreover, there  while granting the recipient the same rights. Moreover, there
228  shall be no restrictions imposed on the recipients to whom those rights  shall be no restrictions imposed on the recipients to whom those rights
229  are granted regarding the work that is exerted with that software.  are granted regarding the work that is exerted with that software.
230  For example, Debian does not consider software as \textit{free} that comes as  For example, Debian does not consider software as \textit{free}, if it only comes as
231  \textit{free for academia}. Such software cannot become part of the Debian  \textit{free for academia}. Such software cannot become part of the Debian
232  system, but may only by offered in supplemental repositories.  system, but may only by offered in supplemental repositories.
233
234  Another important rule is that any granted permission must not be specific to  Another important rule is that any granted permission must not be specific to
235  Debian, but shall be universally applicable to anyone, \emph{i.e.} another software  Debian, but shall be universally applicable to anyone, such as other software
236  vendor or an individual users. This requirement is another indication for an  vendors or individual users. This requirement is another indication of an
237  intrinsic impetus to help Free software at large.  intrinsic impetus to help Free Software at large.
238
239  %The Debian Policy describes the structure and contents of the Debian  %The Debian Policy describes the structure and contents of the Debian
240  %archive and several design issues of the operating system, as well as  %archive and several design issues of the operating system, as well as
# Line 268  availability of software that contribute Line 268  availability of software that contribute
268  and beyond.  and beyond.
269
270  This {\em do-ocracy} principle enables individuals or small groups to  This {\em do-ocracy} principle enables individuals or small groups to
271  actively influence the support of certain work fields.  actively influence the support of certain fields of work.
272  Here, community-driven Linux distributions have an edge over  Here, community-driven Linux distributions have an edge over
273  commercial Linux distributions. The number of users that may use  commercial Linux distributions. The number of users that may use
274  a package, \emph{i.e.} that pay back for an initial packaging effort,  a package, \emph{i.e.} that pay back'' for an initial packaging effort,
275  is not the decisive factor in favor or against the maintenance of a  is not the decisive factor in favor of or against the maintenance of a
276  package. One only needs a sufficiently large community of active  package. One only needs a sufficiently large community of active
277  package maintainers to have confidence that the current  package maintainers to have confidence that the current
278  infrastructure will be maintained, that new packages will  infrastructure will be maintained, that new packages will
279  be brought into the distribution and that one will possibly be  be brought into the distribution, and that one will possibly be
280  allowed to improve current workflows with personal contributions.  allowed to improve current workflows with personal contributions.
281  \DebianMed is actively benefiting from this aspect and is supporting a  \DebianMed is actively benefiting from this aspect and is supporting a
282  lot of applications which are very specific to medical care and are  lot of applications that are very specific to medical care and are
283  not integrated in any other large distribution.  not integrated in any other large distribution.
284
285  The advantage of plugging Free Medical Software directly into a large  The advantage of plugging Free Medical Software directly into a large
# Line 299  upstream developer, usually per email, Line 299  upstream developer, usually per email,
299  %Earlier than this effort was  %Earlier than this effort was
300  the \printurl{www.debian.org/Bugs}{Debian Bug Tracking System} (BTS) offers  the \printurl{www.debian.org/Bugs}{Debian Bug Tracking System} (BTS) offers
301  an additional channel for tracking software defects efficiently. The  an additional channel for tracking software defects efficiently. The
302  maintainer of a software can investigate whether a particular report is actually  maintainer of a piece of software can investigate whether a particular report is actually
303  valid before upstream developers need to deal with it. Moreover, in many cases  valid before upstream developers need to deal with it. Moreover, in many cases
304  the Debian maintainer can suggest or even implement fixes, that are then sent  the Debian maintainer can suggest or even implement fixes, that are then sent
305  to upstream alongside the bug report, if the problem is not Debian-specific.  to upstream alongside the bug report, if the problem is not Debian-specific.
# Line 310  In the case of Free Medical Software the Line 310  In the case of Free Medical Software the
310  do not feature a bug tracking system.  Thus the inclusion of such  do not feature a bug tracking system.  Thus the inclusion of such
311  software into Debian adds extra value to the respective projects, because users can  software into Debian adds extra value to the respective projects, because users can
312  report issues via the Debian BTS and the maintainer of a package  report issues via the Debian BTS and the maintainer of a package
313  work as a proxy to the software authors.  For a user this has  works as a proxy to the software authors.  For a user this has
314  the benefit of a consistent bug reporting interface and software  the benefit of a consistent bug reporting interface and software
315  authors might get extra technical information provided by the Debian  authors might get extra technical information provided by the Debian
316  maintainer who generally has decent technical knowledge.  maintainer who generally has decent technical knowledge.
# Line 357  platforms are available online for every Line 357  platforms are available online for every
357
358  \subsection{Selection of packages}  \subsection{Selection of packages}
359
360  Debian contains more than 20000 binary packages, and this number is  Debian contains more than 20,000 binary packages, and this number is
361  constantly increasing.  There is no single user who needs all these  constantly increasing.  There is no single user who needs all these
362  packages.  packages.
363  % duplication  % duplication
364  %The typical user is interested in a subset of these  %The typical user is interested in a subset of these
365  packages.  %packages.
366  To specify packages of one's particular interest, several  To specify packages of one's particular interest, several
367  options are provided by Debian:  options are provided by Debian:
368
369  \begin{description*}  \begin{description*}
370  \item[tasksel] Provision of a reasonable software selection for rather general  \item[tasksel] Provision of a reasonable software selection for rather general
371    tasks that can be accomplished using a set of packages installed on    tasks that can be accomplished using a set of packages installed on
# Line 397  options are provided by Debian: Line 398  options are provided by Debian:
398  \end{description*}  \end{description*}
399
400  In addition to its 13 officially supported architectures, there are  In addition to its 13 officially supported architectures, there are
401  ports to even more hardware architectures and operating systems kernels.  ports to even more hardware architectures and operating system kernels.
402  Moreover, Debian package management and distribution infrastructure  Moreover, Debian package management and distribution infrastructure
403  has been adopted to other operating systems lacking a built-in equivalent,  has been adopted to other operating systems lacking a built-in equivalent,
404  \emph{i.e.} Fink on Mac OS X  \emph{i.e.} Fink on Mac OS X
# Line 412  There are general distributions, which d Line 413  There are general distributions, which d
413  user group and try to provide a universal coverage,  user group and try to provide a universal coverage,
414  and there are several specialised distributions targeting specific groups of users.  and there are several specialised distributions targeting specific groups of users.
415
416  {\itshape Distributors\/} are those companies that are building these  {\itshape Distributors\/} are those companies or organisations that are building these
417  collections of software.  Since the software provided by GNU/Linux distributions  collections of software.  Since the software provided by GNU/Linux distributions
418  is Free, the user purchasing a copy of the distribution pays for the  is Free, the user purchasing a copy of the distribution pays for the
419  service that the distributor is providing.  These services might be:  service that the distributor is providing.  These services might be:
# Line 448  a product with the following features: Line 449  a product with the following features:
449    \item attractive web appearance    \item attractive web appearance
450  \end{itemize*}  \end{itemize*}
451
452  Due to the complexity of the task these projects had to make compromises  Due to the complexity of the task, these projects had to make compromises
453  regarding the quality of their products and where frequently being  regarding the quality of their products and were frequently being
454  \begin{itemize*}  \begin{itemize*}
455    \item sloppy about policy of the underlying Debian system    \item sloppy about policy of the underlying Debian system
# Line 468  forums, IRC, etc. Line 469  forums, IRC, etc.
469  It turned out that this approach is not sustainable for the distribution of  It turned out that this approach is not sustainable for the distribution of
470  Free Medical Software.  Free Medical Software.
471  Some of these distributions issued only a single  Some of these distributions issued only a single
472  release, others remained longer but were constantly loosing  release, others remained longer but were constantly losing
474  distribution of general software tools stagnated at the point when  distribution of general software tools stagnated at the moment at which
475  the original fork from Debian, Knoppix or other distribution happened.  the original fork from Debian, Knoppix or other distribution happened.
476  Especially the latter aspect made such an approach to distribute software  Especially the latter aspect made such an approach to distribute software
477  unacceptable for sensible medical data.  unacceptable for sensible medical data.
478
479  To prevent these problems \DebianMed took a different approach.  The initial team was  To prevent these problems, \DebianMed took a different approach.  The initial team was
480  also quite small, but has grown in the eight years of existence to more  also quite small, but has grown in the eight years of its existence to more
481  than 20 active maintainers.  The primary idea is to maintain medical  than 20 active maintainers.  The primary idea is to maintain medical
482  applications {\em inside} Debian.  This automatically solves all  applications {\em inside} Debian.  This automatically solves all
483  drawbacks of the separate distributions mentioned above: There are  drawbacks of the separate distributions mentioned above: security
484  security updates provided without any specific effort of the Debian  updates are provided without any specific effort of the Debian
485  Med team.  There is a huge and reliable infrastructure with a bug  Med team.  There is a huge and reliable infrastructure with a bug
486  tracking system, several FTP servers all over the world, autobuilders  tracking system, several FTP servers all over the world, autobuilders
487  and an QA team running intense tests regarding software quality (see  and an QA team running intense tests regarding software quality (see
488  above).  above).
489
490  Similar effort as \DebianMed exists in Fedora as  An effort similar to \DebianMed exists in Fedora as
491  \printurl{http://fedoraproject.org/wiki/SIGs/FedoraMedical}{FedoraMedical  \printurl{http://fedoraproject.org/wiki/SIGs/FedoraMedical}{FedoraMedical
492    SIG (Special Interest Group)} and in openSUSE as    SIG (Special Interest Group)} and in openSUSE as
493  \printurl{http://en.opensuse.org/Portal:Medical}{openSUSE Medical}.  \printurl{http://en.opensuse.org/Portal:Medical}{openSUSE Medical}.
494  Both projects share the same idea to put medical applications inside a  Both projects share the same idea of putting medical applications inside a
495  larger distribution instead of trying to do the work of the  larger distribution instead of trying to do the work of the
496  distributor themselves.  The  distributor themselves.  The
497  difference to \DebianMed (besides of the different distribution) is  difference with \DebianMed (besides of being different distributions) is
498  that both teams are much smaller and thus the number of packaged  that both teams are much smaller and thus the number of packaged
499  applications is in both cases less than 5\% of the applications  applications is in both cases less than 5\% of the applications
500  available for Debian.  Moreover Debian does not distinguish between  available for Debian.  Moreover Debian does not distinguish between
# Line 509  underlying operating system (you can eas Line 510  underlying operating system (you can eas
510  kernel with Debian 6.0) but rather the fact that the same strategy to  kernel with Debian 6.0) but rather the fact that the same strategy to
511  support a specific field as in \DebianMed was followed:  Use a large  support a specific field as in \DebianMed was followed:  Use a large
512  and technically well supported system and put the specific software  and technically well supported system and put the specific software
513  for special use cases {\em into} this instead of deriving the whole  for special use cases {\em into} this system instead of deriving a
514  system.  whole {\em new} system from the existing one.
515
516
517  \subsection{Comparison with \DebianMed}  \subsection{Comparison with \DebianMed}
# Line 520  system. Line 521  system.
521  Looking at all efforts mentioned above (except Fedora  Looking at all efforts mentioned above (except Fedora
522  Medical and openSUSE Medical) it becomes evident that they are all  Medical and openSUSE Medical) it becomes evident that they are all
523  limited to biological software.  Previously it was stated that one  limited to biological software.  Previously it was stated that one
524  strong column of \DebianMed is this specific field and it is for a  strong column of \DebianMed is this specific field. This is the case for a specific
525  reason: The amount of free biological software is large and most of  reason: The amount of free biological software is large and most of
526  these projects are relatively easy to turn into packages -- therefore the  these projects are relatively easy to turn into packages -- therefore the
527  amount of work per package is much smaller compared to for instance  amount of work per package is much smaller compared to, for instance,
528  medical record applications with preparation of databases, dedicated  medical record applications with preparation of databases, dedicated
529  user management.  user management.
530
531  There is one major difference between the projects mentioned above  There is one major difference between the projects mentioned above
532  and \DebianMed: While the biological part is really interesting for  and \DebianMed: While the biological part is really interesting for
533  medical care \DebianMed tries to cover all other fields of medical  medical care, \DebianMed tries to cover all other fields of medical
534  care as well.  This goal is not yet reached but continuous work is  care as well.  This goal is not yet reached but work in this direction
535  done into this direction and some important steps are done.  is continuously performed and some important steps are done.
536
537  \subsubsection{Debian Pure Blend}  \subsubsection{Debian Pure Blend}
538
539  An even more important difference than the more general approach  An even more important difference than the more general approach
540  compared to the other repositories is the fact that \DebianMed is not  compared to the other repositories, is the fact that \DebianMed is not
541  only about just packaging software.  The \DebianMed project is one of  only about just packaging software.  The \DebianMed project is one of
542  the earliest so called {\em Debian Pure Blends} and aims to do  the earliest so called {\em Debian Pure Blends} and aims to do
543  more for the comfort of their users than adding binary packages to the  more for the comfort of their users than adding binary packages to the
544  Debian package pool.  The main goal is to turn Debian into the  Debian package pool.  The main goal is to turn Debian into the
545  distribution of choice for people working in the field of medicine and  distribution of choice for people working in the field of medicine and
546  to make Debian an operating system that is particularly well suited for  to make Debian an operating system that is particularly well suited for
547  the requirements for medical practice and research. The goal of  the requirements of medical practice and research. The goal of
548  \DebianMed is a complete system for all tasks in medical care which is  \DebianMed is a complete system for all tasks in medical care that is
549  build completely on free software.  built completely on Free Software.
550
551
552  \subsubsection{Flexibility in supporting small user groups}  \subsubsection{Flexibility in supporting small user groups}
553
554  On the organisational side the project tries to attract people working  On the organisational side the project tries to attract people working
555  in the field of Free Software in medicine to share the effort of  in the field of Free Software in medicine to share the effort of
556  building a common platform which reduces the amount of work for  building a common platform that reduces the amount of work for
557  developers and users.  Sharing the effort in publishing free medical  developers and users.  Sharing the effort in publishing free medical
558  software to a large user base is a main advantage of \DebianMed.  software to a large user base is a main advantage of \DebianMed.
559
560  The strength of Debian is the huge number of developers (more than  The strength of Debian is the huge number of developers (more than
561  1000) all over the world working in different fields.  Some of them  1,000) all over the world working in different fields.  Some of them
562  are working in the field of biology or medicine and thus have a  are working in the field of biology or medicine and thus have a
563  natural interest in developing a rock solid system they can rely on  natural interest in developing a rock solid system they can rely on
564  for their own work (not only commercial interest to sell service per  for their own work (not only commercial interest to sell service per
# Line 575  somebody who just does the work is calle Line 576  somebody who just does the work is calle
576  just means the doer decides what gets done.  just means the doer decides what gets done.
577
578  That is the reason why Debian is often the platform of choice for  That is the reason why Debian is often the platform of choice for
579  researcher in the field of computational biology: Some biologists are Debian  researchers in the field of computational biology: Some biologists are Debian
580  maintainers and so they added support for biological packages. The  maintainers and so they added support for biological packages. The
581  more the Debian user in the field of biology report back about  more the Debian users in the field of biology report back about
582  problems or wishes the more Debian maintainers are able to enhance  problems or wishes, the more Debian maintainers are able to enhance
583  their system for their own and their users benefit.  their system for their own and their users' benefit.
584
585  \subsubsection{Metapackages}  \subsubsection{Metapackages}
586
587  Debian offers tens of thousands of software, data and documentation packages. It is considered  Debian offers tens of thousands of software, data and documentation packages. It is considered
588  helpful for the users (who might not have the right to install  helpful for the users (who might not have the right to install
589  packages himself) to specify all biomedical software with  packages themselves) to specify all biomedical software with a
590  single instruction given to the local shell or to the local system  single instruction given to the local shell or to the local system
592
593  \DebianMed contains a set of metapackages that  \DebianMed contains a set of metapackages that
594  declare dependencies on other Debian package to thus prepare  declare dependencies on other Debian packages that can be used to prepare
595  the system for solving particular tasks.  The user  the system for solving particular tasks.  The user
596  then needs to seek only for metapackages starting with prefix \package{med-}  only needs to search for metapackages starting with prefix \package{med-},
597  to install just few of them to fulfill his software selection requirements.  and install just few of them to fulfill his or her software selection requirements.
598  The package management system then will take care about  The package management system then will take care about
599  the installation of all packages that are in the list of dependencies  the installation of all packages that are in the list of dependencies
600  of these metapackages -- so the user can be sure that all packages he  of these metapackages -- so the user can be sure that all packages he
601  might need for the job will be installed on his system.  Once any of  or she might need for the job will be installed on his or her system.  If at least one of
602  the metapackages is installed, a special user menu will be created to  the metapackages is installed, a special user menu is created to
603  enhance usability for the user working in the field of medicine.  enhance usability for the user working in the field of medicine.
604
605  Currently, \DebianMed applications are provided in certain  Currently, \DebianMed applications are provided in certain
# Line 607  hospital information systems, medical im Line 608  hospital information systems, medical im
608  molecular biology and medical genetics and others.  molecular biology and medical genetics and others.
609
610  %% This sounds somewhat redundant to me - SM  %% This sounds somewhat redundant to me - SM
611  Each work field has an appropriate metapackage, for instance  Each field of work has an appropriate metapackage, for instance
612  \package{med-bio} for packages concerning molecular biology and  \package{med-bio} for packages concerning molecular biology and
613  medical genetics and \package{med-practice} which are helpful to  medical genetics and \package{med-practice}, which is helpful to
614  manage a medical practice.  The sense of a metapackage is that you  manage a medical practice.  The sense of using metapackages is that you
615  have to install only one single package using a package management  have to install only a single package using a package management
616  software inside Debian to get all interesting packages which are  software tool to get all interesting packages that are
617  necessary for a single task.  For  necessary for a single task.  For
618  instance a single command \\  instance a single command \\
619  \hspace*{10mm}\texttt{apt-get install med-bio} \\  \hspace*{10mm}\texttt{apt-get install med-bio} \\
620  results in installation of all applications inside Debian which are related to the field of  results in installation of all applications inside Debian that are related to the field of
621  molecular biology and medical genetics.  molecular biology and medical genetics.
622
623
# Line 629  molecular biology and medical genetics. Line 630  molecular biology and medical genetics.
630  \label{figure:dmstats}  \label{figure:dmstats}
631  \end{figure}  \end{figure}
632
633  Once a software is packaged, the effort for future maintenance is  Once a piece of software is packaged, the effort needed for its future maintenance is
634  relatively small. Nevertheless, care is needed not to exhaust initial maintainer's  relatively small. Nevertheless, care is needed not to exhaust initial maintainers'
635  enthusiasm since continuous maintenance requires investigation of submitted bug reports and following the "upstream"  enthusiasm since continuous maintenance requires investigation of submitted bug reports and following the upstream''
636  development. Also, for many package maintainers, to understand  development. Also, for many package maintainers, to understand
637  the upstream code, to learn from it and to contribute back is a part  the upstream code, to learn from it, and to contribute back is a part
638  of their motivation - and that often does not scale. In the longer run,  of their motivation -- and that often does not scale. In the longer run,
639  continuous growth can only come through attracting additional contributors  continuous growth can only come through attracting additional contributors
640  to the Debian project.   Debian welcome contributions and setup  to the Debian project.   Debian welcomes contributions and has set up
642  \printurl{wiki.debian.org/DebianMaintainer}{Debian Maintainer} programs  \printurl{wiki.debian.org/DebianMaintainer}{Debian Maintainer} programs
643  to lower the entry barrier.  Those programs allow anyone  to lower the entry barrier.  Those programs allow anyone
# Line 646  obtaining of which requires going throug Line 647  obtaining of which requires going throug
647  \printurl{www.debian.org/devel/join/newmaint}{Debian New Maintainer}  \printurl{www.debian.org/devel/join/newmaint}{Debian New Maintainer}
648  process.    Moreover, the Debian policy is not requiring any kind of  process.    Moreover, the Debian policy is not requiring any kind of
649  a \emph{Contributor Agreement}, thus ownership for any contributed work  a \emph{Contributor Agreement}, thus ownership for any contributed work
650  remains with the authors which is an important insensitive in the true  remains with the authors, which is an important incentive in the true
651  spirit of open-source.  As a result, anyone  spirit of open source.  As a result, anyone
652  interested can easily contribute and acceptance might be only a couple of emails away.  interested can easily contribute and acceptance might be only a couple of emails away.
653
654  % Should the Google Code-In and Google Summer of Code be mentioned?  % Should the Google Code-In and Google Summer of Code be mentioned?
# Line 670  interested can easily contribute and acc Line 671  interested can easily contribute and acc
671
672  \DebianMed is not a derived distribution and is a part of the  \DebianMed is not a derived distribution and is a part of the
673  Debian project. \DebianMed relies on the core Debian infrastructure (\emph{e.g.} build farm  Debian project. \DebianMed relies on the core Debian infrastructure (\emph{e.g.} build farm
674  across variety architectures, online repositories and mirrors, bug  for a variety of architectures, online repositories and mirrors, bug
675  tracking system) and only complements it with an additional thin  tracking system) and only complements it with an additional thin
676  layer yet again functioning within Debian infrastructure.  That guarantees that overall development system remains robust  layer yet again functioning within Debian infrastructure.
677  and not requiring extra effort from the \DebianMed sub-community.  That guarantees that the overall development system remains robust
678  Moreover, adherence to common principles and organization  and does not require extra effort from the \DebianMed sub-community.
679    Moreover, adherence to common principles and organisation
680  helps \DebianMed project members to improve efficiency and share  helps \DebianMed project members to improve efficiency and share
681  overall maintenance cost since many actions could be done on the  overall maintenance cost because many actions can be performed on the
682  entire pool of the maintained packages at once.  Admittedly, quite  entire pool of maintained packages at once.  Admittedly, quite
683  frequently software products maintained by \DebianMed are of generic  frequently software products maintained by \DebianMed are of generic
684  utility, \emph{e.g.}  Java or Python libraries,  and thus of interest to the  utility, such as Java or Python libraries,  and thus of interest to the
685  Debian audience outside of the target scope of \DebianMed -- Medicine,  Debian audience outside of the target scope of \DebianMed -- Medicine,
686  as a result benefiting Debian as a whole.  Due to significant  as a result benefiting Debian as a whole.  Due to significant
687  overlap,  boundaries between different Blends are not clearly defined and  overlap,  boundaries between different Blends are not clearly defined and
# Line 694  artifactual. Line 696  artifactual.
696  \end{figure}  \end{figure}
697
698  The success of the Debian Blends approach finds evidence in \emph{e.g.} a  The success of the Debian Blends approach finds evidence in \emph{e.g.} a
699  continuous growth of the number of packages inside Debian which are of  continuous growth of the number of packages inside Debian that are of
700  interest for health care.  Taking the number of dependencies of some  interest for health care.  Taking the number of dependencies of some
701  metapackages into account (see figure \ref{figure:dmstats}), only a  metapackages into account (see figure \ref{figure:dmstats}), only a
702  small set of packages useful for medical care was available at the  small set of packages useful for medical care was available at the
# Line 703  with a gradient that perfectly reflects Line 705  with a gradient that perfectly reflects
705  in this field can be observed.  in this field can be observed.
706
707  Besides the growth of the output of a project it is useful to  Besides the growth of the output of a project it is useful to
708  characterize the commitment of people involved in the  characterise the commitment of people involved in the
709  project.  It is important to ensure that fresh blood is coming into the  project.  It is important to ensure that fresh blood is coming into the
710  project to compensate for the normal loss of supporters  project to compensate for the normal loss of supporters,
711  which always happens in Free Software projects (people find new jobs  which always happens in Free Software projects (people find new jobs
712  with different orientation or less spare time for private reasons  with different orientations or have less spare time for private reasons
713  etc.).  A raw measure for the activity of members might be their mails  etc.).  A raw measure for the activity of members might be their mails
714  to the project mailing list.  Figure \ref{figure:authorstats}) shows  to the project mailing list.  Figure \ref{figure:authorstats} shows
715  the number of mails from the ten most active posters on the \DebianMed  the number of mails from the ten most active posters on the \DebianMed
716  mailing list.  This graph shows that the number of active supporters  mailing list.  This graph shows that the number of active supporters
717  was growing constantly in the first years and is now at some constant  was growing constantly in the first years and is now at some constant
# Line 739  yet visible in the graphs). Line 741  yet visible in the graphs).
741
742  The most active people committing packaging materials are shown in  The most active people committing packaging materials are shown in
743  Figure \ref{figure:develstats}(a).  In the last year 26 developers did  Figure \ref{figure:develstats}(a).  In the last year 26 developers did
744  1108 commits to the SVN and since the beginning of \DebianMed, 47 developers  1,108 commits to the SVN repository and since the beginning of \DebianMed, 47 developers
745  did 5545 commits regarding packaging medical applications or  did 5,545 commits regarding packaging medical applications or
747
748  \subsubsection{Backports}  \subsubsection{Backports}
# Line 753  whole. For scientific packages and for Line 755  whole. For scientific packages and for
755  packages reacting to continuous changes in the health care system,  packages reacting to continuous changes in the health care system,
756  this is not an adequate situation. The long established  this is not an adequate situation. The long established
757  \printurl{backports.debian.org}{Debian backports}  \printurl{backports.debian.org}{Debian backports}
758  service has being integrated within the official Debian.  It offers updates to  service has being integrated within the official Debian project.  It offers updates to
759  the latest versions of packages while relying on the core components - whenever  the latest versions of packages while relying on the core components -- whenever
760  possible - that were shipped with the official releases. This  possible -- that were shipped with the official releases. This
761  compromise allows to brings maximal usability and maximal robustness  compromise allows to brings maximal usability and maximal robustness
762  together.  together.
763
764  \subsubsection{Role inside Debian}  \subsubsection{Role inside Debian}
765
766  The Debian Pure Blends framework was mainly inspired by the \DebianMed  The Debian Pure Blends framework was mainly inspired by the \DebianMed
767  needs.  The implementation \emph{e.g.} by the Debian Edu project -- another  needs.  The implementation by, for example, the Debian Edu project -- another
768  Blend -- is far more advanced.  There are several reasons for this  Blend -- is far more advanced.  There are several reasons for this
769  fact.  The main reasons is an enormous availability of software for education  fact.  The main reason is an enormous availability of software for education
770  and the fact that a Norwegian company paid developers to work full  and the fact that a Norwegian company paid developers to work full
771  time on this project.  \DebianMed profited from those  time on this project.  \DebianMed profited from those
772  technologies and generalised some tools from Debian Edu for all Blends.  technologies and generalised some tools from Debian Edu for all Blends.
# Line 772  Conversely, inside \DebianMed some new B Line 774  Conversely, inside \DebianMed some new B
774  now enhance the easy preparation of metapackages.  now enhance the easy preparation of metapackages.
775
776  Beyond the metapackages, another service of the Blends is the  Beyond the metapackages, another service of the Blends is the
777  so called web sentinel. It is a web portal to guide the contributors  so-called web sentinel. It is a web portal to guide the contributors
778  to the current active tasks (packages) and their associated  to the current active tasks (packages) and their associated
779  bug reports.  bug reports.
780  The tasks pages are providing an overview about all the work fields  The task pages are providing an overview of all fields of work,
781  like biology, medical imaging, practice management etc.  which are  such as biology, medical imaging, practice management, etc., that are
782  covered by \DebianMed.  The list of all the packages is regenerated  covered by \DebianMed.  The list of all the packages is regenerated
783  on a daily basis and includes some meta information to \emph{e.g.} point to  on a daily basis and includes some meta information to \emph{e.g.} point to
784  relevant scientific publications and the description of the  relevant scientific publications and the description of the
785  packages in this task.  So the output of the project can be easily \marginpar{just have a regular reference to the URL}  packages in this task.  The output of the project can be easily \marginpar{just have a regular reference to the URL}
788
# Line 793  available, give information about the us Line 795  available, give information about the us
795  results and inform about versions packaged for Debian as well as a  results and inform about versions packaged for Debian as well as a
797  these pages gets an easy option to provide a screenshot or a missing  these pages gets an easy option to provide a screenshot or a missing
798  or translations as well as fixing a wrong translation, \emph{i.e.} everyone  translation as well as fixing a wrong translation, \emph{i.e.} everyone
799  is visibly invited to contribute.  is visibly invited to contribute.
800
801  There are also quality assurance tools developed for instance there is  There are also quality assurance tools developed; for instance there is
802  an overview about  an overview of
803  \printurl{http://debian-med.alioth.debian.org/bugs/}{all bugs  \printurl{http://debian-med.alioth.debian.org/bugs/}{all bugs
804    concerning the packages in \DebianMed}.    concerning the packages in \DebianMed}.
805
806  By providing this kind of tools for other Blends as well \DebianMed  By providing this kind of tools for other Blends as well \DebianMed
807  has set some cornerstone in the technical cooperation between user  has set a cornerstone in the technical cooperation between user
808  oriented projects inside Debian.  This in turn awakes the interest of  oriented projects inside Debian.  This in turn awakes the interest of
809  other Debian developers who might provide other tools for \DebianMed.  other Debian developers who might provide other tools for \DebianMed.
810
# Line 810  other Debian developers who might provid Line 812  other Debian developers who might provid
812
813  The \DebianMed project serves as a common platform for all Free  The \DebianMed project serves as a common platform for all Free
814  Software that may be utilised in medical care. Tools developed in  Software that may be utilised in medical care. Tools developed in
815  computational biology are just a part of it because it is an important  computational biology are just a part of it because they are an important
816  brick in medical sciences.  brick in medical sciences.
817
818  The contributors to \DebianMed aim at providing the best possible  The contributors to \DebianMed aim at providing the best possible
819  platform for medical work. The Freedom for users to apply those  platform for medical work. The freedom of users to apply those
820  technologies for local needs, \emph{i.e.} new scientific problems or  technologies for local needs, \emph{e.g.} new scientific problems or
821  particular regulations in health care, are intrinsically connected  particular regulations in health care, are intrinsically connected
822  with that prime ambition. The Debian Free Software Guidelines  with that prime ambition. The Debian Free Software Guidelines
823  match those nicely and are applicable across platforms.  match those nicely and are applicable across platforms.
# Line 851  and shares its developments across platf Line 853  and shares its developments across platf
853
854  That strong support within the community of users is essential for the  That strong support within the community of users is essential for the
855  development of software, for quality assurance, feedback on features,  development of software, for quality assurance, feedback on features,
856  and not at least for the motivation of staff, all commercial  and not at least for the motivation of staff, that all commercial
857  distributors are well aware of.  E.g., Red Hat has initiated Fedora as  distributors are well aware of.  For example, Red Hat has initiated Fedora as
858  a free supplement to their commercial distribution.  It is this reason  a free supplement to their commercial distribution.  This is the reason
859  why \DebianMed is part of Debian and why groups external to the Debian  why \DebianMed is part of Debian and why groups external to the Debian
860  society, like BioLinux\marginpar{ref for BioLinux}, are also keen on close collaborations with the  society, like BioLinux\marginpar{ref for BioLinux}, are also keen on close collaboration with the
861  community.  community.
862
863
864  \subsubsection{Approaching \DebianMed}  \subsubsection{Approaching \DebianMed}
865
866  Anybody already using regular Debian or Ubuntu and having a package installed  Anybody already using regular Debian or Ubuntu and having a package installed
867  the is maintained by \DebianMed, is already a user of \DebianMed.  that is maintained by \DebianMed, is already a user of \DebianMed.
868  To have a new package shipped with the distribution, one  To have a new package shipped with the distribution, one
869  can  can ask on the \printurl{lists.debian.org/debian-med}{\DebianMed
as on the \printurl{lists.debian.org/debian-med}{\DebianMed
870      mailing list}. The developers of the software would      mailing list}. The developers of the software would
871  be helped with the packaging and offered guidance towards  be helped with the packaging process and offered guidance towards
873
874  %% I have difficulties with the remaining items. The style is  %% I have difficulties with the remaining items. The style is
# Line 910  very suitable medium for this purpose. Line 911  very suitable medium for this purpose.
911  for the sharing of data management, \emph{i.e.} the input for their  for the sharing of data management, \emph{i.e.} the input for their
912  tools that should be consistent for all tools contributing  tools that should be consistent for all tools contributing
913  to a scientific workflow. While some ideas like \emph{e.g.} getData \marginpar{wiki.debian.org/getData},  to a scientific workflow. While some ideas like \emph{e.g.} getData \marginpar{wiki.debian.org/getData},
914  have been developed, this still needs to be amended to suite  have been developed, this still needs to be amended to suit
915  the community better.  the community better.
916
917  Another aspect is education. Debian or Ubuntu are used in  Another aspect is education. Debian or Ubuntu are used in
# Line 922  course materials to be shared similarly Line 923  course materials to be shared similarly
923  \section{Conclusions}  \section{Conclusions}
924
925  The real use of Free Software for medical care is very heterogeneous,  The real use of Free Software for medical care is very heterogeneous,
926  even if some fields like micro biology are  even if some fields like microbiology are
927  better covered than others. The continuous updates of data and the  better covered than others. The continuous updates of data and the
928  addition of novel important tools for a general medical environment  addition of novel important tools for a general medical environment
929  cannot be performed by a single individual. The adherence to a policy  cannot be performed by a single individual. The adherence to a policy
930  and the sharing of maintenance are basic technologies to allow  and the sharing of maintenance are basic technologies to allow
931  inter-institutional software projects of different kind in health  inter-institutional software projects of different kinds in health
932  care.  care.
933
934  Debian and its special dedication to medical software in \DebianMed,  Debian and its special dedication to medical software in \DebianMed,
935  but also the technical infrastructure behind this community project  but also the technical infrastructure behind this community project,
936  renders a comfortable solution.  The volunteers behind \DebianMed  renders a comfortable solution.  The volunteers behind \DebianMed
937  strive to support everybody's specific projects as best as they  strive to support everybody's specific projects as well as they
938  possibly can. It is the particular challenge of users of Free  possibly can. It is a particular challenge of users of Free
939  Software, to determine together with the community the available  Software, to determine together with the community the available
941  respectively.  respectively.
# Line 948  of the software that is important. openS Line 949  of the software that is important. openS
949  slight variations, have adopted much of the principles that Debian  slight variations, have adopted much of the principles that Debian
951  format conversion tool \package{alien}  format conversion tool \package{alien}
952  to work together as Linux users, maybe along  to work together as Free Software users, maybe along
953  the lines of the collaboration between Debian and Ubuntu. And we all,  the lines of the collaboration between Debian and Ubuntu. And we all,
954  users, packagers and developers, need to understand more about cross  users, packagers and developers, need to understand more about cross
955  platform developments that also includes Mac OS X and Windows.  platform developments that also includes Mac OS X and Windows.
# Line 964  platform developments that also includes Line 965  platform developments that also includes
965  \section{Acknowledgements}  \section{Acknowledgements}
966
967  Many thanks go to all contributors to Debian and \DebianMed,  Many thanks go to all contributors to Debian and \DebianMed,
968  i.e.  the providers of the packages, the developers of the Free software  \emph{i.e.}, the providers of the packages, the developers of the Free Software
969  and to all those who donate the resources for the project.  and to all those who donate the resources for the project.
970

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