Re: Please proofread paper
2010/12/10 Andreas Tille <andreas@an3as.eu>:
> On Fri, Dec 10, 2010 at 11:29:42AM +0100, Nicolas Barbier wrote:
>
>> I am currently reading through this, checking for minor
>> grammar/spelling mistakes and inconsistent usage of UK/US English. I
>> am not sure whether the text is supposed to be written using the UK or
>> US variant: both variants are currently used in a mixed fashion. I am
>> converting the UK-isms to US English, does that sound OK?
>
> I'm persoanlly using "M-x ispell-changedictionary: british" so I prefer
> UK English. While I'm not very stubborn about this I really think that
> changing it the other way around should be more easy.
I noticed that there were indeed more changes needed in the UK->US
direction, so I switched to UK.
Patch for paper-text.tex attached.
Nicolas
8c8
< with an ambition to apply their talents the biomedical domain. At
---
> with an ambition to apply their talents to the biomedical domain. At
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< The ideas behind the \DebianMed generalised into the concept of
---
> The ideas behind the Debian Med generalised into the concept of
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< which are relevant for a given domain, but not yet integrated into
---
> that are relevant for a given domain, but not yet integrated into
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< procedures ease direct contributions to Debian, thus preventing unnecessary
---
> procedures eases direct contributions to Debian, thus preventing unnecessary
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< 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
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< complete system. For example, due to modularisation updates and fixes in core libraries, most
< of the time, make end-user software upgrades unnecessary. Performing binary builds
---
> complete system. For example, due to modularisation, updates and fixes in core libraries
> make end-user software upgrades unnecessary most of the time. Performing binary builds
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< on a projects manpower.
---
> on a project's manpower.
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< and similar efforts. Mutual interest in neuroimaging software led the
< NeuroDebian project \cite{neurodebian} join forces with \DebianMed to improve
---
> and similar efforts. Mutual interest in neuroimaging software led to the
> NeuroDebian project \cite{neurodebian} joining forces with \DebianMed to improve
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< An even larger task, managing a hospital is also tackled by several
< projects and the most famous is OpenVista\cite{openvista:2008}. As an
---
> The even larger task of managing a hospital is also tackled by several
> projects, of which the most famous is OpenVista\cite{openvista:2008}. As an
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< OpenMRS\cite{openmrs:2010} which is in preparation of being included
---
> OpenMRS\cite{openmrs:2010}, which is in preparation of being included
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< \section{Principles of Free Software Distribution}
---
> \section{Principles of Free Software distribution}
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< To make free Software development work, it requires a critical mass of
---
> To make Free Software development work, it requires a critical mass of
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< not the main concern of a regular Linux Distribution. However, with
---
> not the main concern of a regular Linux distribution. However, with
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< Free Software Guidelines (DFSG)}, that allow to free and open-source
---
> Free Software Guidelines (DFSG)}, that allow to distinguish free and open source
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< 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
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< Debian, but shall be universally applicable to anyone, \emph{i.e.} another software
< vendor or an individual users. This requirement is another indication for an
< intrinsic impetus to help Free software at large.
---
> Debian, but shall be universally applicable to anyone, such as other software
> vendors or individual users. This requirement is another indication of an
> intrinsic impetus to help Free Software at large.
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< actively influence the support of certain work fields.
---
> actively influence the support of certain fields of work.
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< a package, \emph{i.e.} that pay back for an initial packaging effort,
< is not the decisive factor in favor or against the maintenance of a
---
> a package, \emph{i.e.} that ``pay back'' for an initial packaging effort,
> is not the decisive factor in favor of or against the maintenance of a
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< be brought into the distribution and that one will possibly be
---
> be brought into the distribution, and that one will possibly be
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< lot of applications which are very specific to medical care and are
---
> lot of applications that are very specific to medical care and are
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< 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
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< 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
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< Debian contains more than 20000 binary packages, and this number is
---
> Debian contains more than 20,000 binary packages, and this number is
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< packages.
---
> %packages.
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>
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< ports to even more hardware architectures and operating systems kernels.
---
> ports to even more hardware architectures and operating system kernels.
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< {\itshape Distributors\/} are those companies that are building these
---
> {\itshape Distributors\/} are those companies or organisations that are building these
451,452c452,453
< Due to the complexity of the task these projects had to make compromises
< regarding the quality of their products and where frequently being
---
> Due to the complexity of the task, these projects had to make compromises
> regarding the quality of their products and were frequently being
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< release, others remained longer but were constantly loosing
< manpower. Furthermore, no security updates were made available and the
< distribution of general software tools stagnated at the point when
---
> release, others remained longer but were constantly losing
> manpower. Furthermore, no security updates were made available, and the
> distribution of general software tools stagnated at the moment at which
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< To prevent these problems \DebianMed took a different approach. The initial team was
< also quite small, but has grown in the eight years of existence to more
---
> To prevent these problems, \DebianMed took a different approach. The initial team was
> also quite small, but has grown in the eight years of its existence to more
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< drawbacks of the separate distributions mentioned above: There are
< security updates provided without any specific effort of the Debian
---
> drawbacks of the separate distributions mentioned above: security
> updates are provided without any specific effort of the Debian
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< Similar effort as \DebianMed exists in Fedora as
---
> An effort similar to \DebianMed exists in Fedora as
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< Both projects share the same idea to put medical applications inside a
---
> Both projects share the same idea of putting medical applications inside a
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< difference to \DebianMed (besides of the different distribution) is
---
> difference with \DebianMed (besides of being different distributions) is
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< for special use cases {\em into} this instead of deriving the whole
< system.
---
> for special use cases {\em into} this system instead of deriving a
> whole {\em new} system from the existing one.
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< 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
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< amount of work per package is much smaller compared to for instance
---
> amount of work per package is much smaller compared to, for instance,
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< medical care \DebianMed tries to cover all other fields of medical
< care as well. This goal is not yet reached but continuous work is
< done into this direction and some important steps are done.
---
> medical care, \DebianMed tries to cover all other fields of medical
> care as well. This goal is not yet reached but work in this direction
> is continuously performed and some important steps are done.
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< compared to the other repositories is the fact that \DebianMed is not
---
> compared to the other repositories, is the fact that \DebianMed is not
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< the requirements for medical practice and research. The goal of
< \DebianMed is a complete system for all tasks in medical care which is
< build completely on free software.
---
> the requirements of medical practice and research. The goal of
> \DebianMed is a complete system for all tasks in medical care that is
> built completely on Free Software.
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< building a common platform which reduces the amount of work for
---
> building a common platform that reduces the amount of work for
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< 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
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< researcher in the field of computational biology: Some biologists are Debian
---
> researchers in the field of computational biology: Some biologists are Debian
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< more the Debian user in the field of biology report back about
< problems or wishes the more Debian maintainers are able to enhance
< their system for their own and their users benefit.
---
> more the Debian users in the field of biology report back about
> problems or wishes, the more Debian maintainers are able to enhance
> their system for their own and their users' benefit.
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< packages himself) to specify all biomedical software with
---
> packages themselves) to specify all biomedical software with a
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< declare dependencies on other Debian package to thus prepare
---
> declare dependencies on other Debian packages that can be used to prepare
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< then needs to seek only for metapackages starting with prefix \package{med-}
< to install just few of them to fulfill his software selection requirements.
---
> only needs to search for metapackages starting with prefix \package{med-},
> and install just few of them to fulfill his or her software selection requirements.
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< might need for the job will be installed on his system. Once any of
< the metapackages is installed, a special user menu will be created to
---
> or she might need for the job will be installed on his or her system. If at least one of
> the metapackages is installed, a special user menu is created to
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< Each work field has an appropriate metapackage, for instance
---
> Each field of work has an appropriate metapackage, for instance
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< medical genetics and \package{med-practice} which are helpful to
< manage a medical practice. The sense of a metapackage is that you
< have to install only one single package using a package management
< software inside Debian to get all interesting packages which are
---
> medical genetics and \package{med-practice}, which is helpful to
> manage a medical practice. The sense of using metapackages is that you
> have to install only a single package using a package management
> software tool to get all interesting packages that are
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< 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
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< Once a software is packaged, the effort for future maintenance is
< relatively small. Nevertheless, care is needed not to exhaust initial maintainer's
< enthusiasm since continuous maintenance requires investigation of submitted bug reports and following the "upstream"
---
> Once a piece of software is packaged, the effort needed for its future maintenance is
> relatively small. Nevertheless, care is needed not to exhaust initial maintainers'
> enthusiasm since continuous maintenance requires investigation of submitted bug reports and following the ``upstream''
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< the upstream code, to learn from it and to contribute back is a part
< of their motivation - and that often does not scale. In the longer run,
---
> the upstream code, to learn from it, and to contribute back is a part
> of their motivation -- and that often does not scale. In the longer run,
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< to the Debian project. Debian welcome contributions and setup
---
> to the Debian project. Debian welcomes contributions and has set up
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< remains with the authors which is an important insensitive in the true
< spirit of open-source. As a result, anyone
---
> remains with the authors, which is an important incentive in the true
> spirit of open source. As a result, anyone
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< across variety architectures, online repositories and mirrors, bug
---
> for a variety of architectures, online repositories and mirrors, bug
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< layer yet again functioning within Debian infrastructure. That guarantees that overall development system remains robust
< and not requiring extra effort from the \DebianMed sub-community.
< Moreover, adherence to common principles and organization
---
> layer yet again functioning within Debian infrastructure.
> That guarantees that the overall development system remains robust
> and does not require extra effort from the \DebianMed sub-community.
> Moreover, adherence to common principles and organisation
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< overall maintenance cost since many actions could be done on the
< entire pool of the maintained packages at once. Admittedly, quite
---
> overall maintenance cost because many actions can be performed on the
> entire pool of maintained packages at once. Admittedly, quite
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< 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
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< continuous growth of the number of packages inside Debian which are of
---
> continuous growth of the number of packages inside Debian that are of
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< characterize the commitment of people involved in the
---
> characterise the commitment of people involved in the
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< project to compensate for the normal loss of supporters
---
> project to compensate for the normal loss of supporters,
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< with different orientation or less spare time for private reasons
---
> with different orientations or have less spare time for private reasons
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< to the project mailing list. Figure \ref{figure:authorstats}) shows
---
> to the project mailing list. Figure \ref{figure:authorstats} shows
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< 1108 commits to the SVN and since the beginning of \DebianMed, 47 developers
< did 5545 commits regarding packaging medical applications or
---
> 1,108 commits to the SVN repository and since the beginning of \DebianMed, 47 developers
> did 5,545 commits regarding packaging medical applications or
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< service has being integrated within the official Debian. It offers updates to
< the latest versions of packages while relying on the core components - whenever
< possible - that were shipped with the official releases. This
---
> service has being integrated within the official Debian project. It offers updates to
> the latest versions of packages while relying on the core components -- whenever
> possible -- that were shipped with the official releases. This
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< needs. The implementation \emph{e.g.} by the Debian Edu project -- another
---
> needs. The implementation by, for example, the Debian Edu project -- another
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< fact. The main reasons is an enormous availability of software for education
---
> fact. The main reason is an enormous availability of software for education
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< 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
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< The tasks pages are providing an overview about all the work fields
< like biology, medical imaging, practice management etc. which are
---
> The task pages are providing an overview of all fields of work,
> such as biology, medical imaging, practice management, etc., that are
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< 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}
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< 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
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< There are also quality assurance tools developed for instance there is
< an overview about
---
> There are also quality assurance tools developed; for instance there is
> an overview of
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< has set some cornerstone in the technical cooperation between user
---
> has set a cornerstone in the technical cooperation between user
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< 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
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< platform for medical work. The Freedom for users to apply those
< technologies for local needs, \emph{i.e.} new scientific problems or
---
> platform for medical work. The freedom of users to apply those
> technologies for local needs, \emph{e.g.} new scientific problems or
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< and not at least for the motivation of staff, all commercial
< distributors are well aware of. E.g., Red Hat has initiated Fedora as
< a free supplement to their commercial distribution. It is this reason
---
> and not at least for the motivation of staff, that all commercial
> distributors are well aware of. For example, Red Hat has initiated Fedora as
> a free supplement to their commercial distribution. This is the reason
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< 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
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< the is maintained by \DebianMed, is already a user of \DebianMed.
---
> that is maintained by \DebianMed, is already a user of \DebianMed.
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< can
< as on the \printurl{lists.debian.org/debian-med}{\DebianMed
---
> can ask on the \printurl{lists.debian.org/debian-med}{\DebianMed
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< be helped with the packaging and offered guidance towards
---
> be helped with the packaging process and offered guidance towards
913c914
< have been developed, this still needs to be amended to suite
---
> have been developed, this still needs to be amended to suit
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< even if some fields like micro biology are
---
> even if some fields like microbiology are
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< inter-institutional software projects of different kind in health
---
> inter-institutional software projects of different kinds in health
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< but also the technical infrastructure behind this community project
---
> but also the technical infrastructure behind this community project,
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< strive to support everybody's specific projects as best as they
< possibly can. It is the particular challenge of users of Free
---
> strive to support everybody's specific projects as well as they
> possibly can. It is a particular challenge of users of Free
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< to work together as Linux users, maybe along
---
> to work together as Free Software users, maybe along
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< i.e. the providers of the packages, the developers of the Free software
---
> i.e., the providers of the packages, the developers of the Free Software
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