2010/12/10 Andreas Tille <andr...@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 28c28 < The ideas behind the \DebianMed generalised into the concept of --- > The ideas behind the Debian Med generalised into the concept of 35c35 < which are relevant for a given domain, but not yet integrated into --- > that are relevant for a given domain, but not yet integrated into 37c37 < procedures ease direct contributions to Debian, thus preventing unnecessary --- > procedures eases direct contributions to Debian, thus preventing unnecessary 74c74 < 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 76,77c76,77 < 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 121c121 < on a projects manpower. --- > on a project's manpower. 138,139c138,139 < 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 164,165c164,165 < 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 175c175 < OpenMRS\cite{openmrs:2010} which is in preparation of being included --- > OpenMRS\cite{openmrs:2010}, which is in preparation of being included 180c180 < \section{Principles of Free Software Distribution} --- > \section{Principles of Free Software distribution} 199c199 < To make free Software development work, it requires a critical mass of --- > To make Free Software development work, it requires a critical mass of 202c202 < not the main concern of a regular Linux Distribution. However, with --- > not the main concern of a regular Linux distribution. However, with 223c223 < Free Software Guidelines (DFSG)}, that allow to free and open-source --- > Free Software Guidelines (DFSG)}, that allow to distinguish free and open source 230c230 < 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 235,237c235,237 < 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. 271c271 < actively influence the support of certain work fields. --- > actively influence the support of certain fields of work. 274,275c274,275 < 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 279c279 < be brought into the distribution and that one will possibly be --- > be brought into the distribution, and that one will possibly be 282c282 < lot of applications which are very specific to medical care and are --- > lot of applications that are very specific to medical care and are 302c302 < 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 313c313 < 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 360c360 < Debian contains more than 20000 binary packages, and this number is --- > Debian contains more than 20,000 binary packages, and this number is 365c365 < packages. --- > %packages. 367a368 > 400c401 < ports to even more hardware architectures and operating systems kernels. --- > ports to even more hardware architectures and operating system kernels. 415c416 < {\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 471,473c472,474 < 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 478,479c479,480 < 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 482,483c483,484 < 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 489c490 < Similar effort as \DebianMed exists in Fedora as --- > An effort similar to \DebianMed exists in Fedora as 493c494 < Both projects share the same idea to put medical applications inside a --- > Both projects share the same idea of putting medical applications inside a 496c497 < difference to \DebianMed (besides of the different distribution) is --- > difference with \DebianMed (besides of being different distributions) is 512,513c513,514 < 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. 523c524 < 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 526c527 < amount of work per package is much smaller compared to for instance --- > amount of work per package is much smaller compared to, for instance, 532,534c533,535 < 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. 539c540 < compared to the other repositories is the fact that \DebianMed is not --- > compared to the other repositories, is the fact that \DebianMed is not 546,548c547,549 < 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. 555c556 < building a common platform which reduces the amount of work for --- > building a common platform that reduces the amount of work for 560c561 < 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 578c579 < researcher in the field of computational biology: Some biologists are Debian --- > researchers in the field of computational biology: Some biologists are Debian 580,582c581,583 < 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. 588c589 < packages himself) to specify all biomedical software with --- > packages themselves) to specify all biomedical software with a 593c594 < declare dependencies on other Debian package to thus prepare --- > declare dependencies on other Debian packages that can be used to prepare 595,596c596,597 < 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. 600,601c601,602 < 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 610c611 < Each work field has an appropriate metapackage, for instance --- > Each field of work has an appropriate metapackage, for instance 612,615c613,616 < 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 619c620 < 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 632,634c633,635 < 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'' 636,637c637,638 < 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, 639c640 < to the Debian project. Debian welcome contributions and setup --- > to the Debian project. Debian welcomes contributions and has set up 649,650c650,651 < 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 673c674 < across variety architectures, online repositories and mirrors, bug --- > for a variety of architectures, online repositories and mirrors, bug 675,677c676,679 < 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 679,680c681,682 < 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 682c684 < 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 697c699 < continuous growth of the number of packages inside Debian which are of --- > continuous growth of the number of packages inside Debian that are of 706c708 < characterize the commitment of people involved in the --- > characterise the commitment of people involved in the 708c710 < project to compensate for the normal loss of supporters --- > project to compensate for the normal loss of supporters, 710c712 < with different orientation or less spare time for private reasons --- > with different orientations or have less spare time for private reasons 712c714 < to the project mailing list. Figure \ref{figure:authorstats}) shows --- > to the project mailing list. Figure \ref{figure:authorstats} shows 742,743c744,745 < 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 756,758c758,760 < 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 765c767 < needs. The implementation \emph{e.g.} by the Debian Edu project -- another --- > needs. The implementation by, for example, the Debian Edu project -- another 767c769 < fact. The main reasons is an enormous availability of software for education --- > fact. The main reason is an enormous availability of software for education 775c777 < 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 778,779c780,781 < 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 783c785 < 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} 796c798 < 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 799,800c801,802 < 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 805c807 < has set some cornerstone in the technical cooperation between user --- > has set a cornerstone in the technical cooperation between user 813c815 < 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 817,818c819,820 < 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 854,856c856,858 < 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 858c860 < 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 865c867 < the is maintained by \DebianMed, is already a user of \DebianMed. --- > that is maintained by \DebianMed, is already a user of \DebianMed. 867,868c869 < can < as on the \printurl{lists.debian.org/debian-med}{\DebianMed --- > can ask on the \printurl{lists.debian.org/debian-med}{\DebianMed 870c871 < 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 925c926 < even if some fields like micro biology are --- > even if some fields like microbiology are 930c931 < inter-institutional software projects of different kind in health --- > inter-institutional software projects of different kinds in health 934c935 < but also the technical infrastructure behind this community project --- > but also the technical infrastructure behind this community project, 936,937c937,938 < 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 951c952 < to work together as Linux users, maybe along --- > to work together as Free Software users, maybe along 967c968 < 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