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Agile development of science depends on the affiliated barter of advice amid advisers (Woelfle, Olliaro & Todd, 2011). In the past, concrete copies of accurate works had to be produced and distributed. Therefore, publishers bare to advance ample assets for book and printing. Aback the journals were mainly financed by their subscribers, their editors not abandoned had to adjudge on the accurate affection of a submitted manuscript, but additionally on the abeyant absorption to their readers. The availability of globally affiliated computers enabled the accelerated barter of advice at low cost. Yochai Benkler (2006) predicts important changes in the advice assembly economy, which are based on three observations:

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A nonmarket action in areas such as education, arts, science, backroom and theology.

The absolute acceleration of nonmarket production, fabricated attainable through networked individuals and alike effects.

The actualization of all-embracing associate production; for example, of software and encyclopedias.

Immaterial appurtenances such as ability and ability are not absent aback captivated or shared—they are ‘nonrival’—, and they accredit a networked advice economy, which is not commercially apprenticed (Benkler, 2006).

In some areas of science a album culture, i.e., a paper-based barter arrangement of assay account and results, already existed aback Paul Ginsparg in 1991 accomplished a server for the administration of cyberbanking preprints—‘e-prints’—about high-energy atom approach at the Los Alamos National Laboratory (LANL), USA (Ginsparg, 1994). Later, the LANL server confused with Ginsparg to Cornell University, USA, and was renamed as arXiv (Butler, 2001). Currently, arXiv (https://arxiv.org/) publishes e-prints accompanying to physics, mathematics, computer science, quantitative biology, quantitative accounts and statistics. Aloof a few years afterwards the alpha of the aboriginal album servers, their important addition to accurate advice was axiomatic (Ginsparg, 1994; Youngen, 1998; Brown, 2001). In 2014, arXiv accomplished the absorbing cardinal of 1 actor e-prints (Van Noorden, 2014).

In added bourgeois areas, such as allure and biology, accepting the publishing above-mentioned peer-review took added time (Brown, 2003). A album server for activity sciences (http://biorxiv.org/) was launched by the Cold Spring Habor Laboratory, USA, in 2013 (Callaway, 2013). PeerJ preprints (https://peerj.com/preprints/), started in the aforementioned year, accepts manuscripts from biological sciences, medical sciences, bloom sciences and computer sciences.

The agreement ‘preprints’ and ‘e-prints’ are acclimated synonymously, aback the concrete administration of preprints has become obsolete. A aloft check of album publishing are the sometimes akin behavior of accurate publishers. The SHERPA/RoMEO activity informs about absorb behavior and self-archiving options of abandoned publishers (http://www.sherpa.ac.uk/romeo/).

The appellation ‘Open Access’ (OA) was alien 2002 by the Budapest Attainable Admission Initiative and was authentic as:

“Barrier-free admission to online works and added resources. OA abstruse is digital, online, chargeless of allegation (gratis OA), and chargeless of causeless absorb and licensing restrictions (libre OA).” (Suber, 2012)

Frustrated by the adversity to admission alike digitized accurate literature, three scientists founded the Attainable Library of Science (PLoS). In 2003, PLoS Assay was appear as the aboriginal absolutely Attainable Admission account for assay (Brown, Eisen & Varmus, 2003; Eisen, 2003).

Thanks to the abundant success of OA publishing, abounding accustomed book publishers now action a alleged ‘Open Admission option’, i.e., to accomplish accustomed accessories chargeless to apprehend for an added acquittal by the authors. The absorb in these amalgam models ability abide with the publisher, whilst absolutely OA usually accommodate a avant-garde license, such as the Creative Commons Attribution 4.0 International (CC BY 4.0, https://creativecommons.org/licenses/by/4.0/).

OA abstruse is abandoned one basic of a added accustomed attainable philosophy, which additionally includes the admission to scholarships, software, and abstracts (Willinsky, 2005). Interestingly, there are several altered ‘schools of thought’ on how to acquire and ascertain Attainable Science, as able-bodied the position that any science is attainable by definition, because of its cold to accomplish generated ability attainable (Fecher & Friesike, 2014).

In a contempo study, the commodity processing accuse (APCs) for assay accelerated universities in the USA and Canada were estimated to be about 1,800 USD for absolutely OA journals and 3,000 USD for amalgam OA journals (Solomon & Björk, 2016). PeerJ (https://peerj.com/), an OA account for biological and computer sciences launched in 2013, acutely bargain the publishing cost, alms its associates a life-time publishing plan for a baby allotment fee (Van Noorden, 2012); alternatively the authors can acquire to pay an APC of $1,095 USD, which may be cheaper, if assorted co-authors participate.

Examples such as the Account of Statistical Software (JSS, https://www.jstatsoft.org/) and eLife (https://elifesciences.org/) authenticate the achievability of absolutely community-supported OA publications. Amount 1 compares the APCs of altered OA publishing business models.

JSS and eLife are peer-reviewed and indexed by Thomson Reuters. Both journals are amid in the Q1 affection quartile in all their registered accountable categories of the Scimago Account & Country Rank (http://www.scimagojr.com/), demonstrating that high-quality publications can be produced afterwards charging the accurate authors or readers.

In 2009, a abstraction was agitated out apropos the “Economic Implications of Alternative Scholarly Publishing Models”, which demonstrates an all-embracing civic account by application OA publishing models (Houghton et al., 2009). In the aforementioned report, the absolute advertisement costs are evaluated. The about costs of an commodity for the administrator are presented in Fig. 2.

Conventional publishers absolve their aerial cable or APC prices with the added value; for example, journalism (stated in the cartoon as ‘non-article processing’). However, stakeholder profits, which could be as aerial as 50%, additionally charge be considered, and are aloof from the science account (Van Noorden, 2013).

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Generally, the assembly costs of an commodity could be almost disconnected into bartering and academic/technical costs (Fig. 2). For nonmarket production, the bartering costs such as margins/profits, administration etc. can be acutely reduced. Hardware and casework for hosting an beat system, such as Attainable Account Systems of the Attainable Ability Activity (https://pkp.sfu.ca/ojs/) can be provided by attainable institutions. Active advisers can accomplish editor and analyst activities afterwards added amount for the journals. Nevertheless, ‘article processing’, which includes the arrangement administration during associate assay and assembly represents the best big-ticket part.

Therefore, we advised a action for the able formatting of accurate manuscripts.

Generally speaking, a accurate arrangement is composed of capacity and formatting. While the content, i.e., text, figures, tables, citations etc., may abide the aforementioned amid altered publishing forms and account styles, the formatting can be actual different. Best publishers crave the formatting of submitted manuscripts in a assertive format. Ignoring this Guide for Authors, (for example, by appointment a arrangement with a altered advertence style), gives a abrogating consequence with a journal’s beat staff. Manuscripts which are too abominably able can alike abet a beeline ‘desk-reject’ (Volmer & Stokes, 2016).

Currently DOC(X), LATEX and/ or PDF book formats are the best frequently acclimated formats for account acquiescence platforms. However, alike if the agreeable of a submitted arrangement ability be accustomed during the associate assay ‘as is’, the architecture still needs to be acclimatized to the accurate advertisement appearance in the assembly stage. For the cyberbanking administration and archiving of accurate works, which is accepting added and added importance, added formats (EPUB, (X)HTML, JATS) charge to be generated. Table 1 lists the book formats which are currently the best accordant ones for accurate publishing.

Current accustomed formats for accurate publishing.

Although the agreeable elements of documents, such as title, author, abstract, text, figures, tables, etc., abide the same, the syntax of the book formats is rather different. Table 2 demonstrates some simple examples of differences in altered markup languages.

Examples for formatting elements and their implementations in altered markup languages.

Documents with the frequently acclimated Office Attainable XML (DOCX Microsoft Chat files) and OpenDocument (ODT LibreOffice) book formats can be opened in a accustomed argument editor afterwards unzipping. However, agreeable and formatting advice is broadcast into assorted folders and files. Practically speaking, those book formats crave the use of acclimatized chat processing software.

From a writer’s perspective, the use of What You See Is What You Get (WYSIWYG) programs such as Microsoft Word, WPS Office or LibreOffice ability be convenient, because the formatting of the certificate is anon visible. But the complicated syntax blueprint generally aftereffect in problems aback application altered software versions and for collaborative writing. Simple conversions amid book formats can be difficult or impossible. In a worst-case scenario, ‘old’ files cannot be opened any added for abridgement of accordant software.

In some genitalia of the accurate association accordingly LATEX, a book affairs in apparent argument format, is actual popular. With LATEX, abstracts with accomplished typographic affection can be produced. However, the antecedent files are chaotic with LATEX commands and the antecedent argument can be complicated to read. Causes of accumulation errors in LATEX are sometimes difficult to find. Therefore, LATEX is not actual user friendly, abnormally for accidental writers or beginners.

In bookish publishing, it is additionally adorable to actualize altered achievement formats from the aforementioned antecedent text:

For the publishing of a book, with a book adaptation in PDF and an cyberbanking adaptation in EPUB.

For the administration of a academy script, with an online adaptation in HTML and a book adaptation in PDF.

For appointment a account arrangement for peer-review in DOCX, as able-bodied as a album adaptation with addition account appearance in PDF.

For archiving and exchanging commodity abstracts application the Account Commodity Tag Apartment (JATS) (National Advice Standards Organization, 2012), a connected architecture developed by the National Library of Medicine (NLM).

Some of the tasks can be performed with LATEX, but an chip band-aid charcoal a challenge. Several programs for the about-face amid abstracts formats exist, such as the e-book library affairs calibre (http://calibre-ebook.com/). But the after-effects of such conversions are generally not satisfactory and crave abundant chiral corrections.

Therefore, we were attractive for a band-aid that enables the conception of accurate manuscripts in a simple format, with the consecutive bearing of assorted achievement formats. The charge for amalgam publishing has been accustomed alfresco of science (Kielhorn, 2011), but the requirements specific to accurate publishing acquire not been addressed so far. Therefore, we advised the achievability to accomplish assorted advertisement formats from a simple arrangement antecedent file.

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Markdown was originally developed by John Gruber in accord with Aaron Swartz, with the ambition to abridge the autograph of HTML abstracts (http://daringfireball.net/projects/markdown/). Instead of coding a book in HTML syntax, the agreeable of a certificate is accounting in apparent argument and annotated with simple tags which ascertain the formatting. Subsequently, the Markdown (MD) files are parsed to accomplish the final HTML document. With this concept, the antecedent book charcoal calmly clear and the columnist can focus on the capacity rather than formatting. Despite its aboriginal focus on the web, the MD architecture has been accurate to be able-bodied ill-fitted for bookish autograph (Ovadia, 2014). In particular, Pandoc-flavored MD (http://pandoc.org/) adds several extensions which facilitate the assembly of bookish abstracts and their about-face into assorted achievement formats. Table 2 demonstrates the artlessness of MD compared to added markup languages. Figure 3 illustrates the bearing of assorted formatted abstracts from a arrangement in Pandoc MD. Some accordant functions for accurate texts are explained beneath in added detail.

The account of a argument editor is important for the author, either autograph abandoned or with several co-authors. In this area we present software and strategies for altered scenarios. Figure 4 summarizes assorted options for bounded or networked alteration of MD files.

Due to MD’s simple syntax, basically any argument editor is acceptable for alteration markdown files. The formatting tags are accounting in apparent argument and are attainable to remember. Therefore, the columnist is not absent by attractive about for blueprint options with the mouse. For several accepted argument editors, such as vim (http://www.vim.org/), GNU Emacs (https://www.gnu.org/software/emacs/), atom (https://atom.io/) or geany (http://www.geany.org/), plugins accommodate added functionality for markdown editing; for example, syntax highlighting, command helpers, alive examination or anatomy browsing.

Various committed markdown editors acquire been appear as well. Abounding of those are cross-platform compatible, such as Abricotine (http://abricotine.brrd.fr/), columnist (https://github.com/wereturtle/ghostwriter) and CuteMarkEd (https://cloose.github.io/CuteMarkEd/).

The failing architecture is additionally ideal for autograph on adaptable devices. Numerous applications are attainable on the App food for Android and iOS systems. The programs Swype and Dragon (http://www.nuance.com/) facilitate the ascribe of argument on such accessories by bookish words from gestures and accent acceptance (dictation).

Figure 5 shows the alteration of a markdown file, application the cross-platform editor Atom with several markdown plugins.

Storing manuscripts on arrangement drives (The Cloud) has become accepted for several reasons:

Protection adjoin abstracts loss.

Synchronization of abstracts amid several devices.

Collaborative alteration options.

Markdown files on a Google Drive (https://drive.google.com) for instance can be edited online with StackEdit (https://stackedit.io). Amount 6 demonstrates the online alteration of a markdown book on an ownCloud (https://owncloud.com/) installation. OwnCloud is an Attainable Antecedent software platform, which allows the accoutrement of a book server on claimed webspace. The functionality of an ownCloud accession can be added by installing plugins.

Even algebraic formulas are rendered accurately in the HTML alive examination window of the ownCloud markdown plugin (Fig. 6).

The accord and assembly belvedere Authorea (https://www.authorea.com/) additionally supports markdown as one of assorted attainable ascribe formats. This can be benign for collaborations in which one or added authors are not accustomed with markdown syntax.

Programmers, abnormally aback alive in broadcast teams, await on adaptation ascendancy systems to administer changes of code. Currently, Git (https://git-scm.com/), which is additionally acclimated for the development of the Linux kernel, is one of the best active software solutions for versioning. Git allows the alongside assignment of collaborators and has an able amalgamation and battle resolution system. A Git athenaeum may be acclimated by a audible bounded columnist to accumulate clue of changes, or by a aggregation with a alien repository; for example, on Github (https://github.com/) or Bitbucket (https://bitbucket.org/). Because of the apparent argument architecture of markdown, Git can be acclimated for adaptation ascendancy and broadcast writing. For the autograph of the present article, the co-authors (Germany and Mexico) acclimated a alien Git athenaeum on Bitbucket. The apparent argument syntax of markdown facilitates the decision of differences of certificate versions, as apparent in Fig. 7.

In the afterward section, we authenticate the abeyant for book accurate manuscripts with Pandoc application examples for archetypal certificate elements, such as tables, figures, formulas, cipher listings and references. A abrupt addition is accustomed by Dominici (2014). The complete Pandoc User’s Chiral is attainable at http://pandoc.org/MANUAL.html.

There are several options to address tables in markdown. The best adjustable alternative—which was additionally acclimated for this article—are aqueduct tables. The capacity of altered beef are afar by aqueduct syms (—):

gives

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The headings and the alignment of the beef are accustomed in the aboriginal two lines. The corpuscle amplitude is variable. The Pandoc constant –columns=NUM can be acclimated to ascertain the breadth of curve in characters. If capacity do not fit, they will be wrapped.

Complex tables (for example, tables featuring assorted headers or those absolute beef spanning assorted rows or columns), are currently not representable in Markdown format. However, it is attainable to bury LATEX and HTML tables into the document. These format-specific tables will abandoned be included in the achievement if a certificate of the corresponding architecture is produced. This is adjustment can be continued to administer any affectionate of format-specific typographic functionality which would contrarily be bare in Markdown syntax.

Images are amid as follows:

e.g.,

The alt argument is acclimated e.g., in HTML output. Angel ambit can be authentic in braces:

As well, an identifier for the amount can be authentic with #, consistent e.g., in the angel attributes {#figure1 height=30%}.

A branch absolute abandoned an angel is interpreted as a figure. The alt argument is afresh achievement as the figure’s caption.

Scientific texts generally crave acclimatized characters; for example, Greek letters, algebraic and concrete syms, and so on.

The UTF-8 standard, developed and maintained by the Unicode Consortium, enables the use of characters beyond languages and computer platforms. The encoding is authentic as RFC certificate 3629 of the Arrangement Alive accumulation (Yergeau, 2003) and as ISO accustomed ISO/IEC 10646:2014 (International Alignment for Standardization, 2014). Blueprint of Unicode and cipher annal are provided on the Unicode homepage (http://www.unicode.org/).

In Pandoc Markdown documents, Unicode characters such as ∘, α, ä, Å can be amid anon and anesthetized to the altered achievement documents. The actual processing of MD with UTF-8 encoding to LATEX/PDF achievement requires the use of the –latex-engine=xelatex advantage and the use of an acclimatized font. The Times-like XITS chantry (https://github.com/khaledhosny/xits-math), acceptable for aerial affection book of accurate texts, can be set in the LATEX template:

To facilitate the ascribe of specific characters, alleged mnemonics can be enabled in some editors (e.g., in atom by the character-table package). For example, the 2-character mnemonics ‘:u’ gives ‘ü’ (diaeresis), or ‘D*’ the Greek Δ. The attainable appearance mnemonics and appearance sets are listed in RFC 1345: http://www.faqs.org/rfcs/rfc1345.html (Simonsen, 1992).

Formulas are accounting in LATEX approach application the delimiters $. For example, the blueprint for artful the accustomed aberration s of a accidental sampling would be accounting as:

and gives: s=1N−1∑i=1Nxi−x¯2with xi the abandoned observations, x¯ the sample beggarly and N the absolute cardinal of samples.

Pandoc parses formulas into centralized structures and allows about-face into formats added than LATEX. This allows for format-specific blueprint representation and enables computational assay of the formulas (Corbí& Burgos, 2015).

Verbatim cipher blocks are adumbrated by three tilde syms:

Typesetting inline code is attainable by anchor argument amid aback ticks.

These examples are abandoned a abbreviate affirmation of the capacities of Pandoc apropos accurate documents. For added abundant information, we accredit to the official chiral (http://pandoc.org/MANUAL.html).

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The able alignment and book of citations and bibliographies is acute for bookish writing. Pandoc supports assorted strategies for managing references. For processing the citations and the conception of the bibliography, the command band constant –filter pandoc-citeproc is used, with variables for the advertence database and the bibliography style. The bibliography will be amid automatically at the attack # References or # Bibliography.

Pandoc is able to action all boilerplate abstruse database formats, such as RIS, BIB, etc. However, for advancement affinity with LATEX/ BIBTEX, the use of BIB databases is recommended. The acclimated database either can be authentic in the YAML metablock of the MD book (see below) or it can be anesthetized as constant aback calling Pandoc.

For inserting a reference, the database key is accustomed aural aboveboard brackets, and adumbrated by an ‘@’. It is additionally attainable to add information, such as page:

gives (Suber, 2012; Benkler, 2006, p. 57 ff.).

The Commendation Appearance Accent (CSL) (http://citationstyles.org/) is acclimated for the citations and bibliographies. This book architecture is supported, for example, by the advertence administration programs Mendeley (https://www.mendeley.com/), Papers (http://papersapp.com/) and Zotero (https://www.zotero.org/). CSL styles for accurate journals can be begin from the Zotero appearance athenaeum (https://www.zotero.org/styles). The bibliography appearance that Pandoc should use for the ambition certificate can be alleged in the YAML block of the Markdown certificate or can be anesthetized in as an command band option. The closing is added recommendable, because audible bibliography appearance may be acclimated for altered documents.

For citations in accurate manuscripts accounting in LATEX, the natbib amalgamation is broadly used. To actualize a LATEX achievement book with natbib citations, Pandoc artlessly has to be run with the –natbib option, but afterwards the –filter pandoc-citeproc parameter.

To allotment the bibliography for a assertive arrangement with co-authors or the publisher’s assembly team, it is generally adorable to accomplish a subset of a beyond database, which abandoned contains the cited references. If LATEX achievement was generated with the –natbib option, the accumulation of the book with LATEX gives an AUX book (in the archetype alleged md-article.aux), which afterwards can be extracted application BibTool (https://github.com/ge-ne/bibtool):

In this example, the commodity database will be alleged bibshort.bib.

For the absolute conception of an commodity specific BIB database afterwards application LATEX, we wrote a simple Perl calligraphy alleged mdbibexport (https://github.com/robert-winkler/mdbibexport).

Bourne (2005) argues that journals should be finer agnate to biological databases: both accommodate abstracts which can be referenced by altered identifiers like DOI or, for example, gene IDs. Applying the semantic-web account of Berners-Lee & Hendler (2001) to this area can accomplish this eyes a reality. Here we appearance how metadata can be authentic in Markdown. We adduce conventions, and authenticate their adequacy to accredit interlinked and semantically accomplished account articles.

Document advice such as title, authors, abstruse etc. can be authentic in a metadata block accounting in YAML syntax. YAML (“YAML Ain’t Markup Language”, http://yaml.org/) is a abstracts serialization accustomed in simple, animal clear format. Variables authentic in the YAML area are candy by Pandoc and chip into the generated documents. The YAML metadata block is accustomed by three hyphens (—) at the beginning, and three hyphens or dots (…) at the end; for example;

The attainable availability of all accordant advice is a axial aspect of Attainable Science. Analogous to commodity contents, abstracts should be attainable via absence tools. We acquire that this assumption charge additionally be activated to commodity metadata. Thus, we created a custom Pandoc biographer that emits the article’s abstracts as JSON–LD (Lanthaler & Gütl, 2012), acceptance for advisory and abyssal queries of the journal’s abstracts with accustomed accoutrement of the semantic web. The aloft YAML advice would be achievement as:

This architecture allows processing of the advice by accustomed abstracts processing software and browsers.

We developed a adjustment to acquiesce writers the adjustable blueprint of authors and their corresponding affiliations. Columnist names can be accustomed as a string, via the key of a single-element object, or absolutely as a name aspect of an object. Affiliations can be authentic anon as backdrop of the columnist object, or alone in the convention object.

Additional information, for example, email addresses or identifiers like ORCID (Haak et al., 2012), can be added as added values:

The account commodity tag apartment (JATS) was developed by the National Library of Medicine (NLM) and connected by ANSI/NISO as an archiving and barter architecture of account accessories and the associated metadata (National Advice Standards Organization, 2012), including abstracts of the blazon apparent above. The pandoc-jats biographer by Martin Fenner is a plugin accessible with Pandoc to aftermath JATS-formatted output. The biographer was acclimatized to be accordant with our metadata assembly method, acceptance for simple bearing of files which accommodate the accordant metadata.

Writers can add advice about the acumen a commendation is given. This ability advice reviewers and readers, and can abridge the chase for accordant literature. We developed an continued commendation syntax that integrates seamlessly into Markdown and can be acclimated to add commutual advice to citations. Our adjustment is based on CiTO, the Commendation Typing Aesthetics (Shotton, 2010), which specifies a cant for the action aback commendation a resource. The blazon of a citations can be added to a Markdown commendation application @CITO_PROPERTY:KEY, area CITO_PROPERTY is a accurate CiTO property, and KEY is the accepted commendation key. Our apparatus extracts that advice and includes it in the generated affiliated abstracts output. A accustomed CiTO acreage (cites) is used, if no CiTO acreage is begin in a commendation key.

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The assignment at duke will consistently be the accountable of the generated semantic subject–predicate–object triples. Some CiTO predicates cannot be acclimated in a sensical way beneath this condition. Focusing on columnist convenience, we use this actuality to acquiesce abridgement of backdrop aback sensible. For example, if authors of a biological cardboard accommodate a advertence to the cardboard anecdotic a adjustment which was acclimated in their work, this affiliation can be declared by the uses_method_in acreage of the CiTO ontology. The changed property, provides_method_for, would consistently be cool in this ambience as adumbrated by causality. It is accordingly not accurate by our tool. This allows us to acquaint an abridgement (method) for the closing property, as any ambiguity has been eliminated. Users of Western blotting ability appropriately address @method_in:towbin_1979 or alike aloof @method:towbin_1979, area towbin_1979 is the commendation identifier of the anecdotic cardboard by Towbin, Staehelin & Gordon (1979).

Scientific manuscripts acquire to be submitted in a architecture authentic by the account or publisher. At the moment, DOCX is the best accepted book architecture for arrangement submission. Some publishers additionally acquire or crave LATEX or ODT formats. Added to the accustomed appearance of the manuscript—organization of sections, fonts, etc.—the commendation appearance of the account charge additionally be followed. Often, the aforementioned arrangement has to be able for altered journals; for example, if the arrangement was alone by a account and has to be formatted for addition one, or if a album of the cardboard is submitted to an annal that requires a audible certificate architecture than the targeted peer-reviewed journal. In this example, we appetite to actualize a arrangement for a PLoS account in DOCX and ODT architecture for WYSIWYG chat processors. Further, a adaptation in LATEX/ PDF should be produced for PeerJ acquiescence and archiving at the PeerJ album server.

The examples for DOCX/ ODT are kept almost simple, to appearance the proof-of-principle and to accommodate a apparent certificate for the development of own templates. Nevertheless, the generated abstracts should be acceptable for acquiescence afterwards little chiral editing. For specific journals it may be all-important to actualize added adult templates or to copy/ adhesive the all-encompassing DOCX/ ODT achievement into the publisher’s template.

A aboriginal DOCX certificate with bibliography in PLoS architecture is created with Pandoc DOCX output:

The ambit -S -s accomplish a typographically actual (dashes, non-breaking spaces etc.) stand-alone document. A bibliography with the PLoS appearance is created by the citeproc clarify ambience –csl=plos.csl –filter pandoc-citeproc.

The certificate settings and styles of the consistent book pandoc-manuscript.docx can be optimized and be acclimated afresh as certificate arrangement (–reference-docx=pandoc-manuscript.docx): instead of .

It is additionally attainable to anon re-use a antecedent achievement book as arrangement (i.e., arrangement and achievement book acquire the aforementioned book name):

In this way, the arrangement can be incrementally acclimatized to the acclimatized certificate formatting. The final certificate may be active after as Pandoc arrangement for added manuscripts with the aforementioned specifications. In this case, active Pandoc the aboriginal time with the template, the capacity of the new arrangement would be abounding into the provided DOCX template. A folio with DOCX arrangement formatting of this commodity is apparent in Fig. 8.

The aforementioned action can be activated with an ODT formatted document.

The absence Pandoc LATEX arrangement can be accounting into a abstracted book by:

This arrangement can be adjusted; for example, by defining Unicode encoding (see above), by including accurate bales or ambience certificate options (line numbering, chantry size). The arrangement can afresh be acclimated with the Pandoc constant –template=pandoc-peerj.latex.

The templates acclimated for this certificate are included as Supplemental Material (see area ‘Software and Cipher Availability’ below).

The appearance for HTML and EPUB formats can be authentic in .css stylesheets. The Supplemental Material (see area ‘Software and Cipher Availability’ below) contains a simple archetype .css book for modifying the HTML output, which can be acclimated with the Pandoc constant -c pandoc.css.

The commands all-important to aftermath the certificate in a specific formats or styles can be authentic in a simple Makefile. An archetype Makefile is included in the antecedent cipher of this article. The acclimatized achievement book architecture can be alleged aback calling make. For example, make outfile.pdf produces this commodity in PDF format. Calling accomplish afterwards any advantage creates all listed certificate types. A Makefile bearing DOCX, ODT, JATS, PDF, LATEX, HTML and EPUB files of this certificate is provided as Supplemental Material (see area ‘Software and Cipher Availability’ below).

The accomplish action was activated on Windows 10 and Linux 64 bit. All documents—DOCX, ODT, JATS, LATEX, PDF, EPUB and HTML—were generated successfully, which demonstrates the cross-platform affinity of the workflow.

Following the trend to associate production, the formatting of accurate agreeable charge become added efficient. Markdown/Pandoc has the abeyant to comedy a key role in the alteration from proprietary to community-driven bookish production. Important assay tools, such as the statistical accretion and cartoon accent R (R Core Team, 2014) and the Jupyter anthology activity (Kluyver et al., 2016) acquire already adopted the MD syntax (for example, http://rmarkdown.rstudio.com/). The software for autograph manuscripts in MD is complete abundant to be acclimated by bookish writers. Therefore, publishers additionally should accede implementing the MD architecture into their beat platforms.

Relevant software acclimated for this article.

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Authoring accurate manuscripts in markdown (MD) architecture is straight-forward, and chiral formatting is bargain to a minimum. The simple syntax of MD facilitates certificate alteration and collaborative writing. The accelerated about-face of MD to assorted formats such as DOCX, LATEX, PDF, EPUB and HTML can be done calmly application Pandoc, and templates accredit the automatic bearing of abstracts according to specific account styles.

The added appearance we implemented facilitate the actual indexing of meta advice of account accessories according to the ‘semantic web’ philosophy.

Altogether, the MD architecture supports the active autograph and fast assembly of accurate literature. The associated time and amount abridgement abnormally favours community-driven advertisement strategies.

The accordant software for creating this arrangement acclimated is cited according to (Smith, Katz & Niemeyer, 2016) and listed in Table 3. Aback altered identifiers are missing for best software projects, we abandoned accredit to the activity homepages or software repositories:

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