agile-markdown.bib

@article{eisen_publish_2003,
  chapter = {Education},
  title = {Publish and Be Praised},
  issn = {0261-3077},
  abstract = {Michael Eisen on why it's high time the results of scientific research were freely available to everyone},
  language = {en-GB},
  timestamp = {2016-11-11T01:55:27Z},
  urldate = {2016-11-11},
  journal = {The Guardian},
  author = {Eisen, Michael},
  month = oct,
  year = {2003},
  keywords = {Education,Higher education,Research,science},
  file = {Guardian Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/I5IJJKEV/research.html:text/html}
}

@book{benkler_wealth_2006,
  address = {New Haven, CT, USA},
  title = {The {{Wealth}} of {{Networks}}: {{How Social Production Transforms Markets}} and {{Freedom}}},
  isbn = {0-300-11056-1},
  timestamp = {2016-11-21T21:38:24Z},
  publisher = {{Yale University Press}},
  author = {Benkler, Yochai},
  year = {2006}
}

@misc{houghton_economic_2009,
  title = {Economic Implications of Alternative Scholarly Publishing Models: {{Exploring}} the Costs and Benefits},
  copyright = {Copyright Jisc unless explicitly acknowledged otherwise.},
  shorttitle = {Economic Implications of Alternative Scholarly Publishing Models},
  abstract = {This is the final report of the JISC EI-ASPM Project, which was commissioned by JISC to explore whether there are new opportunities and new models for scholarly publishing that would better serve researchers and better communicate and disseminate research findings.},
  language = {en-GB},
  timestamp = {2016-11-16T04:50:33Z},
  urldate = {2016-11-16},
  howpublished = {\url{http://www.webarchive.org.uk/wayback/archive/20140614041628/http://www.jisc.ac.uk/publications/reports/2009/economicpublishingmodelsfinalreport.aspx\#downloads}},
  author = {Houghton, John and Rasmussen, Bruce and Sheehan, Peter and Oppenheim, Charles and Morris, Anne and Creaser, Claire and Greenwood, Helen and Summers, Mark and Gourlay, Adrian},
  month = jan,
  year = {2009},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/W6P43E94/economicpublishingmodelsfinalreport.html:text/html}
}

@article{brown_why_2003,
  title = {Why {{PLoS Became}} a {{Publisher}}},
  volume = {1},
  issn = {1544-9173},
  doi = {10.1371/journal.pbio.0000036},
  abstract = {Public Library of Science has grown from a grassroots movement to a nonprofit publisher, in order to catalyze change towards open-access publishing of the scientific literature},
  timestamp = {2016-11-21T21:38:36Z},
  number = {1},
  urldate = {2016-11-11},
  journal = {PLoS Biol},
  author = {Brown, Patrick O and Eisen, Michael B and Varmus, Harold E},
  month = oct,
  year = {2003},
  file = {PubMed Central Full Text PDF:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/2NT3MAGR/Brown et al. - 2003 - Why PLoS Became a Publisher.pdf:application/pdf},
  pmcid = {PMC212706},
  pmid = {14551926}
}

@article{dominici_pandoc_2014,
  title = {An Overview of {{Pandoc}}},
  volume = {35},
  timestamp = {2016-11-21T21:43:10Z},
  number = {1},
  journal = {TUGboat},
  author = {Dominici, Massimiliano},
  year = {2014},
  pages = {44--50}
}

@techreport{HTML4,
  type = {W3C Recommendation},
  title = {{{HTML}} 4.01 {{Specification}}},
  timestamp = {2016-11-21T21:30:09Z},
  institution = {W3C},
  author = {Raggett, Dave and Hors, Arnaud Le and Jacobs, Ian and Le Hors, Arnaud and Raggett, Dave and Jacobs, Ian},
  month = dec,
  year = {1999}
}

@article{eikebrokk_epub_2014,
  title = {{{EPUB}} as {{Publication Format}} in {{Open Access Journals}}: {{Tools}} and {{Workflow}}},
  issn = {1940-5758},
  timestamp = {2016-11-21T21:30:08Z},
  number = {24},
  journal = {Code4Lib},
  author = {Eikebrokk, Trude and Dahl, Tor Arne and Kessel, Siri},
  month = apr,
  year = {2014}
}

@techreport{rfc7764,
  type = {RFC},
  title = {Guidance on {{Markdown}}: {{Design Philosophies}}, {{Stability Strategies}}, and {{Select Registrations}}},
  timestamp = {2016-11-21T21:30:09Z},
  institution = {RFC Editor},
  author = {Leonard, Sean},
  month = mar,
  year = {2016},
  pages = {1--28},
  howpublished = {Internet Request for Comments},
  shorthand = {RFC7764}
}

@article{callaway_preprints_2013,
  title = {Preprints {{Come}} to {{Life}}},
  volume = {503},
  doi = {10.1038/503180a},
  abstract = {A dedicated website for sharing biology papers before peer review leaves journals divided.},
  timestamp = {2016-11-21T21:37:38Z},
  number = {7475},
  urldate = {2016-11-10},
  journal = {Nature News},
  author = {Callaway, Ewen},
  month = nov,
  year = {2013},
  pages = {180},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/DUTIGWJ9/preprints-come-to-life-1.html:text/html}
}

@book{lamport_latex:_1994,
  address = {Reading, Mass},
  edition = {2 edition},
  title = {{{LaTeX}}: {{A Document Preparation System}}},
  isbn = {978-0-201-52983-8},
  shorttitle = {{{LaTeX}}},
  abstract = {LaTex is a software system for typesetting documents. Because it is especially good for technical documents and is available for almost any computer system, LaTex has become a lingua franca of the scientific world. Researchers, educators, and students in universities, as well as scientists in industry, use LaTex to produce professionally formatted papers, proposals, and books. They also use LaTex input to communicate information electronically to their colleagues around the world. With the release of LaTex 2[subscript epsilon], the new standard version, LaTex has become even more powerful. Among its new features are an improved method for handling different styles of type, and commands for including graphics and producing colors. LaTex 2[subscript epsilon] makes available to all LaTex users valuable enhancements to the software that have been developed over the years by users in many different places to satisfy a variety of needs. This book, written by the original architect and implementer of LaTex is both the user's guide and the reference manual for the software. It has been updated to reflect the changes in the new release. The book begins with instructions for formatting simpler text, and progressively describes commands and techniques for handling larger and more complicated documents. A separate chapter explains how to deal with errors. An added appendix describes what is new and different in LaTex 2[subscript epsilon]. Other additions to the second edition include descriptions of new commands for inserting pictures prepared with other programs and for producing colored output; new sections on how to make books and slides; instructions for making an index with the MakeIndexprogram, and an updated guide to preparing a bibliography with the BibTex program; plus a section on how to send your LaTex documents electronically. Users new to LaTex will find here a book that has earned worldwide praise as a model for clear, concise, and practical documentation. E},
  language = {English},
  timestamp = {2016-11-21T21:03:58Z},
  publisher = {{Addison-Wesley Professional}},
  author = {Lamport, Leslie},
  month = jul,
  year = {1994}
}

@article{brown_role_2003,
  title = {The {{Role}} of {{Electronic Preprints}} in {{Chemical Communication}}: {{Analysis}} of {{Citation}}, {{Usage}}, and {{Acceptance}} in the {{Journal Literature}}},
  volume = {54},
  issn = {1532-2890},
  shorttitle = {The {{Role}} of {{Electronic Preprints}} in {{Chemical Communication}}},
  doi = {10.1002/asi.10223},
  abstract = {This study characterizes the usage and acceptance of electronic preprints (e-prints) in the literature of chemistry. Survey of authors of e-prints appearing in the Chemistry Preprint Server (CPS) at http://preprints.chemweb.com indicates use of the CPS as a convenient vehicle for dissemination of research findings and for receipt of feedback before submitting to a peer-reviewed journal. Reception of CPS e-prints by editors of top chemistry journals is very poor. Only 6\% of editors responding allow publication of articles that have previously appeared as e-prints. Concerns focus on the lack of peer review and the uncertain permanence of e-print storage. Consequently, it was not surprising to discover that citation analysis yielded no citations to CPS e-prints in the traditional literature of chemistry. Yet data collected and posted by the CPS indicates that the e-prints are valued, read, and discussed to a notable extent within the chemistry community. Thirty-two percent of the most highly rated, viewed, and discussed e-prints eventually appear in the journal literature, indicating the validity of the work submitted to the CPS. This investigation illustrates the ambivalence with which editors and authors view the CPS, but also gives an early sense of the potential free and rapid information dissemination, coupled with open, uninhibited discussion and evaluation, has to expand, enrich, and vitalize the scholarly discourse of chemical scientists.},
  language = {en},
  timestamp = {2016-11-21T21:38:11Z},
  number = {5},
  urldate = {2016-11-11},
  journal = {J. Am. Soc. Inf. Sci.},
  author = {Brown, Cecelia},
  month = mar,
  year = {2003},
  pages = {362--371},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/E4Q8WTCG/abstract.html:text/html}
}

@article{van_noorden_journal_2012,
  title = {Journal {{Offers Flat Fee}} for `all {{You Can Publish}}'},
  volume = {486},
  doi = {10.1038/486166a},
  abstract = {Latest venture is part of an explosion of ideas for open-access publishing.},
  timestamp = {2016-11-21T21:36:33Z},
  number = {7402},
  urldate = {2016-11-11},
  journal = {Nature News},
  author = {Van Noorden, Richard},
  month = jun,
  year = {2012},
  pages = {166},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/96IA9MWT/journal-offers-flat-fee-for-all-you-can-publish-1.html:text/html}
}

@techreport{ODF,
  title = {Open {{Document Format}} for {{Office Applications}} ({{OpenDocument}}) v1.0},
  timestamp = {2016-11-21T21:30:08Z},
  institution = {OASIS},
  author = {Brauer, Michael and Durusau, Patrick and Edwards, Gary and Faure, David and Magliery, Tom and Vogelheim, Daniel},
  month = feb,
  year = {2005},
  publischer = {OASIS Consortium}
}

@article{willinsky_unacknowledged_2005,
  title = {The {{Unacknowledged Convergence}} of {{Open Source}}, {{Open Access}}, and {{Open Science}}},
  volume = {10},
  copyright = {Authors submitting a paper to First Monday automatically agree to confer a limited license to First Monday if and when the manuscript is accepted for publication. This license allows First Monday to publish a manuscript in a given issue. Authors have a choice of: 1. Dedicating the article to the public domain. This allows anyone to make any use of the article at any time, including commercial use. A good way to do this is to use the Creative Commons Public Domain Dedication Web form; see http://creativecommons.org/license/publicdomain-2?lang=en . 2. Retaining some rights while allowing some use. For example, authors may decide to disallow commercial use without permission. Authors may also decide whether to allow users to make modifications (e.g. translations, adaptations) without permission. A good way to make these choices is to use a Creative Commons license. * Go to http://creativecommons.org/license/ . * Choose and select a license. * What to do next \textemdash{} you can then e\textendash{}mail the license html code to yourself. Do this, and then forward that e\textendash{}mail to First Monday's editors. Put your name in the subject line of the e\textendash{}mail with your name and article title in the e\textendash{}mail. Background information about Creative Commons licenses can be found at http://creativecommons.org/about/licenses/ . 3. Retaining full rights, including translation and reproduction rights. Authors may use the statement: \textcopyright{} Author 2016 All Rights Reserved. Authors may choose to use their own wording to reserve copyright. If you choose to retain full copyright, please add your copyright statement to the end of the article. Authors submitting a paper to First Monday do so in the understanding that Internet publishing is both an opportunity and challenge. In this environment, authors and publishers do not always have the means to protect against unauthorized copying or editing of copyright\textendash{}protected works.},
  issn = {13960466},
  doi = {10.5210/fm.v10i8.1265},
  abstract = {A number of open initiatives are actively resisting the extension of intellectual property rights. Among these developments, three prominent instances \textemdash{} open source software, open access to research and scholarship, and open science \textemdash{} share not only a commitment to the unrestricted exchange of information and ideas, but economic principles based on (1) the efficacy of free software and research; (2) the reputation\textendash{}building afforded by public access and patronage; and, (3) the emergence of a free\textendash{}or\textendash{}subscribe access model. Still, with this much in common, the strong sense of convergence among these open initiatives has yet to be fully realized, to the detriment of the larger, common issue. By drawing on David's (2004; 2003; 2000; 1998) economic work on open science and Weber's (2004) analysis of open source, this paper seeks to make that convergence all the more apparent, as well as worth pursuing, by those interested in furthering this alternative approach, which would treat intellectual properties as public goods.},
  timestamp = {2016-11-21T21:38:20Z},
  number = {8},
  urldate = {2016-11-11},
  journal = {First Monday},
  author = {Willinsky, John},
  month = aug,
  year = {2005},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/XXPHFQV4/1265.html:text/html}
}

@misc{international_organization_for_standardization_iso_2013,
  title = {{{ISO}} 32000-1:2008 - {{Document}} Management -- {{Portable}} Document Format -- {{Part}} 1: {{PDF}} 1.7},
  shorttitle = {{{ISO}} 32000-1},
  timestamp = {2016-11-21T21:24:46Z},
  urldate = {2016-11-21},
  howpublished = {\url{http://www.iso.org/iso/home/store/catalogue_tc/catalogue_detail.htm?csnumber=51502}},
  journal = {ISO},
  author = {{International Organization for Standardization}},
  year = {2013},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/82CRGVEB/catalogue_detail.html:text/html}
}

@techreport{OOXML,
  title = {{{OFFICE OPEN XML OVERVIEW ECMA TC45}}},
  timestamp = {2016-11-21T21:30:09Z},
  institution = {Ecma International},
  author = {Ngo, Tom},
  month = dec,
  year = {2006},
  publischer = {ECMA International}
}

@article{youngen_citation_1998,
  title = {Citation {{Patterns}} to {{Traditional}} and {{Electronic Preprints}} in the {{Published Literature}}},
  volume = {59},
  issn = {0010-0870, 2150-6701},
  doi = {10.5860/crl.59.5.448},
  abstract = {The number of physics and astronomy preprints available electronically has increased dramatically over the past five years. Internet-accessible preprint servers at the Stanford Linear Accelerator Laboratory (SLAC), Los Alamos National Laboratory (LANL), and elsewhere provide unrestricted access to citations and/or full text of many physics and astronomy papers long before they appear in print. Because of the timeliness of these papers, as well as the increasing demand for current research, physicists and astronomers have found it necessary to cite these pre-prints in their research articles rather than wait until they appear in print. This paper identifies the growing importance of electronic preprints in the published literature and addresses several areas of concern regarding the future role of electronic preprints in scientific communication.},
  language = {en},
  timestamp = {2016-11-21T21:35:44Z},
  number = {5},
  urldate = {2016-11-10},
  journal = {Coll. res. libr.},
  author = {Youngen, Gregory K.},
  month = jan,
  year = {1998},
  pages = {448--456},
  file = {Full Text PDF:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/I4B2C3VJ/Youngen - 1998 - Citation Patterns to Traditional and Electronic Pr.pdf:application/pdf;Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/KDQWGFU5/448.html:text/html}
}

@article{garnet_semiautomatic_2015,
  title = {Semi-{{Automated Correction Tools}} for {{Mathematics}}-{{Based Exercises}} in {{MOOC Environments}}},
  volume = {3},
  issn = {1989-1660},
  doi = {10.9781/ijimai.2015.3312},
  abstract = {Massive Open Online Courses (MOOCs) allow the participation of hundreds of students who are interested in a wide range of areas. Given the huge numbers enrolled, it is almost impossible to give complex homework to students and have it carefully corrected and reviewed by a tutor or assistant professor. In this paper, we present a software framework that aims at assisting teachers in MOOCs during correction tasks for mathematics exercises. This framework might suit maths, physics or technical subjects. As a test experience, we apply it to 300+ physics homework bulletins from 80+ students. Test results show our solution can prove very useful in guiding assistant teachers during correction shifts.},
  timestamp = {2016-11-21T21:30:08Z},
  number = {3},
  journal = {International Journal of Interactive Multimedia and Artificial Intelligence},
  author = {Corb{\'\i}, Alberto and Burgos, Daniel},
  month = jun,
  year = {2015},
  keywords = {Automatic,Education,e-learning,Latex},
  pages = {89--95},
  attachments = {http://www.ijimai.org/journal/sites/default/files/files/2015/06/ijimai20153<sub>3</sub><sub>1</sub>2<sub>p</sub>df<sub>6</sub>7215.pdf}
}

@article{woelfle_open_2011,
  title = {Open {{Science Is}} a {{Research Accelerator}}},
  volume = {3},
  copyright = {\textcopyright{} 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  issn = {1755-4330},
  doi = {10.1038/nchem.1149},
  abstract = {An open-source approach to the problem of producing an off-patent drug in enantiopure form serves as an example of how academic and industrial researchers can join forces to make new scientific discoveries that could have a huge impact on human health.},
  language = {en},
  timestamp = {2016-11-21T21:37:16Z},
  number = {10},
  urldate = {2016-11-11},
  journal = {Nat Chem},
  author = {Woelfle, Michael and Olliaro, Piero and Todd, Matthew H.},
  month = oct,
  year = {2011},
  keywords = {Medicinal chemistry,Medicinal chemistry,Natural product synthesis,Natural product synthesis},
  pages = {745--748},
  file = {Full Text PDF:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/48CEBMK2/Woelfle et al. - 2011 - Open science is a research accelerator.pdf:application/pdf;Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/SIVM5D65/nchem.1149.html:text/html}
}

@article{kielhorn_multi_2011,
  title = {Multi-Target Publishing-{{Generating ePub}}, {{PDF}}, and More, from {{Markdown}} Using Pandoc},
  volume = {32},
  timestamp = {2016-11-21T21:30:09Z},
  number = {3},
  journal = {TUGboat-TeX Users Group},
  author = {Kielhorn, Axel},
  year = {2011},
  pages = {272}
}

@article{van_noorden_open_2013,
  title = {Open {{Access}}: {{The True Cost}} of {{Science Publishing}}},
  volume = {495},
  issn = {1476-4687},
  shorttitle = {Open {{Access}}},
  doi = {10.1038/495426a},
  language = {ENG},
  timestamp = {2016-11-21T21:37:10Z},
  number = {7442},
  journal = {Nature},
  author = {Van Noorden, Richard},
  month = mar,
  year = {2013},
  keywords = {Access to Information,Access to Information,Costs and Cost Analysis,Costs and Cost Analysis,Internet,Internet,Libraries,Libraries,Peer Review,Peer Review; Research,Periodicals as Topic,Periodicals as Topic,Publishing,Publishing,Research,Research Personnel,Research Personnel},
  pages = {426--429},
  pmid = {23538808}
}

@incollection{fecher_open_2014,
  title = {Open {{Science}}: {{One Term}}, {{Five Schools}} of {{Thought}}},
  copyright = {\textcopyright{}2014 The Author(s)},
  isbn = {978-3-319-00025-1 978-3-319-00026-8},
  shorttitle = {Open {{Science}}},
  abstract = {Open Science is an umbrella term encompassing a multitude of assumptions about the future of knowledge creation and dissemination. Based on a literature review, this chapter aims at structuring the overall discourse by proposing five Open Science schools of thought: The infrastructure school (which is concerned with the technological architecture), the public school (which is concerned with the accessibility of knowledge creation), the measurement school (which is concerned with alternative impact measurement), the democratic school (which is concerned with access to knowledge) and the pragmatic school (which is concerned with collaborative research).},
  language = {en},
  timestamp = {2016-11-21T21:37:31Z},
  urldate = {2016-11-11},
  booktitle = {Opening {{Science}}},
  publisher = {{Springer International Publishing}},
  author = {Fecher, Benedikt and Friesike, Sascha},
  editor = {Bartling, S{\"o}nke and Friesike, Sascha},
  year = {2014},
  keywords = {Communication Studies,Communication Studies,Computers and Society,Computers and Society,Job Careers in Science and Engineering,Job Careers in Science and Engineering},
  pages = {17--47},
  file = {Full Text PDF:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/E459Z4C7/Fecher and Friesike - 2014 - Open Science One Term, Five Schools of Thought.pdf:application/pdf;Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/7DA6FUGM/978-3-319-00026-8_2.html:text/html}
}

@article{volmer_how_2016,
  title = {How to {{Prepare}} a {{Manuscript Fit}}-for-{{Purpose}} for {{Submission}} and {{Avoid Getting}} a ``desk-{{Reject}}''},
  issn = {1097-0231},
  doi = {10.1002/rcm.7746},
  abstract = {First impressions are very important and when these are negative, they can adversely affect a manuscript's journey through the scientific publication system. This short guide highlights some crucial factors to take into consideration before submitting a manuscript for review in a scientific journal. The aim is to advise authors on the best way to present their research, to comply with formal requirements of the journal and to optimize the first impression made.},
  language = {en},
  timestamp = {2016-11-21T21:36:18Z},
  urldate = {2016-11-04},
  journal = {Rapid Commun. Mass Spectrom.},
  author = {Volmer, Dietrich A. and Stokes, Caroline S.},
  month = jan,
  year = {2016},
  keywords = {Desk rejection,Desk rejection,Manuscript submission,Manuscript submission,Unsubmission,Unsubmission},
  pages = {n/a--n/a},
  file = {Full Text PDF:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/44HT6I6U/Volmer and Stokes - 2016 - How to prepare a manuscript fit-for-purpose for su.pdf:application/pdf;Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/UQ5H9Q4P/abstract\;jsessionid=375898CD95E9BF372525FE95434DE5BF.html:text/html}
}

@article{brown_e-volution_2001,
  title = {The {{E}}-{{Volution}} of {{Preprints}} in the {{Scholarly Communication}} of {{Physicists}} and {{Astronomers}}},
  volume = {52},
  issn = {1532-2890},
  doi = {10.1002/1097-4571(2000)9999:9999<::AID-ASI1586>3.0.CO;2-D},
  abstract = {To learn how e-prints are cited, used, and accepted in the literature of physics and astronomy, the philosophies, policies, and practices of top-tier physics and astronomy journals regarding e-prints from the Los Alamos e-print archive, arXiv.org, were examined. Citation analysis illustrated e-prints were cited with increasing frequency by a variety of journals in a wide range of physics and astronomy fields from 1998 to 1999. The peak e-print citation rate of 3 years observed was comparable to that of print journals, suggesting a similarity in citation patterns of e-prints and printed articles. The number of citations made to 37 premier physics and astronomy journals and their impact factors have remained constant since arXiv.org's inception in 1991, indicating that e-prints have yet to make an impact on the use of the printed literature. The degree of acceptance stated by the journals' editors and the policies given in the journal's instructions to authors sections concerning the citing of e-prints and subsequent publication of papers that have appeared as e-prints differed from journal to journal, ranging from emphatically unacceptable to ``why not?'' Even though the use of the traditional literature has not changed since arXiv.org began and the policies concerning e-print citation and publication were inconsistent, the number of citations (35,928) and citations rates (34.1\%) to 12 arXiv.org archives were found to be large and increasing. It is, therefore, evident that arXiv.org e-prints have evolved into an important facet of the scholarly communication of physics and astronomy.},
  language = {en},
  timestamp = {2016-11-21T21:38:02Z},
  number = {3},
  urldate = {2016-11-10},
  journal = {J. Am. Soc. Inf. Sci.},
  author = {Brown, Cecelia},
  month = jan,
  year = {2001},
  pages = {187--200},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/5UFUX6W7/abstract.html:text/html}
}

@article{smith_software_2016,
  title = {Software {{Citation Principles}}},
  volume = {2},
  issn = {2376-5992},
  doi = {10.7717/peerj-cs.86},
  abstract = {Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.},
  timestamp = {2016-11-21T21:37:46Z},
  journal = {PeerJ Computer Science},
  author = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E.},
  editor = {Peroni, Silvio},
  month = sep,
  year = {2016},
  keywords = {Attribution,Software citation,Software credit},
  pages = {e86}
}

@article{butler_alamos_2001,
  title = {Los {{Alamos Loses Physics Archive}} as {{Preprint Pioneer Heads East}}},
  volume = {412},
  copyright = {\textcopyright{} 2001 Nature Publishing Group},
  issn = {0028-0836},
  doi = {10.1038/35083708},
  abstract = {The Los Alamos preprint server, which has established itself as physicists' favourite place for early circulation of their research, is leaving the New Mexico laboratory to set up shop at Cornell University in New York state.Paul Ginsparg, who founded the server \textemdash{} now known as arXiv \textemdash{} 10 years ago, is leaving the Los Alamos National Laboratory (LANL) to take up a faculty position at Cornell, and the server will move with him.},
  language = {en},
  timestamp = {2016-11-21T21:36:41Z},
  number = {6842},
  urldate = {2016-11-10},
  journal = {Nature},
  author = {Butler, Declan},
  month = jul,
  year = {2001},
  pages = {3--4},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/VID6G5U8/412003a0.html:text/html}
}

@incollection{dptcollective_toolkit_2015,
  title = {From {{Print}} to {{Ebooks}}: {{A Hybrid Publishing Toolkit}} for the {{Arts}}},
  isbn = {987-9082234534},
  timestamp = {2016-11-21T21:30:08Z},
  publisher = {{Institute of Network Cultures}},
  author = {{DPT Collective}},
  editor = {Monk, Joe and Rasch, Miriam and Cramer, Florian and Wu, Amy},
  month = feb,
  year = {2015}
}

@techreport{HTML5,
  type = {W3C Recommendation},
  title = {{{HTML5}}},
  timestamp = {2016-11-21T21:30:09Z},
  institution = {W3C},
  author = {Hickson, Ian and Berjon, Robin and Faulkner, Steve and Leithead, Travis and Navara, Erika Doyle and O'Connor, Edward and Pfeiffer, Silvia and Faulkner, Steve and Navara, Erika Doyle and Leithead, Travis and Berjon, Robin and Hickson, Ian and Pfeiffer, Silvia and O'Connor, Theresa},
  month = oct,
  year = {2014}
}

@article{solomon_article_2016,
  title = {Article {{Processing Charges}} for {{Open Access Publication}}\textemdash{}the {{Situation}} for {{Research Intensive Universities}} in the {{USA}} and {{Canada}}},
  volume = {4},
  issn = {2167-8359},
  doi = {10.7717/peerj.2264},
  abstract = {Background. Open access (OA) publishing via article processing charges (APCs) is growing as an alternative to subscription publishing. The Pay It Forward (PIF) Project is exploring the feasibility of transitioning from paying subscriptions to funding APCs for faculty at research intensive universities. Estimating of the cost of APCs for the journals authors at research intensive universities tend to publish is essential for the PIF project and similar initiatives. This paper presents our research into this question. Methods. We identified APC prices for publications by authors at the 4 research intensive United States (US) and Canadian universities involved in the study. We also obtained APC payment records from several Western European universities and funding agencies. Both data sets were merged with Web of Science (WoS) metadata. We calculated the average APCs for articles and proceedings in 13 discipline categories published by researchers at research intensive universities. We also identified 41 journals published by traditionally subscription publishers which have recently converted to APC funded OA and recorded the APCs they charge. Results. We identified 7,629 payment records from the 4 European APC payment databases and 14,356 OA articles authored by PIF partner university faculty for which we had listed APC prices. APCs for full OA journals published by PIF authors averaged 1,775 USD; full OA journal APCs paid by Western European funders averaged 1,865 USD; hybrid APCs paid by Western European funders averaged 2,887 USD. The APC for converted journals published by major subscription publishers averaged 1,825 USD. APC funded OA is concentrated in the life and basic sciences. APCs funded articles in the social sciences and humanities are often multidisciplinary and published in journals such as PLOS ONE that largely publish in the life sciences. Conclusions. Full OA journal APCs average a little under 2,000 USD while hybrid articles average about 3,000 USD for publications by researchers at research intensive universities. There is a lack of information on discipline differences in APCs due to the concentration of APC funded publications in a few fields and the multidisciplinary nature of research.},
  language = {en},
  timestamp = {2016-11-21T21:35:29Z},
  urldate = {2016-11-11},
  journal = {PeerJ},
  author = {Solomon, David and Bj{\"o}rk, Bo-Christer},
  month = jul,
  year = {2016},
  pages = {e2264},
  file = {Full Text PDF:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/CWWITCVG/Solomon and Björk - 2016 - Article processing charges for open access publica.pdf:application/pdf;Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/ZFFGXTSN/2264.html:text/html}
}

@article{ginsparg_first_1994,
  title = {First {{Steps Towards Electronic Research Communication}}},
  volume = {8},
  issn = {0894-1866},
  doi = {10.1063/1.4823313},
  abstract = {Scitation is the online home of leading journals and conference proceedings from AIP Publishing and AIP Member Societies},
  timestamp = {2016-11-21T21:36:05Z},
  number = {4},
  urldate = {2016-11-10},
  journal = {Computers in Physics},
  author = {Ginsparg, Paul},
  month = jul,
  year = {1994},
  pages = {390--396},
  file = {Full Text PDF:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/9GPFWMPQ/Ginsparg - 1994 - First Steps Towards Electronic Research Communicat.pdf:application/pdf;Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/269TD62I/1.html:text/html}
}

@article{van_noorden_arxiv_2014,
  title = {The {{arXiv Preprint Server Hits}} 1 {{Million Articles}}},
  doi = {10.1038/nature.2014.16643},
  abstract = {Website where scientists flock to upload manuscripts before peer review has doubled its holdings in six years.},
  timestamp = {2016-11-21T21:37:53Z},
  urldate = {2016-11-11},
  journal = {Nature News},
  author = {Van Noorden, Richard},
  year = {2014},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/C4I83FAN/2496.html:text/html}
}

@techreport{rfc7763,
  type = {RFC},
  title = {The Text/Markdown {{Media Type}}},
  timestamp = {2016-11-21T21:30:09Z},
  institution = {RFC Editor},
  author = {Leonard, Sean},
  year = {2016},
  pages = {1--15},
  howpublished = {Internet Request for Comments},
  shorthand = {RFC7763}
}

@book{suber_open_2012,
  address = {Cambridge, Mass},
  title = {Open {{Access}}},
  isbn = {978-0-262-51763-8},
  abstract = {The Internet lets us share perfect copies of our work with a worldwide audience at virtually no cost. We take advantage of this revolutionary opportunity when we make our work "open access": digital, online, free of charge, and free of most copyright and licensing restrictions. Open access is made possible by the Internet and copyright-holder consent, and many authors, musicians, filmmakers, and other creators who depend on royalties are understandably unwilling to give their consent. But for 350 years, scholars have written peer-reviewed journal articles for impact, not for money, and are free to consent to open access without losing revenue. In this concise introduction, Peter Suber tells us what open access is and isn't, how it benefits authors and readers of research, how we pay for it, how it avoids copyright problems, how it has moved from the periphery to the mainstream, and what its future may hold. Distilling a decade of Suber's influential writing and thinking about open access, this is the indispensable book on the subject for researchers, librarians, administrators, funders, publishers, and policy makers.},
  language = {English},
  timestamp = {2016-11-21T21:37:03Z},
  publisher = {{The MIT Press}},
  author = {Suber, Peter},
  month = jul,
  year = {2012}
}

@article{ovadia_markdown_2014,
  title = {Markdown for {{Librarians}} and {{Academics}}},
  volume = {33},
  issn = {0163-9269},
  doi = {10.1080/01639269.2014.904696},
  timestamp = {2016-11-21T21:36:59Z},
  number = {2},
  urldate = {2016-11-06},
  journal = {Behavioral \& Social Sciences Librarian},
  author = {Ovadia, Steven},
  month = apr,
  year = {2014},
  pages = {120--124},
  shortjournal = {Behavioral  Social Sciences Librarian}
}

@techreport{rfc3629,
  type = {RFC},
  title = {{{UTF}}-8, a Transformation Format of {{ISO}} 10646},
  timestamp = {2016-12-06T17:14:05Z},
  institution = {Alis Technologies},
  author = {Yergeau, F},
  year = {2003},
  pages = {1--15}
}

@misc{international_organization_for_standardization_iso/iec_2014,
  title = {{{ISO}}/{{IEC}} 10646:2014 - {{Information}} Technology -- {{Universal Coded Character Set}} ({{UCS}})},
  shorttitle = {{{ISO}}/{{IEC}} 10646},
  timestamp = {2016-12-06T17:17:55Z},
  urldate = {2016-12-06},
  howpublished = {\url{http://www.iso.org/iso/home/store/catalogue_tc/catalogue_detail.htm?csnumber=63182}},
  journal = {ISO},
  author = {{International Organization for Standardization}},
  year = {2014},
  file = {Snapshot:/home/rob/.mozilla/firefox/x4ox4i88.default/zotero/storage/35RSZHTQ/catalogue_detail.html:text/html}
}

@techreport{rfc1345,
  type = {RFC},
  title = {Character {{Mnemonics}} \& {{Character Sets}}},
  timestamp = {2016-12-06T17:32:25Z},
  institution = {Rationel Almen Planlaegning},
  author = {Simonsen, K},
  year = {1992},
  pages = {1--15},
  howpublished = {Internet Request for Comments},
  shorthand = {RFC1345}
}

@article{bourne_database_2005,
	title = {Will a Biological Database Be Different from a Biological Journal?},
	volume = {1},
	issn = {1553-7358},
	url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0010034},
	doi = {10.1371/journal.pcbi.0010034},
	number = {3},
	urldate = {2017-01-27},
	journal = {PLOS Computational Biology},
	author = {Bourne, Philip},
	month = aug,
	year = {2005},
	keywords = {Biological databases, Computational biology, Computers, Internet, Perception, Sequence alignment, Sequence databases, Sequence motif analysis},
	pages = {e34}
}

@article{shotton_cito_2010,
	title = {{CiTO}, the {Citation} {Typing} {Ontology}},
	volume = {1},
	issn = {2041-1480},
	url = {http://dx.doi.org/10.1186/2041-1480-1-S1-S6},
	doi = {10.1186/2041-1480-1-S1-S6},
	abstract = {CiTO, the Citation Typing Ontology, is an ontology for describing
                  the nature of reference citations in scientific research
                  articles and other scholarly works, both to other such
                  publications and also to Web information resources, and for
                  publishing these descriptions on the Semantic Web. Citation
                  are described in terms of the factual and rhetorical
                  relationships between citing publication and cited
                  publication, the in-text and global citation frequencies of
                  each cited work, and the nature of the cited work itself,
                  including its publication and peer review status. This paper
                  describes CiTO and illustrates its usefulness both for the
                  annotation of bibliographic reference lists and for the
                  visualization of citation networks. The latest version of
                  CiTO, which this paper describes, is CiTO Version 1.6,
                  published on 19 March 2010. CiTO is written in the Web
                  Ontology Language OWL, uses the namespace
                  http://purl.org/net/cito/, and is available from
                  http://purl.org/net/cito/ . This site uses content negotiation
                  to deliver to the user an OWLDoc Web version of the ontology
                  if accessed via a Web browser, or the OWL ontology itself if
                  accessed from an ontology management tool such as Protégé 4 (
                  http://protege.stanford.edu/ ). Collaborative work is
                  currently under way to harmonize CiTO with other ontologies
                  describing bibliographies and the rhetorical structure of
                  scientific discourse.},
	number = {1},
	urldate = {2017-02-05},
	journal = {Journal of Biomedical Semantics},
	author = {Shotton, David},
	year = {2010},
	pages = {S6},
}

@article{berners-lee_publishing_2001,
	title = {Publishing on the semantic web},
	volume = {410},
	issn = {0028-0836},
	url = {http://dx.doi.org/10.1038/35074206},
	doi = {10.1038/35074206},
	number = {6832},
	journal = {Nature},
	author = {Berners-Lee, Tim and Hendler, James},
	month = apr,
	year = {2001},
	pages = {1023--1024},
	annote = {10.1038/35074206}
}

@article{haak_orcid_2012,
	title = {{ORCID}: a system to uniquely identify researchers},
	volume = {25},
	shorttitle = {{ORCID}},
	doi = {10.1087/20120404},
	abstract = {The Open Researcher \& Contributor ID (ORCID) registry presents a unique opportunity to solve the problem of author name ambiguity. At its core the value of the ORCID registry is that it crosses disciplines, organizations, and countries, linking ORCID with both existing identifier schemes as well as publications and other research activities. By supporting linkages across multiple datasets – clinical trials, publications, patents, datasets – such a registry becomes a switchboard for researchers and publishers alike in managing the dissemination of research findings. We describe use cases for embedding ORCID identifiers in manuscript submission workflows, prior work searches, manuscript citations, and repository deposition. We make recommendations for storing and displaying ORCID identifiers in publication metadata to include ORCID identifiers, with CrossRef integration as a specific example. Finally, we provide an overview of ORCID membership and integration tools and resources.},
	number = {4},
	journal = {Learned Publishing},
	author = {Haak, Laurel L. and Fenner, Martin and Paglione, Laura and Pentz, Ed and Ratner, Howard},
	month = oct,
	year = {2012},
	pages = {259--264}
}

@article{towbin_electrophoretic_1979,
	title = {Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications},
	volume = {76},
	issn = {0027-8424, 1091-6490},
	shorttitle = {Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets},
	url = {http://www.pnas.org/content/76/9/4350},
	abstract = {A method has been devised for the electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets. The method results in quantitative transfer of ribosomal proteins from gels containing urea. For sodium dodecyl sulfate gels, the original band pattern was obtained with no loss of resolution, but the transfer was not quantitative. The method allows detection of proteins by autoradiography and is simpler than conventional procedures. The immobilized proteins were detectable by immunological procedures. All additional binding capacity on the nitrocellulose was blocked with excess protein; then a specific antibody was bound and, finally, a second antibody directed against the first antibody. The second antibody was either radioactively labeled or conjugated to fluorescein or to peroxidase. The specific protein was then detected by either autoradiography, under UV light, or by the peroxidase reaction product, respectively. In the latter case, as little as 100 pg of protein was clearly detectable. It is anticipated that the procedure will be applicable to analysis of a wide variety of proteins with specific reactions or ligands.},
	language = {en},
	number = {9},
	urldate = {2017-02-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Towbin, H. and Staehelin, T. and Gordon, J.},
	month = sep,
	year = {1979},
	pmid = {388439},
	pages = {4350--4354},
}

@inproceedings{lanthaler_jsonld_2012,
  title = {On using {JSON-LD} to create evolvable {RESTful} services},
  author = {Lanthaler, Markus and Gütl, Christian},
  booktitle = {Proceedings of the Third International Workshop on {RESTful} Design},
  pages = {25--32},
  year = {2012},
  organization = {ACM}
}

@Manual{R_2014,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = 2014,
  url = {https://www.R-project.org}
}

@inbook{kluyver_jupyter_2016,
  title = {Jupyter Notebooks—a publishing format for reproducible computational workflows},
  author = {Kluyver, Thomas and Ragan-Kelley, Benjamin and Pérez, Fernando and
                  Granger, Brian and Bussonnier, Matthias and Frederic, Jonathan
                  and Kelley, Kyle and Hamrick, Jessica and Grout, Jason and
                  Corlay, Sylvain and others},
  booktitle = {Positioning and Power in Academic Publishing: Players, Agents and Agendas},
  editors = {Fernando Loizides and Birgit Schmidt},
  pages = {87--90},
  year = {2016},
  doi = {10.3233/978-1-61499-649-1-87}
}

@techreport{JATS,
  title = {{JATS: Journal Article Tag Suite}},
  number = {{ANSI/NISO Z39.96}},
  isbn = {978-1-937522-09-4},
  author = {{National Information Standards Organization}},
  year = 2012,
  pages = {iv, 503},
  abstract = {The Journal Article Tag Suite provides a common XML format in
                  which publishers and archives can exchange journal content.
                  The JATS provides a set of XML elements and attributes for
                  describing the textual and graphical content of journal
                  articles as well as some non-article material such as letters,
                  editorials, and book and product reviews.}
}