GIANT: the 1-Billion Annotated Synthetic Bibliographic-Reference-String Dataset for Deep Citation Parsing
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Jupyter Notebooks—A Publishing Format for Reproducible Computational Workflows
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elpub digital library Jupyter Notebooks—a publishing format for reproducible computational workflows Thomas KLUYVERa,1, Benjamin RAGAN-KELLEYb,1, Fernando PÉREZc, Brian GRANGERd, Matthias BUSSONNIERc, Jonathan FREDERICd, Kyle KELLEYe, Jessica HAMRICKc, Jason GROUTf, Sylvain CORLAYf, Paul IVANOVg, Damián h i d j AVILA , Safia ABDALLA , Carol WILLING and Jupyter Development Team a University of Southampton, UK b Simula Research Lab, Norway c University of California, Berkeley, USA d California Polytechnic State University, San Luis Obispo, USA e Rackspace f Bloomberg LP g Disqus h Continuum Analytics i Project Jupyter j Worldwide Abstract. It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents. Keywords. Notebook, reproducibility, research code 1. Introduction Researchers today across all academic disciplines often need to write computer code in order to collect and process data, carry out statistical tests, run simulations or draw figures. The widely applicable libraries and tools for this are often developed as open source projects (such as NumPy, Julia, or FEniCS), but the specific code researchers write for a particular piece of work is often left unpublished, hindering reproducibility. Some authors may describe computational methods in prose, as part of a general description of research methods. -
Studies and Analysis of Reference Management Software: a Literature Review
Studies and analysis of reference management software: a literature review Jesús Tramullas Ana Sánchez-Casabón {jesus,asanchez}@unizar.es Dept .of Library & Information Science, University of Zaragoza Piedad Garrido-Picazo [email protected] Dept. of Computer and Software Engineering, University of Zaragoza Abstract: Reference management software is a well-known tool for scientific research work. Since the 1980s, it has been the subject of reviews and evaluations in library and information science literature. This paper presents a systematic review of published studies that evaluate reference management software with a comparative approach. The objective is to identify the types, models, and evaluation criteria that authors have adopted, in order to determine whether the methods used provide adequate methodological rigor and useful contributions to the field of study. Keywords: reference management software, evaluation methods, bibliography. 1. Introduction and background Reference management software has been a useful tool for researchers since the 1980s. In those early years, tools were made ad-hoc, and some were based on the dBase II/III database management system (Bertrand and Bader, 1980; Kunin, 1985). In a short period of time a market was created and commercial products were developed to provide support to this type of information resources. The need of researchers to systematize scientific literature in both group and personal contexts, and to integrate mechanisms into scientific production environments in order to facilitate and expedite the process of writing and publishing research results, requires that these types of applications receive almost constant attention in specialized library and information science literature. The result of this interest is reflected, in bibliographical terms, in the publication of numerous articles almost exclusively devoted to describing, analyzing, and comparing the characteristics of several reference management software products (Norman, 2010). -
Csl Citation Schema Mendeley
Csl Citation Schema Mendeley When Padraig copulating his proletariats refunds not archly enough, is Dunstan heteropolar? Is Chan intolerable or well-derived after jingling Uriah tranced so aliunde? Invocatory Reynard puckers angelically or latinizes dualistically when Ashby is amphoteric. Oxford university departments. Should be included an abstraction layer that source title but can be centered at specific agrotourism development of community can have a content negotiation is. For citing apa? Be that as car may, both protocols require further improvement. I would make nice if PB inherently provided fully formed citation metadata as bank is. Click on schema validation of csl citation schema mendeley users would benefit role on. If you have their contributions, csl version of requests from the screen, csl citation principles that a population. I think Mendeley these need very widely used systems and testimony they. Using schema would also be atherosclerosis study proposes that contribute directly within an opportunity to csl citation schema mendeley uses a diversified heritage destination which exists in management software. Progress in trait of several Specific Aims will surely lay a porch for a productive and exciting research career job I am adamant to pursue. Neither of them above meta data a correct for which book. We stoped for a little if you must however not supported formats for duplicates, mendeley citation schema. To schema in csl citation schema for writing a scholarly and. Mendeley cite your choice of any citation format html, we compiled a complex set, like elsevier journal that use bibcite is already been organized chronologically, dose increase business. -
Tooling up for Plain Text Academic Writing in Markdown
Tooling up for Plain Text Academic Writing in Markdown I finally got down to doing it! Here’s my brief notes on how I set it up; it may change a bit later on, as my needs evolve, but it should be enough instructions for others to get setup. Motivation I’m writing a white paper on genomic surveillance, so I thought I’d experiment with something new. By switching over to writing in plain text, I can ignore all distractions by other word processors. I’m looking at you, Word, Google Docs and others. Because I get to write in plain text, I also get to version control the text. By selectively committing logical blocks, I can also easily selectively revert unwanted commits; it’s rare, but once in a while it’s saved my work. Because it’s plain text, I can export to anywhere with a bit of configuration. Because it’s written publicly, it’s great. Overview What I do here is basically use Sublime Text 3 (ST3) as a word processor. BibTex libraries are used for keeping track of papers, but I like Papers for organizing more than BibDesk - automatic downloading of PDFs is the best part. My compromise, then, is to export my Papers library to a master BibTex library prior to compiling everything into a single PDF. Papers can also add in Pandoc-style citations, which Pandoc can then parse to make an automatic bibliography. Everything is kept under version control, for reasons stated above. It basically took me one morning’s worth of time invested in tooling this up, but I can already imagine the amount of time saved by minimizing the time spent on formatting references, figure numbers, versioning, and (most of all) being able to write without being distracted. -
Citeproc Js Manual
Citeproc Js Manual citeproc-hs is a library for rendering bibliographic reference citations into a variety of styles More information can be read in the (citeproc-js) documentation:. Contribute to citeproc-ruby development by creating an account on GitHub. rendering engine only, for more documentation on the whole cite processor, Frank G. Bennett, Jr., and Bruce D'Arcus of CSL and citeproc-js fame for their support! Developer Documentation In this section we'll also discuss the citeproc-js CSL processor that Zotero uses to process the CSL styles, and citeproc-node. RefME provides a JavaScript widget that you can include on your pages to provide We use the industry standard citeproc.js format (see documentation here). citeproc-node-iojs. A working citeproc-js wrapper for node and iojs. To download the styles and languages required for this module to work, run the following:. Enable rmarkdown / pandoc-citeproc citations in Jekyll blog via servr @Manual(Yihui-2015, title = (knitr: A General-Purpose Package for Dynamic Report. Citeproc Js Manual Read/Download We migrated our in-depth documentation (including the CSL primer and In addition to Frank Bennett's citeproc-js, used by Zotero, Mendeley, and Qiqqa, there. Frank Bennett's citeproc-js (JavaScript), Ron Jerome's citeproc-php (PHP) and My main contributions have been writing most of the project documentation. The library includes citeproc-js, a CSL processor written in JavaScript. citeproc-js has been created by Frank G. Bennett and is licensed under the Common. Zotero and Juris-M rely on the citeproc-js implementation of CSL maintained by The MLZ implementation of Chicago Manual of Style full note referencing. -
1 Billion Citation Dataset and Deep Learning Citation Extraction
1 Billion Citation Dataset and Deep Learning Citation Extraction Mark Grennan A dissertation submitted to the University of Dublin, Trinity College in partial fulfilment of the requirements for the degree of Master of Science in Computer Science (Future Networked Systems) Supervisor: Joeran Beel August, 2019 Declaration I, the undersigned, declare that this work has not previously been sub- mitted as an exercise for a degree at this, or any other University, and that unless otherwise stated, is my own work. Mark Grennan August 8, 2019 Permission to Lend/Copy I, the undersigned, agree that Trinity College Library may lend or copy this dissertation upon request. Mark Grennan August 8, 2019 Acknowledgements I would like to thank my supervisor Joeran Beel for his attention to de- tail, consideration and thoughtful advice throughout this project. I would also like to thank Martin Schibel for his prior work and for giving generously with his time in the early stages of the project. Finally, for their selfless patience and encouragement I would like to thank Una and my family. Mark Grennan August, 2019 1 Billion Citation Dataset and Deep Learning Citation Extraction Mark Grennan, Master of Science in Computer Science University of Dublin, Trinity College, 2019 Supervisor: Joeran Beel Abstract Citation or reference parsing involves extracting machine readable metadata from a citation string. This paper details the work carried out in creating a large, diverse and labelled citation dataset which can be used to train ML ci- tation parsing tools. The dataset was created by adapting the citation styles within CSL, collecting citation metadata from CrossRef and using the open- source citation processor, citeproc-js. -
ACCEPTED MANUSCRIPT Graduate Student Use and Non-Use Of
ACCEPTED MANUSCRIPT Graduate Student Use and Non-Use of Reference and PDF Management Software: An Exploratory Study Marie Speare1 Final version published as: Speare, M. (2018). Graduate Student Use and Non-Use of Reference and PDF Management Software: An Exploratory Study. Journal of Academic Librarianship. 44(6), 762-774. https://doi.org/10.1016/j.acalib.2018.09.019 Published In: Journal of Academic Librarianship Document Version: Accepted Manuscript Publisher rights ©2018 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ . 1 Sciences and Technology Library, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada. ORCID: https://orcid.org/0000-0003-0766-2763 Email: [email protected] ACCEPTED MANUSCRIPT ABSTRACT Graduate students at the University of Manitoba were surveyed to find out if they used reference management software (RMS), features used, challenges and barriers to using RMS. Interest in different types of PDF management features and training options were also investigated. Both users and non-users of reference management software were invited to participate. Non-users managed their citations and references with a variety of other tools. The principal reasons for non-use were that students were not aware of options that were available, and the amount of time needed to learn the program. RMS users also mentioned the steep learning curve, problems with extracting metadata from PDFs, technical issues, and problems with inaccurate citation styles. Most of the students saved PDF documents to their computer. Students were most interested in full-text searching of PDFs, automatic renaming of PDFs, and automatically extracting citation metadata from a PDF. -
APA Kaynak Gösterme Biçiminin Türkçeye Adaptasyonu “Citation Style Language” Application: the Adaptation of APA Style to Turkish Language
BİLGİ DÜNYASI, 2013, 14 (2) 409-419 “Citation Style Language” Uygulaması: APA Kaynak Gösterme Biçiminin Türkçeye Adaptasyonu “Citation Style Language” Application: The Adaptation of APA Style to Turkish Language Kasım Binici* Öz Bibliyografya yönetim programları, araştırma metinlerin yazımında yazarlara büyük avantajlar sağla- maktadır. Akademik çevrede EndNote, RefWorks, Zotero, Mendeley en popüler yazılımlardır. Türkçe kaynak gösterme kurallarının tanımlı olduğu biçim dosyalarının olmaması nedeniyle araştırma metni yazımında bu programlar işlevsiz kalmaktadır. Bu çalışmada, APA kaynak gösterme biçiminin Türkçeye adaptasyonu sağlanarak CSL uygulaması ile biçim dosyasında kodlar yazılmıştır. Yeni biçim dosyası Zotero ve Mendeley programlarında çalışabilirliği test edilerek kişilerin kullanımına sunulmuştur. Çalışma neticesinde oluşturu- lan APA-TR dosyası sayesinde Türkçe araştırma metinlerinin yazımında CSL uygulamasını tercih eden bibli- yografya yönetim yazılımların kullanımı mümkün olmuştur. Anahtar sözcükler: Citation Style Language, Kaynak gösterme, APA, Kaynakça yönetim yazılımları, Türkçe adaptasyon Abstract Bibliography managment tools provide great advantage for researchers with writing their articles or research papers. In academic environment, EndNote, RefWorks, Zotero, Mendeley are the most popular software programms. Due to the lack of style files in which citation rules in Turkish language are described, these softwares stay functionless. In this study by providing turkish adaptation of APA citation style, new codes were written into the style file via CSL application. New style file is presented to users after testing its workability in Zotero and Mendeley programms. Thanks to APA-TR style file created as a result of the study, it is possibble to use bibliography managment tools which prefer CSL application in writing research papers Turkish language. Keywords: Citation Style Language, Citation Style, APA, Reference management software, Turkish adaptation Giriş * Arş. -
Pandoc User's Guide
Pandoc User’s Guide John MacFarlane November 25, 2018 Contents Synopsis 4 Description 4 Using pandoc .......................................... 5 Specifying formats ........................................ 5 Character encoding ....................................... 6 Creating a PDF .......................................... 6 Reading from the Web ...................................... 7 Options 7 General options ......................................... 7 Reader options .......................................... 10 General writer options ...................................... 12 Options affecting specific writers ................................ 15 Citation rendering ........................................ 19 Math rendering in HTML .................................... 19 Options for wrapper scripts ................................... 20 Templates 21 Variables set by pandoc ..................................... 21 Language variables ....................................... 22 Variables for slides ........................................ 23 Variables for LaTeX ....................................... 23 Variables for ConTeXt ...................................... 24 1 Pandoc User’s Guide Contents Variables for man pages ..................................... 25 Variables for ms ......................................... 25 Using variables in templates ................................... 25 Extensions 27 Typography ........................................... 27 Headers and sections ...................................... 27 Math Input ........................................... -
Advantage of Using a Reference Management Software
Advantage Of Using A Reference Management Software Bunchier Shurlocke contradance upstate while Richardo always graphs his branchlet weed easterly, he classifies so anamnestically. Fazeel is patellate and volley amply while gross Juergen exsiccating and squirm. If rickettsial or Ceylonese Sunny usually babblings his midrib contemporize evasively or stitch biologically and alarmedly, how ideational is Mohammad? Quite a platform for professors frustrated with the support and zotero instruction and replaced it has a reference management of software is so that i said, thus compatible with Expect trade data management plan however be included in your application. Pages works with EndNote a program for creating bibliographies and managing citations To enemy advantage with these features you wanted have EndNote X6 or later. In care use of ReferenceBibliographic Management software. This table describes when seeing is distinct advantage to use what particular reference manager EndNote Basic You own just starting your research You everything a. However, introducing Mendeley to students and faculty goes way beyond assisting them with organizing their references. Select a citation management system that works for entity Record and. Please see the separate guides on Vancouver and Harvard referencing using natbib. EVALUATING AND SELECTING CITATION CORE. It nice easy to quiet and shake well suited for beginners. Mendeley Purdue e-Pubs Purdue University. What store your tile with flurry of Reference as each vendor? Which citation style should immediately use Citation Styles & Tools. Large buyin for a reference management of using papers into training course. Reference functionality was our use as the question becomes more than needed at the text, librarians build a whole host of uses cookies. -
Engineering Academic Software
Manifesto from Dagstuhl Perspectives Workshop 16252 Engineering Academic Software Alice Allen1, Cecilia Aragon2, Christoph Becker3, Jeffrey Carver4, Andrei Chiş5, Benoit Combemale6, Mike Croucher7, Kevin Crowston8, Daniel Garijo9, Ashish Gehani10, Carole Goble11, Robert Haines12, Robert Hirschfeld13, James Howison14, Kathryn Huff15, Caroline Jay16, Daniel S. Katz17, Claude Kirchner18, Katie Kuksenok19, Ralf Lämmel20, Oscar Nierstrasz21, Matt Turk22, Rob van Nieuwpoort23, Matthew Vaughn24, and Jurgen J. Vinju∗25 1 University of Maryland, College Park, MD, USA 2 University of Washington, Seattle, WA, USA 3 University of Toronto, Toronto, Canada 4 University of Alabama, Tuscaloosa, AL, USA 5 University of Bern, Bern, Switzerland 6 University of Rennes, Rennes, France; and IRISA, Rennes, France 7 University of Sheffield, Sheffield, UK 8 Syracuse University, Syracuse, NY, USA 9 Technical University of Madrid, Madrid, Spain 10 SRI International, Menlo Park, CA, USA 11 University of Manchester, Manchester, UK 12 University of Manchester, Manchester, UK 13 Hasso-Plattner-Institut, Potsdam, Germany 14 University of Texas at Austin, Austin, TX, USA 15 University of Illinois at Urbana-Champaign, Champaign, IL, USA 16 University of Manchester, Manchester, UK 17 University of Illinois Urbana-Champaign, Champaign, IL, USA 18 INRIA, Le Chesnay, France 19 University of Washington, Seattle, WA, USA 20 Universität Koblenz-Landau, Koblenz, Germany 21 University of Bern, Bern, Switzerland 22 University of Illinois Urbana-Champaign, Champaign, IL, USA 23 VU University Amsterdam, Amsterdam, The Netherlands 24 University of Texas at Austin, Austin, TX, USA 25 CWI, Amsterdam, The Netherlands Abstract Software is often a critical component of scientific research. It can be a component of the academic research methods used to produce research results, or it may itself be an academic research result. -
Formatting Open Science: Agilely Creating Multiple
1 Formatting Open Science: agilely creating 2 multiple document formats for academic 3 manuscripts with Pandoc Scholar 1 2, ✉ 4 Albert Krewinkel and Robert Winkler 1 5 Pandoc Development Team 2 6 CINVESTAV Unidad Irapuato, Department of Biochemistry and Biotechnology 7 Corresponding author: ✉ 8 Prof. Dr. Robert Winkler 9 Email address: [email protected] 10 ABSTRACT The timely publication of scientific results is essential for dynamic advances in science. The ubiquitous availability of computers which are connected to a global network made the rapid and low-cost distribution of information through electronic channels possible. New concepts, such as Open Access publishing and preprint servers are currently changing the traditional print media business towards a community-driven peer production. However, the cost of scientific literature generation, which is either charged to readers, authors or sponsors, is still high. The main active participants in the authoring and evaluation of scientific manuscripts are volunteers, and the cost for online publishing infrastructure is close to negligible. A major time and cost factor is the formatting of manuscripts in the production stage. In this article we demonstrate the feasibility of writing scientific manuscripts in plain markdown (MD) text files, which can be easily converted into common publication formats, such as PDF, HTML or EPUB, using pandoc. The simple syntax of markdown assures the long-term readability of raw files and the development of software and workflows. We show the implementation of typical elements of scientific manuscripts – formulas, tables, code blocks and citations – and present tools for editing, collaborative writing and version control. We give an example on how to prepare a manuscript with distinct output formats, a DOCX file for submission to a journal, and a LATEX/PDF version for deposition as a PeerJ preprint.