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references.bib
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@book{Dominik201408,
Title = {The Org Mode 8 Reference Manual - Organize your life with GNU
Emacs},
Author = {Carsten Dominik},
Publisher = {Samurai Media Limited},
Year = 2014,
Month = 8,
Isbn = 9789881327703,
Url = {http://amazon.com/o/ASIN/9881327709/},
Price = {\$19.99},
Totalpages = 286,
Timestamp = {2015.02.03},
Keywords = {org-mode},
}
@article{bahn-2002,
title = {An Object-Oriented Scripting Interface To a Legacy Electronic
Structure Code},
author = {S. R. Bahn and K. W. Jacobsen},
journal = CSE,
year = 2002,
volume = 4,
number = 3,
pages = {56-66},
month = {MAY-JUN},
abstract = {The authors have created an object-oriented scripting
interface to a mature density functional theory code. The
interface gives users a high-level, flexible handle on the
code without rewriting the underlying number-crunching
code. The authors also discuss the design issues and
advantages of homogeneous interfaces},
publisher = {IEEE COMPUTER SOC},
address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA
90720-1314 USA},
type = {Article},
language = {English},
affiliation = {Bahn, SR (Reprint Author), Tech Univ Denmark, Dept Phys, CAMP,
Bldg 307, DK-2800 Lyngby, Denmark. Tech Univ Denmark, Dept
Phys, CAMP, DK-2800 Lyngby, Denmark.},
issn = {1521-9615},
keywords-plus ={MULTISCALE SIMULATION; GOLD ATOMS},
subject-category ={Computer Science, Interdisciplinary Applications},
author-email = {[email protected] [email protected]},
number-of-cited-references =19,
journal-iso = {Comput. Sci. Eng.},
journal = {Comput. Sci. Eng.},
doc-delivery-number ={543YL},
unique-id = {ISI:000175131400009},
doi = {10.1109/5992.998641},
}
@misc{python,
Author = {{Python Software Foundation}},
Title = {Python},
Howpublished = {https://www.python.org}}
@misc{emacs,
Author = {{Free Software Foundation}},
Title = {Emacs},
Howpublished = {https://www.gnu.org/software/emacs/emacs.html},
Note = {v24.3}}
@misc{foundation-dissem-sharin,
Author = {{National Science Foundation}},
Url = http://www.nsf.gov/bfa/dias/policy/dmp.jsp,
Howpublished = {http://www.nsf.gov/bfa/dias/policy/dmp.jsp},
Title = {Dissemination and Sharing of Research Results},
Note = {Last accessed 02/23/2015}}
@misc{foundation-nsf-data,
Author = {{National Science Foundation}},
Title = {{NSF} Data Management Plan Requirements},
Howpublished = {http://www.nsf.gov/eng/general/dmp.jsp},
Note = {Last accessed 02/23/2015}}
@misc{energy-statem-digit,
Author = {{Department of Energy}},
Title = {Statement on Digital Data Management},
Howpublished = {http://science.energy.gov/funding-opportunities/digital-data-management/}}
@misc{health-nih-data,
Author = {{National Institutes of Health}},
Url = http://grants.nih.gov/grants/policy/data_sharing/,
Title = {{NIH} Data Sharing Policy},
Howpublished = {http://grants.nih.gov/grants/policy/data\_sharing/},
Note = {Last accessed 02/23/2015}}
@misc{labs-pdftk,
Author = {{PDF Labs}},
Url = {https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/},
Howpublished = {https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/},
Title = {{PDFtk} the pdf toolkit}}
@misc{pakin-attachfile,
Url = http://www.ctan.org/tex-archive/macros/latex/contrib/attachfile,
Howpublished = {http://www.ctan.org/tex-archive/macros/latex/contrib/attachfile},
Author = {Scott Pakin},
Title = {attachfile},
Note = {v1.5b}}
@book{stodden-2014-implem-reprod-resear,
Editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
Title = {Implementing Reproducible Research},
Publisher = {Chapman and Hall/CRC},
Year = 2014}
@article{hallenbeck-2013-effec-o2,
author = "Hallenbeck, Alexander P. and Kitchin, John R.",
title = {Effects of \ce{O_2} and \ce{SO_2} on the capture capacity of a
primary-amine based polymeric \ce{CO_2} sorbent},
keywords = {RUA, orgmode},
journal = IECR,
pages = "10788-10794",
year = 2013,
volume = {52},
number = {31},
doi = "10.1021/ie400582a",
url = "http://pubs.acs.org/doi/abs/10.1021/ie400582a",
eprint = "http://pubs.acs.org/doi/pdf/10.1021/ie400582a",
}
@article{mehta-2014-ident-poten,
author = {Prateek Mehta and Paul A. Salvador and John R. Kitchin},
title = {Identifying Potential \ce{BO2} Oxide Polymorphs for Epitaxial
Growth Candidates},
keywords = {orgmode, },
journal = AAMI,
volume = 6,
number = 5,
pages = {3630-3639},
year = 2014,
doi = {10.1021/am4059149},
url = {http://dx.doi.org/10.1021/am4059149},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/am4059149},
}
@article{schulte-2011-activ-docum,
author = {Schulte, E. and Davison, D.},
journal = CSE,
title = {Active documents with org-mode},
year = 2011,
volume = 13,
number = 3,
pages = {66-73},
keywords = {Org-mode language;active documents;code intermingling;data
intermingling;hierarchical documents;plain-text markup
language;prose intermingling;document handling;specification
languages;},
doi = {10.1109/MCSE.2011.41},
issn = {1521-9615},
}
@article{xu-2014-relat,
author = {Zhongnan Xu and John R. Kitchin},
title = {Relating the Electronic Structure and Reactivity of the 3d
Transition Metal Monoxide Surfaces},
keywords = {DESC0004031, early-career, orgmode, },
journal = CC,
volume = 52,
pages = {60-64},
year = 2014,
doi = {10.1016/j.catcom.2013.10.028},
url = {http://dx.doi.org/10.1016/j.catcom.2013.10.028},
issn = "1566-7367",
abstract = "Abstract We performed a series of density functional theory
calculations of dissociative oxygen adsorption on fcc metals
and their corresponding rocksalt monoxides to elucidate the
relationship between the oxide electronic structure and its
corresponding reactivity. We decomposed the dissociative
adsorption energy of oxygen on an oxide surface into a sum of
the adsorption energy on the metal and a change in adsorption
energy caused by both expanding and oxidizing the lattice. We
were able to identify the key features of the electronic
structure that explains the trends in adsorption energies on
3d transition metal monoxide surfaces. ",
}
@article{schulte-2012-multi-languag,
author = "Eric Schulte and Dan Davison and Thomas Dye and Carsten
Dominik",
title = {A multi-language computing environment for literate
programming and reproducible research},
journal = "Journal of Statistical Software",
volume = 46,
number = 3,
pages = "1--24",
day = 25,
month = 1,
year = 2012,
coden = "JSSOBK",
issn = "1548-7660",
bibdate = "2011-10-03",
url = "http://www.jstatsoft.org/v46/i03",
accepted = "2011-10-03",
submitted = "2010-12-22",
}
@article{millman-2011-python-scien-engin,
author = {K. Jarrod Millman and Michael Aivazis},
title = {Python for scientists and engineers},
journal = CSE,
volume = 13,
number = 2,
pages = {9-12},
year = 2011,
doi = {10.1109/mcse.2011.36},
url = {http://dx.doi.org/10.1109/MCSE.2011.36},
}
@article{xu-2014-probin-cover,
author = {Zhongnan Xu and John R. Kitchin},
title = {Probing the Coverage Dependence of Site and Adsorbate
Configurational Correlations on (111) Surfaces of Late
Transition Metals},
keywords = {DESC0004031, early-career, orgmode, },
journal = JPCC,
volume = 118,
number = 44,
pages = {25597-25602},
year = 2014,
doi = {10.1021/jp508805h},
url = {http://dx.doi.org/10.1021/jp508805h},
}
@article{miller-2014-simul-temper,
author = {Spencer D. Miller and Vladimir V. Pushkarev and Andrew
J. Gellman and John R. Kitchin},
title = {Simulating Temperature Programmed Desorption of Oxygen on
{P}t(111) Using {DFT} Derived Coverage Dependent Desorption
Barriers},
keywords = {DESC0004031, early-career, orgmode, },
journal = TC,
volume = 57,
number = {1-4},
pages = {106-117},
year = 2014,
doi = {10.1007/s11244-013-0166-3},
url = {http://dx.doi.org/10.1007/s11244-013-0166-3},
}
@misc{xu-suppor,
author = {Zhongnan Xu and Jan Rossmeisl and John R. Kitchin},
title = {Supporting data for: A linear response, {DFT+U} study of trends
in the oxygen evolution activity of transition metal rutile
dioxides. doi:10.5281/zenodo.12635},
keywords = {DESC0004031, early-career, },
url = {https://zenodo.org/record/12635},
doi = {10.5281/zenodo.12635}
}
@article{curnan-2014-effec-concen,
author = {Curnan, Matthew T. and Kitchin, John R.},
title = {Effects of Concentration, Crystal Structure, Magnetism, and
Electronic Structure Method on First-Principles Oxygen Vacancy
Formation Energy Trends in Perovskites},
keywords = {orgmode, },
journal = JPCC,
volume = 118,
number = 49,
pages = {28776-28790},
year = 2014,
doi = {10.1021/jp507957n},
url = {http://dx.doi.org/10.1021/jp507957n},
eprint = { http://dx.doi.org/10.1021/jp507957n },
}
@article{boes-2015-estim-bulk,
author = {Jacob R. Boes and Gamze Gumuslu and James B. Miller and Andrew
J. Gellman and John R. Kitchin},
title = {Estimating Bulk-Composition-Dependent \ce{H2} Adsorption
Energies on \ce{Cu_{x}Pd_{1-x}} Alloy (111) Surfaces},
journal = ACAT,
keywords = {orgmode},
volume = 5,
number = {2},
pages = {1020-1026},
year = 2015,
doi = {10.1021/cs501585k},
url = {http://dx.doi.org/10.1021/cs501585k},
}
@article{boes-2015-estim-bulk-si,
author = {Jacob R. Boes and Gamze Gumuslu and James B. Miller and Andrew
J. Gellman and John R. Kitchin},
title = {Supporting Information: Estimating Bulk-Composition-Dependent
\ce{H2} Adsorption Energies on \ce{Cu_{x}Pd_{1-x}} Alloy (111)
Surfaces},
keywords = {orgmode},
journal = ACAT,
volume = {},
pages = {Supporting information},
year = 2015,
doi = {10.1021/cs501585k},
url =
{http://pubs.acs.org/doi/suppl/10.1021/cs501585k/suppl_file/cs501585k_si_001.pdf},
}
@article{perkel-2015-progr,
author = {Jeffrey M. Perkel},
title = {Programming: Pick Up Python},
journal = Nature,
volume = 518,
number = {7537},
pages = {125-126},
year = 2015,
doi = {10.1038/518125a},
url = {http://dx.doi.org/10.1038/518125a},
}
@article{borgman-2012,
author = {Christine L. Borgman},
title = {The Conundrum of Sharing Research Data},
journal = JASIST,
volume = 63,
number = 6,
pages = {1059-1078},
year = 2012,
doi = {10.1002/asi.22634},
url = {http://dx.doi.org/10.1002/asi.22634},
}
@misc{the-datav-projec,
Author = {{Data Science at The Institute for Quantitative and Social
Science}},
Title = {The Dataverse Project},
Howpublished = {web},
Note = {Last accessed Feb. 23, 2015},
Url = {http://dataverse.org}
}
@article{hinsen-2011,
author = {Konrad Hinsen},
title = {A Data and Code Model for Reproducible Research and Executable
Papers},
journal = {Procedia Computer Science},
volume = 4,
pages = {579-588},
year = 2011,
doi = {10.1016/j.procs.2011.04.061},
url = {http://dx.doi.org/10.1016/j.procs.2011.04.061},
}
@article{fomel-2009-guest-editor-introd,
author = {Sergey Fomel and Jon F. Claerbout},
title = {Guest Editors' Introduction: Reproducible Research},
journal = CSE,
volume = 11,
number = 1,
pages = {5-7},
year = 2009,
doi = {10.1109/mcse.2009.14},
url = {http://dx.doi.org/10.1109/mcse.2009.14},
}
@misc{zenodo-zenod,
Title = {Zenodo},
Howpublished = {https://zenodo.org},
Note = {Zenodo builds and operate a simple and innovative service that
enables researchers, scientists, EU projects and institutions
to share and showcase multidisciplinary research results (data
and publications) that are not part of the existing
institutional or subject-based repositories of the research
communities.}}
@misc{figshare,
Title = {figshare},
Howpublished = {http://figshare.com},
Note = {figshare helps academic institutions store, share and manage
all of their research outputs}}
@Misc{mathworks-matlab-noteb,
author = {{MathWorks}},
title = {MATLAB Notebook},
howpublished = {http://www.mathworks.com/help/matlab/matlab\_prog/create-a-matlab-notebook-with-microsoft-word.html},
note = {The MATLAB notebook integrates Microsoft Word and MATLAB to create a functional document with integrated code and results.}}
@Misc{projec-juypy,
title = {Project Juypyter},
howpublished = {http://jupyter.org/},
note = {The Jupyter Project provides a web-browser based computational notebook with a range of computational backends including Python, Julia, R and others.}}
@article{perez-2007-ipyth,
author = {P\'erez, Fernando and Granger, Brian E.},
title = {{IP}ython: a System for Interactive Scientific Computing},
journal = CSE,
volume = 9,
number = 3,
pages = {21--29},
year = 2007,
doi = {10.1109/MCSE.2007.53},
url = "http://ipython.org",
month = may,
issn = "1521-9615",
publisher = {IEEE Computer Society},
}
@BOOK{Stephenson199911,
title = {In the Beginning...was the Command Line},
author = {Neal Stephenson},
publisher = {William Morrow Paperbacks},
year = {1999},
month = {11},
edition = {First Edition},
isbn = {9780380815937},
url = {http://amazon.com/o/ASIN/0380815931/},
}