git_ms.bib

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@article{Peng2011a,
abstract = {Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.},
archivePrefix = {arXiv},
arxivId = {0901.4552},
author = {Peng, Roger D},
doi = {10.1126/science.1213847},
eprint = {0901.4552},
isbn = {0036807510959},
issn = {00368075},
journal = {Science},
number = {6060},
pages = {1226--1227},
pmid = {22144613},
publisher = {American Association for the Advancement of Science},
title = {{Reproducible Research in Computational Science}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1213847},
volume = {334},
year = {2011}
}
@article{DBLP:journals/corr/abs-1210-0530,
abstract = {Scientists spend an increasing amount of time building and using software. However, most scientists are never taught how to do this efficiently. As a result, many are unaware of tools and practices that would allow them to write more reliable and maintainable code with less effort. We describe a set of best practices for scientific software development that have solid foundations in research and experience, and that improve scientists' productivity and the reliability of their software.},
archivePrefix = {arXiv},
arxivId = {1210.0530},
author = {Wilson, Greg and Aruliah, D A and Brown, C Titus and Hong, Neil P Chue and Davis, Matt and Guy, Richard T and Haddock, Steven H D and Huff, Katy and Mitchell, Ian M. and Plumbley, Mark and Waugh, Ben and White, Ethan P and Wilson, Paul},
eprint = {1210.0530},
file = {:Users/karthik/Library/Application Support/Mendeley Desktop/Downloaded/Wilson et al. - 2012 - Best Practices for Scientific Computing.pdf:pdf},
journal = {Arxiv},
month = sep,
pages = {6},
title = {{Best Practices for Scientific Computing}},
url = {http://arxiv.org/abs/1210.0530},
year = {2012}
}
@article{Piwowar2013,
author = {Piwowar, Heather},
doi = {10.1038/493159a},
file = {:Users/karthik/Library/Application Support/Mendeley Desktop/Downloaded/Piwowar - 2013 - Altmetrics Value all research products.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
month = jan,
number = {7431},
pages = {159--159},
title = {{Altmetrics: Value all research products}},
url = {http://www.nature.com/doifinder/10.1038/493159a},
volume = {493},
year = {2013}
}
@article{Greenland2012,
author = {Greenland, Philip and Fontanarosa, Phil B},
doi = {10.1126/science.1224988},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Authorship,Policy,Science,Science: ethics},
month = aug,
number = {6098},
pages = {1019},
pmid = {22936744},
title = {{Ending honorary authorship.}},
url = {http://www.sciencemag.org/content/337/6098/1019.short},
volume = {337},
year = {2012}
}
@article{Vines2013,
abstract = {The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, structure. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost 1000-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with ∼8 d delay and some disagreement with authors. Given the long-term benefits of data accessibility to the academic community, we believe that journal-based mandatory data archiving policies and mandatory data availability statements should be more widely adopted.},
archivePrefix = {arXiv},
arxivId = {1301.3744},
author = {Vines, Timothy H and Andrew, Rose L and Bock, Dan G and Franklin, Michelle T and Gilbert, Kimberly J and Kane, Nolan C and Moore, Jean-S\'{e}bastien and Moyers, Brook T and Renaut, S\'{e}bastien and Rennison, Diana J and Veen, Thor and Yeaman, Sam},
doi = {10.1096/fj.12-218164},
eprint = {1301.3744},
issn = {1530-6860},
journal = {FASEB journal official publication of the Federation of American Societies for Experimental Biology},
month = jan,
pmid = {23288929},
title = {{Mandated data archiving greatly improves access to research data.}},
url = {http://arxiv.org/abs/1301.3744},
year = {2013}
}
@misc{github_2013,
abstract = {Collaborative development network showing exponential growth},
author = {Pearson, Dan PearsonDan},
booktitle = {\{GamesIndustry\} International},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Pearson - 2013 - GitHub sees 3 millionth member account.html:html},
howpublished = {http://www.gamesindustry.biz/articles/2013-01-17-github-sees-3-millionth-member-account},
keywords = {development},
title = {{GitHub sees 3 millionth member account}},
url = {http://www.gamesindustry.biz/articles/2013-01-17-github-sees-3-millionth-member-account},
urldate = {2013-01-18},
year = {2013}
}
@article{Ince2012a,
abstract = {Scientific communication relies on evidence that cannot be entirely included in publications, but the rise of computational science has added a new layer of inaccessibility. Although it is now accepted that data should be made available on request, the current regulations regarding the availability of software are inconsistent. We argue that, with some exceptions, anything less than the release of source programs is intolerable for results that depend on computation. The vagaries of hardware, software and natural language will always ensure that exact reproducibility remains uncertain, but withholding code increases the chances that efforts to reproduce results will fail.},
author = {Ince, Darrel C and Hatton, Leslie and Graham-Cumming, John},
doi = {10.1038/nature10836},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Ince, Hatton, Graham-Cumming - 2012 - The case for open computer programs.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Algorithms,Editorial Policies,Information Dissemination,Intellectual Property,Periodicals as Topic,Periodicals as Topic: standards,Publishing,Publishing: standards,Reproducibility of Results,Research,Research Design,Research: standards,Software},
month = feb,
number = {7386},
pages = {485--8},
pmid = {22358837},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
shorttitle = {Nature},
title = {{The case for open computer programs.}},
url = {http://dx.doi.org/10.1038/nature10836},
volume = {482},
year = {2012}
}
@article{Alsheikh-Ali2011,
abstract = {There is increasing interest to make primary data from published research publicly available. We aimed to assess the current status of making research data available in highly-cited journals across the scientific literature.},
author = {Alsheikh-Ali, Alawi a and Qureshi, Waqas and Al-Mallah, Mouaz H and Ioannidis, John P a},
doi = {10.1371/journal.pone.0024357},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Alsheikh-Ali et al. - 2011 - Public availability of published research data in high-impact journals.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Access to Information,Journal Impact Factor,Periodicals as Topic,Publishing,Publishing: standards},
month = jan,
number = {9},
pages = {e24357},
pmid = {21915316},
title = {{Public availability of published research data in high-impact journals.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3168487\&tool=pmcentrez\&rendertype=abstract},
volume = {6},
year = {2011}
}
@article{Prlic2012b,
author = {Prli\'{c}, Andreas and Procter, James B.},
doi = {10.1371/journal.pcbi.1002802},
file = {:Users/karthik/Library/Application Support/Mendeley Desktop/Downloaded/Prli\'{c}, Procter - 2012 - Ten Simple Rules for the Open Development of Scientific Software.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Computational Biology},
keywords = {Biology,Computational Biology,Editorial},
month = dec,
number = {12},
pages = {e1002802},
publisher = {Public Library of Science},
title = {{Ten Simple Rules for the Open Development of Scientific Software}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1002802},
volume = {8},
year = {2012}
}
@article{Piwowar2007a,
author = {Piwowar, H A and Day, Roger S and Fridsma, B},
file = {:Users/karthik/Library/Application Support/Mendeley Desktop/Downloaded/Piwowar et al. - 2007 - Sharing Detailed Research Data Is Associated with Increased Citation Rate.pdf:pdf},
journal = {PLOS One},
title = {{Sharing Detailed Research Data Is Associated with Increased Citation Rate}},
year = {2007}
}
@article{Wolkovich2012,
abstract = {Understanding how species and ecosystems respond to climate change requires spatially and temporally rich data for a diverse set of species and habitats, combined with models that test and predict responses. Yet current study is hampered by the long-known problems of inadequate management of data and insufficient description of analytical procedures, especially in the field of ecology. Despite recent institutional incentives to share data and new data archiving infrastructure, many ecologists do not archive and publish their data and code. Given current rapid rates of global change, the consequences of this are extreme: because an ecological dataset collected at a certain place and time represents an irreproducible set of observations, ecologists doing local, independent research possess, in their file cabinets and spreadsheets, a wealth of information about the natural world and how it is changing. Although large-scale initiatives will increasingly enable and reward open science, we believe that change demands action and personal commitment by individuals from students and PIs. Herein, we outline the major benefits of sharing data and analytical procedures in the context of global change ecology, and provide guidelines for overcoming common obstacles and concerns. If individual scientists and laboratories can embrace a culture of archiving and sharing we can accelerate the pace of the scientific method and redefine how local science can most robustly scale up to globally relevant questions.},
author = {Wolkovich, Elizabeth M. and Regetz, James and O'Connor, Mary I.},
issn = {13541013},
journal = {Global Change Biology},
keywords = {ATTRIBUTION,AUTHORS,CLIMATE-CHANGE,CYBERINFRASTRUCTURE,ECOLOGY,IMPACTS,METAANALYSIS,PLANTS,TRIALS,code management,data management,global change ecology,open science,scientific method},
month = jul,
number = {7},
pages = {2102--2110},
publisher = {WILEY-BLACKWELL},
title = {{Advances in global change research require open science by individual researchers}},
url = {http://apps.webofknowledge.com/full\_record.do?product=UA\&search\_mode=GeneralSearch\&qid=1\&SID=1CfaPnJ9gbl5bo171Jc\&page=1\&doc=4},
volume = {18},
year = {2012}
}
@article{niedermeyer2012,
abstract = {Natural or synthetic cyclic peptides often possess pronounced bioactivity. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic monomers and the complex fragmentation patterns observed. Even though several software tools for cyclic peptide tandem mass spectra annotation have been published, these tools are still unable to annotate a majority of the signals observed in experimentally obtained mass spectra. They are thus not suitable for extensive mass spectrometric characterization of these compounds. This lack of advanced and user-friendly software tools has motivated us to extend the fragmentation module of a freely available open-source software, mMass (http://www.mmass.org), to allow for cyclic peptide tandem mass spectra annotation and interpretation. The resulting software has been tested on several cyanobacterial and other naturally occurring peptides. It has been found to be superior to other currently available tools concerning both usability and annotation extensiveness. Thus it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides.},
author = {Niedermeyer, Timo H J and Strohalm, Martin},
doi = {10.1371/journal.pone.0044913},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Niedermeyer, Strohalm - 2012 - mMass as a software tool for the annotation of cyclic peptide tandem mass spectra.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
month = jan,
number = {9},
pages = {e44913},
pmid = {23028676},
title = {{mMass as a software tool for the annotation of cyclic peptide tandem mass spectra.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3441486\&tool=pmcentrez\&rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Schultheiss2011,
abstract = {We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009. We found that 72\% of Web sites are still available at the published addresses, only 9\% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33\%, we could not test functionality because there was no example data or a related problem; 13\% were truly no longer working as expected; we could positively confirm functionality only for 45\% of all services. Additionally, we conducted a survey among 872 Web Server Issue corresponding authors; 274 replied. 78\% of all respondents indicate their services have been developed solely by students and researchers without a permanent position. Consequently, these services are in danger of falling into disrepair after the original developers move to another institution, and indeed, for 24\% of services, there is no plan for maintenance, according to the respondents. We introduce a Web service quality scoring system that correlates with the number of citations: services with a high score are cited 1.8 times more often than low-scoring services. We have identified key characteristics that are predictive of a service's survival, providing reviewers, editors, and Web service developers with the means to assess or improve Web services. A Web service conforming to these criteria receives more citations and provides more reliable service for its users. The most effective way of ensuring continued access to a service is a persistent Web address, offered either by the publishing journal, or created on the authors' own initiative, for example at http://bioweb.me. The community would benefit the most from a policy requiring any source code needed to reproduce results to be deposited in a public repository.},
author = {Schultheiss, Sebastian J and M\"{u}nch, Marc-Christian and Andreeva, Gergana D and R\"{a}tsch, Gunnar},
doi = {10.1371/journal.pone.0024914},
editor = {Zhu, Dongxiao},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Schultheiss et al. - 2011 - Persistence and availability of Web services in computational biology.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Computational Biology,Computational Biology: methods,Computational Biology: standards,Humans,Information Storage and Retrieval,Information Storage and Retrieval: standards,Internet,Internet: standards,Periodicals as Topic,Reproducibility of Results},
month = jan,
number = {9},
pages = {e24914},
pmid = {21966383},
publisher = {Public Library of Science},
title = {{Persistence and availability of Web services in computational biology.}},
url = {http://dx.plos.org/10.1371/journal.pone.0024914},
volume = {6},
year = {2011}
}
@article{Kapitzaa,
author = {Kapitza, R and Baumann, P and Reiser, H P},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Kapitza, Baumann, Reiser - Unknown - Using object replication for building a dependable version control system.pdf:pdf},
title = {{Using object replication for building a dependable version control system}},
url = {http://apps.webofknowledge.com/full\_record.do?product=UA\&search\_mode=GeneralSearch\&qid=4\&SID=3FnA8iEApFn6MAKofib\&page=1\&doc=10}
}
@article{Vink2012b,
author = {Vink, Cor J. and Paquin, Pierre and Cruickshank, Robert H.},
doi = {10.1525/bio.2012.62.5.3},
issn = {00063568},
journal = {BioScience},
month = may,
number = {5},
pages = {451--452},
publisher = {American Institute of Biological Sciences},
title = {{Taxonomy and Irreproducible Biological Science}},
url = {http://www.bioone.org/doi/abs/10.1525/bio.2012.62.5.3},
volume = {62},
year = {2012}
}
@article{Piwowar2007a,
abstract = {Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available.},
author = {Piwowar, Heather A and Day, Roger S and Fridsma, Douglas B},
doi = {10.1371/journal.pone.0000308},
issn = {1932-6203},
journal = {PloS one},
keywords = {Biomedical Research,Biomedical Research: economics,Biomedical Research: trends,Clinical Trials as Topic,Cost-Benefit Analysis,Humans,Information Dissemination,Information Dissemination: methods,Internet,Journal Impact Factor,Neoplasms,Neoplasms: therapy,Oligonucleotide Array Sequence Analysis,Periodicals as Topic,Periodicals as Topic: statistics \& numerical data,Publications,Publications: statistics \& numerical data,Regression Analysis},
month = jan,
number = {3},
pages = {e308},
pmid = {17375194},
title = {{Sharing detailed research data is associated with increased citation rate.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1817752\&tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2007}
}
@article{Schwab2000a,
abstract = {To verify a research paper's computational results, readers typically have to recreate them from scratch. ReDoc is a simple software filing system for authors that lets readers easily reproduce computational results using standardized rules and commands},
author = {Schwab, Matthias and Karrenbach, Martin and Claerbout, Jon},
doi = {10.1109/5992.881708},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Schwab, Karrenbach, Claerbout - 2000 - Making Scientific Computations Reproducible.pdf:pdf},
institution = {SEP},
issn = {15219615},
journal = {Computing in Science Engineering},
number = {6},
pages = {61--67},
publisher = {IEEE},
title = {{Making Scientific Computations Reproducible}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=881708},
volume = {2},
year = {2000}
}
@article{Reichman2011,
annote = {I think this paper and Roger Peng's paper, both from the Data Special Issue on Science, are 100\% crucial.  Science also modifies its data archiving policy in that issue.  },
author = {Reichman, O.J. and Jones, Matthew B. and Schildhauer, M. P.},
doi = {10.1126/science.1197962},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Reichman, Jones, Schildhauer - 2011 - Challenges and Opportunities of Open Data in Ecology(3).pdf:pdf},
issn = {0036-8075},
journal = {Science},
month = feb,
number = {6018},
pages = {692--693},
title = {{Challenges and Opportunities of Open Data in Ecology}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1197962 http://www.sciencemag.org/cgi/doi/10.1126/science.331.6018.692},
volume = {331},
year = {2011}
}
@article{Morin2012b,
author = {Morin, Andrew and Urban, Jennifer and Sliz, Piotr},
doi = {10.1371/journal.pcbi.1002598},
editor = {Lewitter, Fran},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Morin, Urban, Sliz - 2012 - A Quick Guide to Software Licensing for the Scientist-Programmer.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
keywords = {Biology,Computational Biology,Computer Science,Education,Engineering,Intellectual property,Science Policy,Science education,Software design,Software engineering,Software tools,Technology development},
month = jul,
number = {7},
pages = {e1002598},
pmid = {22844236},
publisher = {Public Library of Science},
title = {{A quick guide to software licensing for the scientist-programmer.}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1002598},
volume = {8},
year = {2012}
}
@article{Wren2004,
abstract = {The advent of the World Wide Web has enabled unprecedented supplementation of traditional journal publications, allowing access to resources, such as video, sound, software, databases, datasets too large to publish, and even supplementary information and discussion. However, unlike traditional publications, continued availability of these online resources is not guaranteed. An automated survey was conducted to quantify the growth in Uniform Resource Locators (URLs) published to date in MEDLINE abstracts, their current availability and distribution by journal.},
author = {Wren, Jonathan D},
doi = {10.1093/bioinformatics/btg465},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Wren - 2004 - 404 not found the stability and persistence of URLs published in MEDLINE.pdf:pdf},
issn = {1367-4803},
journal = {Bioinformatics (Oxford, England)},
keywords = {Abstracting and Indexing as Topic,Abstracting and Indexing as Topic: methods,Bibliographic,Bibliometrics,Database Management Systems,Databases,Hypermedia,Information Dissemination,Information Dissemination: methods,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,MEDLINE,Reproducibility of Results,Sensitivity and Specificity,Terminology as Topic,Time Factors},
month = mar,
number = {5},
pages = {668--72},
pmid = {15033874},
title = {{404 not found: the stability and persistence of URLs published in MEDLINE.}},
url = {http://bioinformatics.oxfordjournals.org/content/20/5/668.abstract},
volume = {20},
year = {2004}
}
@misc{Wald2010,
annote = {Chelsea Wald},
author = {Wald, C},
booktitle = {Sciencemag.org},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Wald - 2010 - Issues \& Perspectives Scientists Embrace Openness.html:html},
title = {{Issues \& Perspectives Scientists Embrace Openness}},
url = {http://sciencecareers.sciencemag.org/career\_magazine/previous\_issues/articles/2010\_04\_09/caredit.a1000036},
urldate = {2013-01-16},
year = {2010}
}
@article{VanNoorden2011,
author = {{Van Noorden}, Richard},
doi = {10.1038/478026a},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Van Noorden - 2011 - The trouble with retractions.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Editorial Policies,Guidelines as Topic,Humans,Periodicals as Topic,Periodicals as Topic: standards,Research Design,Research Design: statistics \& numerical data,Retraction of Publication as Topic,Science,Science: ethics,Science: standards,Scientific Misconduct,Scientific Misconduct: statistics \& numerical data},
language = {en},
month = oct,
number = {7367},
pages = {6--8},
pmid = {21979026},
publisher = {Nature Publishing Group},
title = {{The trouble with retractions}},
url = {http://www.nature.com/news/2011/111005/full/478026a.html},
volume = {478},
year = {2011}
}
@article{Piwowar2011a,
abstract = {Many initiatives encourage investigators to share their raw datasets in hopes of increasing research efficiency and quality. Despite these investments of time and money, we do not have a firm grasp of who openly shares raw research data, who doesn't, and which initiatives are correlated with high rates of data sharing. In this analysis I use bibliometric methods to identify patterns in the frequency with which investigators openly archive their raw gene expression microarray datasets after study publication. Automated methods identified 11,603 articles published between 2000 and 2009 that describe the creation of gene expression microarray data. Associated datasets in best-practice repositories were found for 25\% of these articles, increasing from less than 5\% in 2001 to 30\%-35\% in 2007-2009. Accounting for sensitivity of the automated methods, approximately 45\% of recent gene expression studies made their data publicly available. First-order factor analysis on 124 diverse bibliometric attributes of the data creation articles revealed 15 factors describing authorship, funding, institution, publication, and domain environments. In multivariate regression, authors were most likely to share data if they had prior experience sharing or reusing data, if their study was published in an open access journal or a journal with a relatively strong data sharing policy, or if the study was funded by a large number of NIH grants. Authors of studies on cancer and human subjects were least likely to make their datasets available. These results suggest research data sharing levels are still low and increasing only slowly, and data is least available in areas where it could make the biggest impact. Let's learn from those with high rates of sharing to embrace the full potential of our research output.},
author = {Piwowar, Heather a},
doi = {10.1371/journal.pone.0018657},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Piwowar - 2011 - Who shares Who doesn't Factors associated with openly archiving raw research data.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Archives,Cooperative Behavior,Databases, Genetic,Humans,Information Dissemination,Multivariate Analysis,Odds Ratio,Periodicals as Topic,Research,Research: statistics \& numerical data},
month = jan,
number = {7},
pages = {e18657},
pmid = {21765886},
title = {{Who shares? Who doesn't? Factors associated with openly archiving raw research data.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3135593\&tool=pmcentrez\&rendertype=abstract},
volume = {6},
year = {2011}
}
@misc{git2013,
file = {::},
title = {{The Octoverse in 2012 · GitHub Blog}},
url = {https://github.com/blog/1359-the-octoverse-in-2012},
urldate = {01/02/13}
}
@article{Desjardins-Proulx2013,
author = {Desjardins-Proulx, P and White, Ethan P. and Adamson, J J and Ram, Karthik and Poisot, Timoth\'{e}e and Gravel, Dominique},
journal = {PLoS Biology},
title = {{The Case for Open Preprints in Biology}},
volume = {Accepted},
year = {2013}
}
@article{Begley2012,
author = {Begley, C Glenn and Ellis, Lee M},
doi = {10.1038/483531a},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Begley, Ellis - 2012 - Drug development Raise standards for preclinical cancer research.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Animals,Biomedical Research,Biomedical Research: standards,Cell Line,Clinical Trials as Topic,Clinical Trials as Topic: statistics \& numerical d,Drug Evaluation,Humans,Mice,Neoplasms,Neoplasms: drug therapy,Neoplasms: genetics,Preclinical,Preclinical: standards,Reproducibility of Results,Research Design,Research Design: statistics \& numerical data,Survival Analysis,Translational Medical Research,Translational Medical Research: standards,Translational Medical Research: statistics \& numer,Translational Medical Research: trends,Treatment Failure,Tumor},
month = mar,
number = {7391},
pages = {531--3},
pmid = {22460880},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
shorttitle = {Nature},
title = {{Drug development: Raise standards for preclinical cancer research.}},
url = {http://dx.doi.org/10.1038/483531a},
volume = {483},
year = {2012}
}
@article{Neylon2012,
annote = {10.1038/492348a},
author = {Neylon, Cameron},
issn = {0028-0836},
journal = {Nature},
month = dec,
number = {7429},
pages = {348--349},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
title = {{Science publishing: Open access must enable open use}},
url = {http://dx.doi.org/10.1038/492348a},
volume = {492},
year = {2012}
}
@misc{github_popularity,
author = {Finley, K},
file = {::},
title = {{Github Has Surpassed Sourceforge and Google Code in Popularity}},
url = {http://readwrite.com/2011/06/02/github-has-passed-sourceforge},
urldate = {2013-01-15},
year = {2011}
}
@article{Whitlock2010a,
author = {Whitlock, Michael C and McPeek, Mark A and Rausher, Mark D and Rieseberg, Loren and Moore, Allen J},
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Whitlock et al. - 2010 - Data archiving.pdf:pdf},
issn = {1537-5323},
journal = {The American naturalist},
keywords = {Access to Information,Biological Evolution,Ecology,Information Management,Information Management: methods,Research,Research: standards},
language = {en},
month = feb,
number = {2},
pages = {145--6},
publisher = {The University of Chicago Press},
title = {{Data archiving.}},
url = {http://www.jstor.org/stable/10.1086/650340},
volume = {175},
year = {2010}
}
@misc{nsf2012,
file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Unknown - Unknown - US NSF - Dear Colleague Letter - Issuance of a new NSF Proposal \& Award Policies and Procedures Guide (NSF13004).html:html},
title = {{US NSF - Dear Colleague Letter - Issuance of a new NSF Proposal \& Award Policies and Procedures Guide (NSF13004)}},
url = {http://www.nsf.gov/pubs/2013/nsf13004/nsf13004.jsp?WT.mc\_id=USNSF\_109},
urldate = {2012-11-11},
year = {2012}
}