diff --git a/git_manuscript.md b/git_manuscript.md index a3a2b9e..e28e39f 100644 --- a/git_manuscript.md +++ b/git_manuscript.md @@ -13,6 +13,7 @@ Berkeley, CA 94720. USA. # Keywords reproducible research, version control, open science. +\newpage # Findings # Introduction diff --git a/git_manuscript.pdf b/git_manuscript.pdf index 4217a73..15c2c4b 100644 Binary files a/git_manuscript.pdf and b/git_manuscript.pdf differ diff --git a/git_ms.bib b/git_ms.bib index fc0dcd5..445ce6a 100644 --- a/git_ms.bib +++ b/git_ms.bib @@ -1,21 +1,124 @@ -Automatically generated by Mendeley 1.7.1 +Automatically generated by Mendeley 1.8 Any changes to this file will be lost if it is regenerated by Mendeley. -@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} +@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{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{Wilson2012, +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/Documents/Work/Reference/Mendeley Desktop//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} +} +@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} +} +@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{Neylon2013, +author = {Neylon, Cameron}, +file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Neylon - 2013 - Open access must enable open use.pdf:pdf}, +journal = {Nature}, +pages = {8--9}, +title = {{Open access must enable open use}}, +volume = {492}, +year = {2013} +} +@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{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{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{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{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.}, @@ -36,6 +139,30 @@ @article{Ince2012a volume = {482}, year = {2012} } +@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{VanNoorden2011a, +author = {{Van Noorden}, Richard}, +file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Van Noorden - 2011 - The trouble with retractions.pdf:pdf}, +journal = {Nature}, +pages = {6--8}, +title = {{The trouble with retractions}}, +year = {2011} +} @article{Prlic2012b, author = {Prli\'{c}, Andreas and Procter, James B.}, doi = {10.1371/journal.pcbi.1002802}, @@ -52,6 +179,38 @@ @article{Prlic2012b volume = {8}, year = {2012} } +@article{Peng2011, +author = {Peng, Roger D}, +doi = {10.1126/science.1213847}, +file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Peng - 2011 - Reproducible Research in Computational Science.pdf:pdf}, +issn = {0036-8075}, +journal = {Science}, +month = dec, +number = {6060}, +pages = {1226--1227}, +title = {{Reproducible Research in Computational Science}}, +url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1213847}, +volume = {334}, +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{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}, @@ -71,59 +230,6 @@ @article{Schultheiss2011 volume = {6}, year = {2011} } -@article{Neylon2013, -author = {Neylon, Cameron}, -file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Neylon - 2013 - Open access must enable open use.pdf:pdf}, -journal = {Nature}, -pages = {8--9}, -title = {{Open access must enable open use}}, -volume = {492}, -year = {2013} -} -@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{Wilson2012, -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/Documents/Work/Reference/Mendeley Desktop//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{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} -} @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}, @@ -159,63 +265,33 @@ @article{Begley2012 volume = {483}, year = {2012} } -@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}, +@article{Piwowar2013, +author = {Piwowar, Heather}, +doi = {10.1038/493159a}, +file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/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{Peng2011, -author = {Peng, Roger D}, -doi = {10.1126/science.1213847}, -file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Peng - 2011 - Reproducible Research in Computational Science.pdf:pdf}, +@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 = dec, -number = {6060}, -pages = {1226--1227}, -title = {{Reproducible Research in Computational Science}}, -url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1213847}, -volume = {334}, -year = {2011} -} -@article{VanNoorden2011a, -author = {{Van Noorden}, Richard}, -file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/Van Noorden - 2011 - The trouble with retractions.pdf:pdf}, -journal = {Nature}, -pages = {6--8}, -title = {{The trouble with retractions}}, -year = {2011} -} -@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{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}, +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{niedermeyer2012, @@ -234,75 +310,6 @@ @article{niedermeyer2012 volume = {7}, year = {2012} } -@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{Piwowar2013, -author = {Piwowar, Heather}, -doi = {10.1038/493159a}, -file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop/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} -} -@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} -} -@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{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{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{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}, @@ -319,21 +326,6 @@ @article{Whitlock2010a volume = {175}, year = {2010} } -@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{Piwowar2007a, author = {Piwowar, H A and Day, Roger S and Fridsma, B}, file = {:Users/karthik/Documents/Work/Reference/Mendeley Desktop//Piwowar et al. - 2007 - Sharing Detailed Research Data Is Associated with Increased Citation Rate.pdf:pdf}, @@ -341,20 +333,28 @@ @article{Piwowar2007a title = {{Sharing Detailed Research Data Is Associated with Increased Citation Rate}}, year = {2007} } -@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{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} +} +@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{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.},