# coding: utf-8
from snowballing.models import *
from snowballing import dbindex
dbindex.last_citation_file = dbindex.this_file(__file__)

from ..work.y1991 import descartes1991a
from ..work.y1992 import claerbout1992a
from ..work.y1995 import buckheit1995a
from ..work.y1998 import newham1998a
from ..work.y1999 import halpin1999a
from ..work.y1999 import mylopoulos1999a
from ..work.y2002 import lerdorf2002a
from ..work.y2003 import agrawal2003a
from ..work.y2003 import angelov2003a
from ..work.y2003 import bezivin2003a
from ..work.y2003 import cuban2003a
from ..work.y2005 import barrett2005a
from ..work.y2005 import margaria2005a
from ..work.y2006 import steffen2006a
from ..work.y2006 import winter2006a
from ..work.y2006 import zhu2006a
from ..work.y2007 import biermann2007a
from ..work.y2007 import geiger2007a
from ..work.y2007 import brand2007a
from ..work.y2007 import chen2007a
from ..work.y2007 import dittner2007a
from ..work.y2007 import jensen2007a
from ..work.y2007 import piwowar2007a
from ..work.y2007 import agtive2007a
from ..work.y2007 import rensink2007a
from ..work.y2008 import decker2008a
from ..work.y2008 import gorp2008a
from ..work.y2008 import hong2008a
from ..work.y2008 import kurp2008a
from ..work.y2008 import varro2008a
from ..work.y2008 import vaquero2008a
from ..work.y2009 import buyya2009a
from ..work.y2009 import deelman2009a
from ..work.y2009 import donoho2009a
from ..work.y2009 import fomel2009a
from ..work.y2009 import jensen2009a
from ..work.y2009 import keahey2009a
from ..work.y2009 import nurmi2009a
from ..work.y2009 import stodden2009a
from ..work.y2009 import vandewalle2009a
from ..work.y2009 import wang2009a
from ..work.y2010 import bezivin2010a
from ..work.y2010 import gorp2010a


DB(Citation(
    gorp2010a, agrawal2003a, ref="[1]",
    contexts=[
        "In the graph transformation domain, GReAT [1] for examplerequires users to register for and install different partsof a tool chain manually",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Amazon Elastic Compute Cloud (Amazon EC2)", "http://aws.amazon.com/ec2/#pricing"),
    ref="[2]",
    contexts=[
        "Amazon EC2 [2]",
        
    ],
    accessed="2009",
))

DB(Citation(
    gorp2010a,
    Site("A UML profile for data modeling", "http://www.agiledata.org/essays/umlDataModelingProfile.html"),
    ref="[3]",
    contexts=[
        "Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].",
        
    ],
    accessed="2009",
))

DB(Citation(
    gorp2010a, angelov2003a, ref="[4]",
    contexts=[
        "In our ongoing work,we are investigating how this trust relationship can be supportedby electronic contracts that are based on a new licensetype [4].",
        
    ],
))

DB(Citation(
    gorp2010a, barrett2005a, ref="[5]",
    contexts=[
        "The web server communicates with these machinesvia a secure protocol (SSH [5]).",
        
    ],
))

DB(Citation(
    gorp2010a, bezivin2003a, ref="[6]",
    contexts=[
        "In fact, often articles are published before the underlying softwareis ready for distribution under any license (see [6] foran example from the model transformation domain).",
        
    ],
))

DB(Citation(
    gorp2010a, bezivin2010a, ref="[7]",
    contexts=[
        "The repository has already beenmoved due to intellectual property issues with the Eclipseinitiative [7].",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, biermann2007a, ref="[8]",
    contexts=[
        ". Even tools based on the Eclipseintegration platform often require readers to install pluginsfrom various sources (see [8] for an example from the modeltransformation domain).",
        
    ],
))

DB(Citation(
    gorp2010a, buckheit1995a, ref="[9]",
    contexts=[
        "This may haveinspired Donoho et al. to develop the WaveLab library [9,18].",
        ". If one were interested in a figure, one would clickon it with a mouse, and a new window would instantlyappear, containing the code that the author of the articleused to create the figure. [9]",
        "Wavelab,Madagascar[9,19,20]",
        
    ],
))

DB(Citation(
    gorp2010a, buyya2009a, ref="[10]",
    contexts=[
        "Buyya et al. point tovarious industrial sources to motivate the economical impactof the paradigm and derive the following running definition:“A Cloud is a type of parallel and distributed systemconsisting of a collection of inter-connected and virtualisedcomputers that are dynamically provisioned and presented asone or more unified computing resources based on servicelevelagreements established through negotiation betweenthe service provider and consumers.” [10].",
        
    ],
))

DB(Citation(
    gorp2010a, chen2007a, ref="[11]",
    contexts=[
        "Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].",
        
    ],
))

DB(Citation(
    gorp2010a, claerbout1992a, ref="[12]",
    contexts=[
        "Probably the most influential contribution to computationalresearch reproducibility was developed in the geophysicsdomain, by the team of Claerbout between 1990 and1995 [12].",
        
    ],
))

DB(Citation(
    gorp2010a, cuban2003a, ref="[13]",
    contexts=[
        "WAN-Deployable As an academic research cloud,SHARE can rely on academic infrastructure, that islargely underused in most cases [13].",
        
    ],
))

DB(Citation(
    gorp2010a, decker2008a, ref="[14]",
    contexts=[
        "At level 4, the installation of a modeling and transformationenvironment is fully automatic (or the tool runs from abrowser, as presented in [14]).",
        
    ],
))

DB(Citation(
    gorp2010a, deelman2009a, ref="[15]",
    contexts=[
        "Executing longrunningjobs according to SLAs is a typical scenario inhigh-performance computing in general and in e-Science inparticular [15].",
        
    ],
))

DB(Citation(
    gorp2010a, descartes1991a, ref="[16]",
    contexts=[
        "Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].",
        
    ],
))

DB(Citation(
    gorp2010a, dittner2007a, ref="[17]",
    contexts=[
        "For the second edition of the contest, the organizers aimedto anticipate reproducibility problems by giving participantsaccess to virtual machines (VMs [17]) running on a localserver during the workshop. I",
        "From a platform perspective, SHARE relies on Apacheas a web container, MySQL as a database engine, and VirtualBoxas a hypervisor [17].",
        
    ],
))

DB(Citation(
    gorp2010a, donoho2009a, ref="[18]",
    contexts=[
        "This may haveinspired Donoho et al. to develop the WaveLab library [9,18].",
        "Moreover, evenif a community adopts a standard platform (such as MATLABin the signal-processing domain [18]), we advocate thatdemonstrations should be made available via a platform suchas SHARE, because (1) results should be reproducible withminimal effort by readers from outside that community too,and (2) because of the durability concern.",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Madagascar—reproducible documents", "http://www.reproducibility.org/wiki/Reproducible_Documents"),
    ref="[19]",
    contexts=[
        "Wavelab (and similar successors such as Madagascar [19]) isan online repository of research code and data, organized byresearch article.",
        "Wavelab,Madagascar[9,19,20]",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, fomel2009a, ref="[20]",
    contexts=[
        "Regarding durability, we support Claerbout’s observationthat every platform eventually becomes obsolete [20]. S",
        "Wavelab,Madagascar[9,19,20]",
        
    ],
))


DB(Citation(
    gorp2010a, geiger2007a, ref="[21]",
    contexts=[
        "In this context, uncontrolled updatesfrom third-party components often lead to inconsistenciessome years after the related article was published (see [21]for an example from the graph-based software engineeringdomain).",
        
    ],
))

DB(Citation(
    gorp2010a, halpin1999a, ref="[22]",
    contexts=[
        "Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].",
        
    ],
))

DB(Citation(
    gorp2010a, hong2008a, ref="[23]",
    contexts=[
        "The third bannerintegrates with a website for collaborative bookmarkingand tagging [23].",
        
    ],
))

DB(Citation(
    gorp2010a, jensen2009a, ref="[24]",
    contexts=[
        "The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].",
        
    ],
))

DB(Citation(
    gorp2010a, jensen2007a, ref="[25]",
    contexts=[
        "The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].",
        
    ],
))

DB(Citation(
    gorp2010a, keahey2009a, ref="[26]",
    contexts=[
        "As a running example, the authors dynamicallyaggregate computational resources from three different universitiesto satisfy the service level agreements (SLAs) forheavyweight biomedical computations [26].",
        "Nimbus [26], Eucalyptus [34], GVE [34]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Wink", "http://www.debugmode.com/wink/"),
    ref="[27]",
    contexts=[
        "This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, kurp2008a, ref="[28]",
    contexts=[
        "Notice that thelatter property enables SHARE administrators to keep someservers shut down outside peak hours (or days), in order tosave energy or perform maintenance tasks [28].",
        
    ],
))

DB(Citation(
    gorp2010a, lerdorf2002a, ref="[29]",
    contexts=[
        "The website is implementedin PHP [29]",
        
    ],
))

DB(Citation(
    gorp2010a, margaria2005a, ref="[30]",
    contexts=[
        "Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).",
        "ETI, dETI, jETI[30,32,42]",
        
    ],
))

DB(Citation(
    gorp2010a, mylopoulos1999a, ref="[31]",
    contexts=[
        "Besides these functional requirements, the system wasimplemented with the following non-functional requirements(NFRs [31]) in mind:",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("How to setup a jETI service provider (jETI server)", "http://jabc.cs.tu-dortmund.de/manual/index.php/JETI#Additional_Documentation"),
    ref="[32]",
    contexts=[
        "Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).",
        "ETI, dETI, jETI[30,32,42]",
        
    ],
    accessed="June 2006",
))

DB(Citation(
    gorp2010a, newham1998a, ref="[33]",
    contexts=[
        "The communication between web andvirtual machine servers is realized via Bash cron jobs [33].",
        
    ],
))

DB(Citation(
    gorp2010a, nurmi2009a, ref="[34]",
    contexts=[
        "Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.",
        "Nimbus [26], Eucalyptus [34], GVE [34]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("3TU Data Centre", "http://datacentrum.3tu.nl/"),
    ref="[35]",
    contexts=[
        "So far, the scarcest resource ishard drive space and we are working with an academic partnerto address that [35].",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a,
    Site("Open source licenses by category", "http://www.opensource.org/licenses/category"),
    ref="[36]",
    contexts=[
        "Open source [36]",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a,
    Site("Research data! Who cares?", "http://w3.tue.nl/nl/diensten/bib/over/minisymposium/"),
    ref="[37]",
    contexts=[
        "Additionally,we wish to thank Leon Osinski for organizing an excellentworkshop related to reproducible research [37].",
        
    ],
    accessed="Sept 2009",
))

DB(Citation(
    gorp2010a, piwowar2007a, ref="[38]",
    contexts=[
        "Similarly, Piwowar et al. [38] have examined the citationhistory of 85 biomedical publications",
        
    ],
))

DB(Citation(
    gorp2010a, rensink2007a, ref="[39]",
    contexts=[
        "Coming back to the transformationtool contest, these risks were exposed most in thefirst edition of the event [39].",
        
    ],
))

DB(Citation(
    gorp2010a, agtive2007a, ref="[40]",
    contexts=[
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Fences", "http://en.wikipedia.org/wiki/Fences_(software)"),
    ref="[41]",
    contexts=[
        "This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, steffen2006a, ref="[42]",
    contexts=[
        "Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).",
        "ETI, dETI, jETI[30,32,42]",
        
    ],
))

DB(Citation(
    gorp2010a, stodden2009a, ref="[43]",
    contexts=[
        "Apart from the technical aspects mentioned above, Stoddenanalyzes different license forms (for media as wellas software) with computational science reproducibility inmind [43].",
        "New licensetypes [43]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Top 10 RDP Protocol Misconceptions—part 2", "http://blogs.msdn.com/rds/archive/2009/03/12/top-10-rdp-protocol-misconceptions-part-2.aspx"),
    ref="[44]",
    contexts=[
        "The underlying protocol (Remote Desktop Protocol, or RDP)supports modern encryption methods [44].",
        
    ],
    accessed="Mar 2009",
))

DB(Citation(
    gorp2010a, brand2007a, ref="[45]",
    contexts=[
        "In a special issue on experimental software engineering, van den Brand observes that “the pressure to publish is much higher than the pressure to develop good software” [45].",
        "Van den Brand confirms that, “in physics or chemistry papersabout experiments contain a lot of technical details in order tofacilitate other researchers to replay the experiments in orderto validate the results described in these papers”, and advocatesthat in software engineering, more attention should bepaid to reviewing the software artifacts that support researchcontributions [45].",
        "Van den Brand indicates that “more and more computerscientists use the open source community to distributetheir tools. In this way it is not necessary to reimplementtools, only to download and install them.” [45]. H",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("SHARE image with CPNtools and behavioral models of SHARE", "http://is.ieis.tue.nl/staff/pvgorp/share/?page=ConfigureNewSession&vdi=ModelsOfSHARE_v1.vdi"),
    ref="[46]",
    contexts=[
        "Therefore, users are invited to connect to a SHARE demothat automatically starts the right modeling tool and loadsthe simulation model for evaluation purposes [46]",
        "By usingcitations such as [46] (cfr., discussion of Fig. 5), authors canenable readers to jump directly to the optimal environment.",
        
    ],
    accessed="Feb 2009",
))

DB(Citation(
    gorp2010a,
    Site("VRDP connection count bug? (wrong value of mcVRDPC lients)", "http://www.virtualbox.org/ticket/4655"),
    ref="[47]",
    contexts=[
        "Apart from a minor bug (see [47]) the software performedremarkably well even for users on lower bandwidth wirelessnetworks.",
        
    ],
    accessed="July 2009",
))

DB(Citation(
    gorp2010a,
    Site("SHARE group with basic operating system images", "http://is.ieis.tue.nl/staff/pvgorp/share/?page=Signup&bundlename=Operating\%20Systems"),
    ref="[48]",
    contexts=[
        "John signs up to the group “Operating Systems”[48],using his e-mail address john.doe@uni.ac.eu and a passwordof his choice.",
        
    ],
    accessed="Mar 2009",
))

DB(Citation(
    gorp2010a,
    Site("SHARE–Sharing Hosted Autonomous Research Environments", "http://is.ieis.tue.nl/staff/pvgorp/share/"),
    ref="[49]",
    contexts=[
        "More specifically, they describewhy we are applying cloud-computing technologies, how weare integrating them, and how others can use our supportiveinformation system—SHARE (Sharing Hosted AutonomousResearch Environments [49]).",
        "This article describes SHARE [49], a system that hasbeen constructed for solving such organizational problems.",
        
    ],
    accessed="2009",
))

DB(Citation(
    gorp2010a,
    Site("SHARE documentation", "http://fmt.cs.utwente.nl/redmine/wiki/5/SHARE"),
    ref="[50]",
    contexts=[
        "John can now evaluate the operating systems that areavailable in SHARE by default, following the stepsdescribed in Sect. 3.1 or following the online documentation[50].S",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, gorp2008a, ref="[51]",
    contexts=[
        "In fact, we are also working on a UML-based techniqueto model transformation interoperability [51]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Call for papers: STTT special section on Graph-Based tool comparison", "http://www.fots.ua.ac.be/events/grabats2008/sttt-section-cfp.pdf"),
    ref="[52]",
    contexts=[
        "Additionally, itturned out that too much effort was required from the organizersas well as from participants when applying this approachover the Internet, for example when editing a journal [52].",
        "It should be noted that the graphbasedtools contest involved several case studies, some ofwhich could be solved in advance (offline case studies) andone of which had to be solved during the workshop (thelive contest) [52]",
        "Again,in the context of the transformation tool contest, we haveinvited all participants to investigate: (1) how to call the relevantpart of their tool with some standard inputs, (2) howto get the transformed results (and some statistics), and (3)how to pass that to a visualizer, which could be a serviceitself [52].",
        
    ],
    accessed="Nov 2008",
))

DB(Citation(
    gorp2010a, vandewalle2009a, ref="[53]",
    contexts=[
        "Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].",
        "“Can we suppose that programssuch as MATLAB, Mathematica, or even Windows areavailable, or should we constrain ourselves to the use ofopen-source programs such as R, Octave, or SciLab in aLinux environment?” [53]",
        "“There exists a largevariety of computer platforms, and making even somesimple code work on most platforms requires a lot ofwork. We need to balance the ease of use for a readerwith the additional work to be done after development ofthe algorithms and initial code. ... ” [53]",
        "“In this tradeoff, it is also important to considerthe long-term availability of a platform. Due to changes indata formats, compilers, and research platforms, researchis often only reproducible in a limited time window.” [53]",
        
    ],
))

DB(Citation(
    gorp2010a, vaquero2008a, ref="[54]",
    contexts=[
        "“Cloud computing” is an emerging paradigm for the provisionof computing infrastructure [54].",
        "This conforms with the definitionof cloud computing as “the user-friendly version ofgrid computing”, in which case grid computing is definedas “reduce computing costs and increase flexibility and reliabilityby using third-party operated hardware” [54].",
        
    ],
))

DB(Citation(
    gorp2010a, varro2008a, ref="[55]",
    contexts=[
        "At the timeof writing this article (2 years after the first contest), the disadvantagesof this approach are clear: it is already impossibleto reproduce the submissions to a particular case study [55]within one man-week",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("VMware ESXi", "http://www.vmware.com/"),
    ref="[56]",
    contexts=[
        ". Interestingly, VirtualBox can evenuse virtual machine images from other hypervisor tools suchas VMware [56].",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, wang2009a, ref="[57]",
    contexts=[
        "Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Hwang woo-suk-wikipedia, the free encyclopedia", "http://en.wikipedia.org/wiki/Hwang_Woo-Suk"),
    ref="[58]",
    contexts=[
        "Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].",
        
    ],
    accessed="2006",
))

DB(Citation(
    gorp2010a, winter2006a, ref="[59]",
    contexts=[
        "Figure 2 shows an enterprise architectural model of SHARE.Following Winter and Fischer’s terminology [59], the diagramaggregates elements from the infrastructure layer(machine and network elements) and the software layer.",
        
    ],
))

DB(Citation(
    gorp2010a, zhu2006a, ref="[60]",
    contexts=[
        "Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].",
        
    ],
))
b2952e6ac0404af09d1f45f3f8a9135afe51536c
<mask token>

<mask token>
DB(Citation(gorp2010a, agrawal2003a, ref='[1]', contexts=[
    'In the graph transformation domain, GReAT [1] for examplerequires users to register for and install different partsof a tool chain manually'
    ]))
DB(Citation(gorp2010a, Site('Amazon Elastic Compute Cloud (Amazon EC2)',
    'http://aws.amazon.com/ec2/#pricing'), ref='[2]', contexts=[
    'Amazon EC2 [2]'], accessed='2009'))
DB(Citation(gorp2010a, Site('A UML profile for data modeling',
    'http://www.agiledata.org/essays/umlDataModelingProfile.html'), ref=
    '[3]', contexts=[
    'Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].'
    ], accessed='2009'))
DB(Citation(gorp2010a, angelov2003a, ref='[4]', contexts=[
    'In our ongoing work,we are investigating how this trust relationship can be supportedby electronic contracts that are based on a new licensetype [4].'
    ]))
DB(Citation(gorp2010a, barrett2005a, ref='[5]', contexts=[
    'The web server communicates with these machinesvia a secure protocol (SSH [5]).'
    ]))
DB(Citation(gorp2010a, bezivin2003a, ref='[6]', contexts=[
    'In fact, often articles are published before the underlying softwareis ready for distribution under any license (see [6] foran example from the model transformation domain).'
    ]))
DB(Citation(gorp2010a, bezivin2010a, ref='[7]', contexts=[
    'The repository has already beenmoved due to intellectual property issues with the Eclipseinitiative [7].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, biermann2007a, ref='[8]', contexts=[
    '. Even tools based on the Eclipseintegration platform often require readers to install pluginsfrom various sources (see [8] for an example from the modeltransformation domain).'
    ]))
DB(Citation(gorp2010a, buckheit1995a, ref='[9]', contexts=[
    'This may haveinspired Donoho et al. to develop the WaveLab library [9,18].'
    ,
    '. If one were interested in a figure, one would clickon it with a mouse, and a new window would instantlyappear, containing the code that the author of the articleused to create the figure. [9]'
    , 'Wavelab,Madagascar[9,19,20]']))
DB(Citation(gorp2010a, buyya2009a, ref='[10]', contexts=[
    'Buyya et al. point tovarious industrial sources to motivate the economical impactof the paradigm and derive the following running definition:“A Cloud is a type of parallel and distributed systemconsisting of a collection of inter-connected and virtualisedcomputers that are dynamically provisioned and presented asone or more unified computing resources based on servicelevelagreements established through negotiation betweenthe service provider and consumers.” [10].'
    ]))
DB(Citation(gorp2010a, chen2007a, ref='[11]', contexts=[
    'Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].'
    ]))
DB(Citation(gorp2010a, claerbout1992a, ref='[12]', contexts=[
    'Probably the most influential contribution to computationalresearch reproducibility was developed in the geophysicsdomain, by the team of Claerbout between 1990 and1995 [12].'
    ]))
DB(Citation(gorp2010a, cuban2003a, ref='[13]', contexts=[
    'WAN-Deployable As an academic research cloud,SHARE can rely on academic infrastructure, that islargely underused in most cases [13].'
    ]))
DB(Citation(gorp2010a, decker2008a, ref='[14]', contexts=[
    'At level 4, the installation of a modeling and transformationenvironment is fully automatic (or the tool runs from abrowser, as presented in [14]).'
    ]))
DB(Citation(gorp2010a, deelman2009a, ref='[15]', contexts=[
    'Executing longrunningjobs according to SLAs is a typical scenario inhigh-performance computing in general and in e-Science inparticular [15].'
    ]))
DB(Citation(gorp2010a, descartes1991a, ref='[16]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ]))
DB(Citation(gorp2010a, dittner2007a, ref='[17]', contexts=[
    'For the second edition of the contest, the organizers aimedto anticipate reproducibility problems by giving participantsaccess to virtual machines (VMs [17]) running on a localserver during the workshop. I'
    ,
    'From a platform perspective, SHARE relies on Apacheas a web container, MySQL as a database engine, and VirtualBoxas a hypervisor [17].'
    ]))
DB(Citation(gorp2010a, donoho2009a, ref='[18]', contexts=[
    'This may haveinspired Donoho et al. to develop the WaveLab library [9,18].'
    ,
    'Moreover, evenif a community adopts a standard platform (such as MATLABin the signal-processing domain [18]), we advocate thatdemonstrations should be made available via a platform suchas SHARE, because (1) results should be reproducible withminimal effort by readers from outside that community too,and (2) because of the durability concern.'
    ]))
DB(Citation(gorp2010a, Site('Madagascar—reproducible documents',
    'http://www.reproducibility.org/wiki/Reproducible_Documents'), ref=
    '[19]', contexts=[
    'Wavelab (and similar successors such as Madagascar [19]) isan online repository of research code and data, organized byresearch article.'
    , 'Wavelab,Madagascar[9,19,20]'], accessed='Mar 2010'))
DB(Citation(gorp2010a, fomel2009a, ref='[20]', contexts=[
    'Regarding durability, we support Claerbout’s observationthat every platform eventually becomes obsolete [20]. S'
    , 'Wavelab,Madagascar[9,19,20]']))
DB(Citation(gorp2010a, geiger2007a, ref='[21]', contexts=[
    'In this context, uncontrolled updatesfrom third-party components often lead to inconsistenciessome years after the related article was published (see [21]for an example from the graph-based software engineeringdomain).'
    ]))
DB(Citation(gorp2010a, halpin1999a, ref='[22]', contexts=[
    'Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].'
    ]))
DB(Citation(gorp2010a, hong2008a, ref='[23]', contexts=[
    'The third bannerintegrates with a website for collaborative bookmarkingand tagging [23].'
    ]))
DB(Citation(gorp2010a, jensen2009a, ref='[24]', contexts=[
    'The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].'
    ]))
DB(Citation(gorp2010a, jensen2007a, ref='[25]', contexts=[
    'The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].'
    ]))
DB(Citation(gorp2010a, keahey2009a, ref='[26]', contexts=[
    'As a running example, the authors dynamicallyaggregate computational resources from three different universitiesto satisfy the service level agreements (SLAs) forheavyweight biomedical computations [26].'
    , 'Nimbus [26], Eucalyptus [34], GVE [34]']))
DB(Citation(gorp2010a, Site('Wink', 'http://www.debugmode.com/wink/'), ref=
    '[27]', contexts=[
    'This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, kurp2008a, ref='[28]', contexts=[
    'Notice that thelatter property enables SHARE administrators to keep someservers shut down outside peak hours (or days), in order tosave energy or perform maintenance tasks [28].'
    ]))
DB(Citation(gorp2010a, lerdorf2002a, ref='[29]', contexts=[
    'The website is implementedin PHP [29]']))
DB(Citation(gorp2010a, margaria2005a, ref='[30]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]']))
DB(Citation(gorp2010a, mylopoulos1999a, ref='[31]', contexts=[
    'Besides these functional requirements, the system wasimplemented with the following non-functional requirements(NFRs [31]) in mind:'
    ]))
DB(Citation(gorp2010a, Site(
    'How to setup a jETI service provider (jETI server)',
    'http://jabc.cs.tu-dortmund.de/manual/index.php/JETI#Additional_Documentation'
    ), ref='[32]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]'], accessed='June 2006'))
DB(Citation(gorp2010a, newham1998a, ref='[33]', contexts=[
    'The communication between web andvirtual machine servers is realized via Bash cron jobs [33].'
    ]))
DB(Citation(gorp2010a, nurmi2009a, ref='[34]', contexts=[
    'Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.'
    , 'Nimbus [26], Eucalyptus [34], GVE [34]']))
DB(Citation(gorp2010a, Site('3TU Data Centre', 'http://datacentrum.3tu.nl/'
    ), ref='[35]', contexts=[
    'So far, the scarcest resource ishard drive space and we are working with an academic partnerto address that [35].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, Site('Open source licenses by category',
    'http://www.opensource.org/licenses/category'), ref='[36]', contexts=[
    'Open source [36]'], accessed='Mar 2010'))
DB(Citation(gorp2010a, Site('Research data! Who cares?',
    'http://w3.tue.nl/nl/diensten/bib/over/minisymposium/'), ref='[37]',
    contexts=[
    'Additionally,we wish to thank Leon Osinski for organizing an excellentworkshop related to reproducible research [37].'
    ], accessed='Sept 2009'))
DB(Citation(gorp2010a, piwowar2007a, ref='[38]', contexts=[
    'Similarly, Piwowar et al. [38] have examined the citationhistory of 85 biomedical publications'
    ]))
DB(Citation(gorp2010a, rensink2007a, ref='[39]', contexts=[
    'Coming back to the transformationtool contest, these risks were exposed most in thefirst edition of the event [39].'
    ]))
DB(Citation(gorp2010a, agtive2007a, ref='[40]', contexts=[]))
DB(Citation(gorp2010a, Site('Fences',
    'http://en.wikipedia.org/wiki/Fences_(software)'), ref='[41]', contexts
    =[
    'This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, steffen2006a, ref='[42]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]']))
DB(Citation(gorp2010a, stodden2009a, ref='[43]', contexts=[
    'Apart from the technical aspects mentioned above, Stoddenanalyzes different license forms (for media as wellas software) with computational science reproducibility inmind [43].'
    , 'New licensetypes [43]']))
DB(Citation(gorp2010a, Site('Top 10 RDP Protocol Misconceptions—part 2',
    'http://blogs.msdn.com/rds/archive/2009/03/12/top-10-rdp-protocol-misconceptions-part-2.aspx'
    ), ref='[44]', contexts=[
    'The underlying protocol (Remote Desktop Protocol, or RDP)supports modern encryption methods [44].'
    ], accessed='Mar 2009'))
DB(Citation(gorp2010a, brand2007a, ref='[45]', contexts=[
    'In a special issue on experimental software engineering, van den Brand observes that “the pressure to publish is much higher than the pressure to develop good software” [45].'
    ,
    'Van den Brand confirms that, “in physics or chemistry papersabout experiments contain a lot of technical details in order tofacilitate other researchers to replay the experiments in orderto validate the results described in these papers”, and advocatesthat in software engineering, more attention should bepaid to reviewing the software artifacts that support researchcontributions [45].'
    ,
    'Van den Brand indicates that “more and more computerscientists use the open source community to distributetheir tools. In this way it is not necessary to reimplementtools, only to download and install them.” [45]. H'
    ]))
DB(Citation(gorp2010a, Site(
    'SHARE image with CPNtools and behavioral models of SHARE',
    'http://is.ieis.tue.nl/staff/pvgorp/share/?page=ConfigureNewSession&vdi=ModelsOfSHARE_v1.vdi'
    ), ref='[46]', contexts=[
    'Therefore, users are invited to connect to a SHARE demothat automatically starts the right modeling tool and loadsthe simulation model for evaluation purposes [46]'
    ,
    'By usingcitations such as [46] (cfr., discussion of Fig. 5), authors canenable readers to jump directly to the optimal environment.'
    ], accessed='Feb 2009'))
DB(Citation(gorp2010a, Site(
    'VRDP connection count bug? (wrong value of mcVRDPC lients)',
    'http://www.virtualbox.org/ticket/4655'), ref='[47]', contexts=[
    'Apart from a minor bug (see [47]) the software performedremarkably well even for users on lower bandwidth wirelessnetworks.'
    ], accessed='July 2009'))
DB(Citation(gorp2010a, Site(
    'SHARE group with basic operating system images',
    'http://is.ieis.tue.nl/staff/pvgorp/share/?page=Signup&bundlename=Operating\\%20Systems'
    ), ref='[48]', contexts=[
    'John signs up to the group “Operating Systems”[48],using his e-mail address john.doe@uni.ac.eu and a passwordof his choice.'
    ], accessed='Mar 2009'))
DB(Citation(gorp2010a, Site(
    'SHARE–Sharing Hosted Autonomous Research Environments',
    'http://is.ieis.tue.nl/staff/pvgorp/share/'), ref='[49]', contexts=[
    'More specifically, they describewhy we are applying cloud-computing technologies, how weare integrating them, and how others can use our supportiveinformation system—SHARE (Sharing Hosted AutonomousResearch Environments [49]).'
    ,
    'This article describes SHARE [49], a system that hasbeen constructed for solving such organizational problems.'
    ], accessed='2009'))
DB(Citation(gorp2010a, Site('SHARE documentation',
    'http://fmt.cs.utwente.nl/redmine/wiki/5/SHARE'), ref='[50]', contexts=
    [
    'John can now evaluate the operating systems that areavailable in SHARE by default, following the stepsdescribed in Sect. 3.1 or following the online documentation[50].S'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, gorp2008a, ref='[51]', contexts=[
    'In fact, we are also working on a UML-based techniqueto model transformation interoperability [51]'
    ]))
DB(Citation(gorp2010a, Site(
    'Call for papers: STTT special section on Graph-Based tool comparison',
    'http://www.fots.ua.ac.be/events/grabats2008/sttt-section-cfp.pdf'),
    ref='[52]', contexts=[
    'Additionally, itturned out that too much effort was required from the organizersas well as from participants when applying this approachover the Internet, for example when editing a journal [52].'
    ,
    'It should be noted that the graphbasedtools contest involved several case studies, some ofwhich could be solved in advance (offline case studies) andone of which had to be solved during the workshop (thelive contest) [52]'
    ,
    'Again,in the context of the transformation tool contest, we haveinvited all participants to investigate: (1) how to call the relevantpart of their tool with some standard inputs, (2) howto get the transformed results (and some statistics), and (3)how to pass that to a visualizer, which could be a serviceitself [52].'
    ], accessed='Nov 2008'))
DB(Citation(gorp2010a, vandewalle2009a, ref='[53]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ,
    '“Can we suppose that programssuch as MATLAB, Mathematica, or even Windows areavailable, or should we constrain ourselves to the use ofopen-source programs such as R, Octave, or SciLab in aLinux environment?” [53]'
    ,
    '“There exists a largevariety of computer platforms, and making even somesimple code work on most platforms requires a lot ofwork. We need to balance the ease of use for a readerwith the additional work to be done after development ofthe algorithms and initial code. ... ” [53]'
    ,
    '“In this tradeoff, it is also important to considerthe long-term availability of a platform. Due to changes indata formats, compilers, and research platforms, researchis often only reproducible in a limited time window.” [53]'
    ]))
DB(Citation(gorp2010a, vaquero2008a, ref='[54]', contexts=[
    '“Cloud computing” is an emerging paradigm for the provisionof computing infrastructure [54].'
    ,
    'This conforms with the definitionof cloud computing as “the user-friendly version ofgrid computing”, in which case grid computing is definedas “reduce computing costs and increase flexibility and reliabilityby using third-party operated hardware” [54].'
    ]))
DB(Citation(gorp2010a, varro2008a, ref='[55]', contexts=[
    'At the timeof writing this article (2 years after the first contest), the disadvantagesof this approach are clear: it is already impossibleto reproduce the submissions to a particular case study [55]within one man-week'
    ]))
DB(Citation(gorp2010a, Site('VMware ESXi', 'http://www.vmware.com/'), ref=
    '[56]', contexts=[
    '. Interestingly, VirtualBox can evenuse virtual machine images from other hypervisor tools suchas VMware [56].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, wang2009a, ref='[57]', contexts=[
    'Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.'
    ]))
DB(Citation(gorp2010a, Site(
    'Hwang woo-suk-wikipedia, the free encyclopedia',
    'http://en.wikipedia.org/wiki/Hwang_Woo-Suk'), ref='[58]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ], accessed='2006'))
DB(Citation(gorp2010a, winter2006a, ref='[59]', contexts=[
    'Figure 2 shows an enterprise architectural model of SHARE.Following Winter and Fischer’s terminology [59], the diagramaggregates elements from the infrastructure layer(machine and network elements) and the software layer.'
    ]))
DB(Citation(gorp2010a, zhu2006a, ref='[60]', contexts=[
    'Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].'
    ]))

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DB(Citation(gorp2010a, agrawal2003a, ref='[1]', contexts=[
    'In the graph transformation domain, GReAT [1] for examplerequires users to register for and install different partsof a tool chain manually'
    ]))
DB(Citation(gorp2010a, Site('Amazon Elastic Compute Cloud (Amazon EC2)',
    'http://aws.amazon.com/ec2/#pricing'), ref='[2]', contexts=[
    'Amazon EC2 [2]'], accessed='2009'))
DB(Citation(gorp2010a, Site('A UML profile for data modeling',
    'http://www.agiledata.org/essays/umlDataModelingProfile.html'), ref=
    '[3]', contexts=[
    'Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].'
    ], accessed='2009'))
DB(Citation(gorp2010a, angelov2003a, ref='[4]', contexts=[
    'In our ongoing work,we are investigating how this trust relationship can be supportedby electronic contracts that are based on a new licensetype [4].'
    ]))
DB(Citation(gorp2010a, barrett2005a, ref='[5]', contexts=[
    'The web server communicates with these machinesvia a secure protocol (SSH [5]).'
    ]))
DB(Citation(gorp2010a, bezivin2003a, ref='[6]', contexts=[
    'In fact, often articles are published before the underlying softwareis ready for distribution under any license (see [6] foran example from the model transformation domain).'
    ]))
DB(Citation(gorp2010a, bezivin2010a, ref='[7]', contexts=[
    'The repository has already beenmoved due to intellectual property issues with the Eclipseinitiative [7].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, biermann2007a, ref='[8]', contexts=[
    '. Even tools based on the Eclipseintegration platform often require readers to install pluginsfrom various sources (see [8] for an example from the modeltransformation domain).'
    ]))
DB(Citation(gorp2010a, buckheit1995a, ref='[9]', contexts=[
    'This may haveinspired Donoho et al. to develop the WaveLab library [9,18].'
    ,
    '. If one were interested in a figure, one would clickon it with a mouse, and a new window would instantlyappear, containing the code that the author of the articleused to create the figure. [9]'
    , 'Wavelab,Madagascar[9,19,20]']))
DB(Citation(gorp2010a, buyya2009a, ref='[10]', contexts=[
    'Buyya et al. point tovarious industrial sources to motivate the economical impactof the paradigm and derive the following running definition:“A Cloud is a type of parallel and distributed systemconsisting of a collection of inter-connected and virtualisedcomputers that are dynamically provisioned and presented asone or more unified computing resources based on servicelevelagreements established through negotiation betweenthe service provider and consumers.” [10].'
    ]))
DB(Citation(gorp2010a, chen2007a, ref='[11]', contexts=[
    'Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].'
    ]))
DB(Citation(gorp2010a, claerbout1992a, ref='[12]', contexts=[
    'Probably the most influential contribution to computationalresearch reproducibility was developed in the geophysicsdomain, by the team of Claerbout between 1990 and1995 [12].'
    ]))
DB(Citation(gorp2010a, cuban2003a, ref='[13]', contexts=[
    'WAN-Deployable As an academic research cloud,SHARE can rely on academic infrastructure, that islargely underused in most cases [13].'
    ]))
DB(Citation(gorp2010a, decker2008a, ref='[14]', contexts=[
    'At level 4, the installation of a modeling and transformationenvironment is fully automatic (or the tool runs from abrowser, as presented in [14]).'
    ]))
DB(Citation(gorp2010a, deelman2009a, ref='[15]', contexts=[
    'Executing longrunningjobs according to SLAs is a typical scenario inhigh-performance computing in general and in e-Science inparticular [15].'
    ]))
DB(Citation(gorp2010a, descartes1991a, ref='[16]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ]))
DB(Citation(gorp2010a, dittner2007a, ref='[17]', contexts=[
    'For the second edition of the contest, the organizers aimedto anticipate reproducibility problems by giving participantsaccess to virtual machines (VMs [17]) running on a localserver during the workshop. I'
    ,
    'From a platform perspective, SHARE relies on Apacheas a web container, MySQL as a database engine, and VirtualBoxas a hypervisor [17].'
    ]))
DB(Citation(gorp2010a, donoho2009a, ref='[18]', contexts=[
    'This may haveinspired Donoho et al. to develop the WaveLab library [9,18].'
    ,
    'Moreover, evenif a community adopts a standard platform (such as MATLABin the signal-processing domain [18]), we advocate thatdemonstrations should be made available via a platform suchas SHARE, because (1) results should be reproducible withminimal effort by readers from outside that community too,and (2) because of the durability concern.'
    ]))
DB(Citation(gorp2010a, Site('Madagascar—reproducible documents',
    'http://www.reproducibility.org/wiki/Reproducible_Documents'), ref=
    '[19]', contexts=[
    'Wavelab (and similar successors such as Madagascar [19]) isan online repository of research code and data, organized byresearch article.'
    , 'Wavelab,Madagascar[9,19,20]'], accessed='Mar 2010'))
DB(Citation(gorp2010a, fomel2009a, ref='[20]', contexts=[
    'Regarding durability, we support Claerbout’s observationthat every platform eventually becomes obsolete [20]. S'
    , 'Wavelab,Madagascar[9,19,20]']))
DB(Citation(gorp2010a, geiger2007a, ref='[21]', contexts=[
    'In this context, uncontrolled updatesfrom third-party components often lead to inconsistenciessome years after the related article was published (see [21]for an example from the graph-based software engineeringdomain).'
    ]))
DB(Citation(gorp2010a, halpin1999a, ref='[22]', contexts=[
    'Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].'
    ]))
DB(Citation(gorp2010a, hong2008a, ref='[23]', contexts=[
    'The third bannerintegrates with a website for collaborative bookmarkingand tagging [23].'
    ]))
DB(Citation(gorp2010a, jensen2009a, ref='[24]', contexts=[
    'The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].'
    ]))
DB(Citation(gorp2010a, jensen2007a, ref='[25]', contexts=[
    'The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].'
    ]))
DB(Citation(gorp2010a, keahey2009a, ref='[26]', contexts=[
    'As a running example, the authors dynamicallyaggregate computational resources from three different universitiesto satisfy the service level agreements (SLAs) forheavyweight biomedical computations [26].'
    , 'Nimbus [26], Eucalyptus [34], GVE [34]']))
DB(Citation(gorp2010a, Site('Wink', 'http://www.debugmode.com/wink/'), ref=
    '[27]', contexts=[
    'This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, kurp2008a, ref='[28]', contexts=[
    'Notice that thelatter property enables SHARE administrators to keep someservers shut down outside peak hours (or days), in order tosave energy or perform maintenance tasks [28].'
    ]))
DB(Citation(gorp2010a, lerdorf2002a, ref='[29]', contexts=[
    'The website is implementedin PHP [29]']))
DB(Citation(gorp2010a, margaria2005a, ref='[30]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]']))
DB(Citation(gorp2010a, mylopoulos1999a, ref='[31]', contexts=[
    'Besides these functional requirements, the system wasimplemented with the following non-functional requirements(NFRs [31]) in mind:'
    ]))
DB(Citation(gorp2010a, Site(
    'How to setup a jETI service provider (jETI server)',
    'http://jabc.cs.tu-dortmund.de/manual/index.php/JETI#Additional_Documentation'
    ), ref='[32]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]'], accessed='June 2006'))
DB(Citation(gorp2010a, newham1998a, ref='[33]', contexts=[
    'The communication between web andvirtual machine servers is realized via Bash cron jobs [33].'
    ]))
DB(Citation(gorp2010a, nurmi2009a, ref='[34]', contexts=[
    'Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.'
    , 'Nimbus [26], Eucalyptus [34], GVE [34]']))
DB(Citation(gorp2010a, Site('3TU Data Centre', 'http://datacentrum.3tu.nl/'
    ), ref='[35]', contexts=[
    'So far, the scarcest resource ishard drive space and we are working with an academic partnerto address that [35].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, Site('Open source licenses by category',
    'http://www.opensource.org/licenses/category'), ref='[36]', contexts=[
    'Open source [36]'], accessed='Mar 2010'))
DB(Citation(gorp2010a, Site('Research data! Who cares?',
    'http://w3.tue.nl/nl/diensten/bib/over/minisymposium/'), ref='[37]',
    contexts=[
    'Additionally,we wish to thank Leon Osinski for organizing an excellentworkshop related to reproducible research [37].'
    ], accessed='Sept 2009'))
DB(Citation(gorp2010a, piwowar2007a, ref='[38]', contexts=[
    'Similarly, Piwowar et al. [38] have examined the citationhistory of 85 biomedical publications'
    ]))
DB(Citation(gorp2010a, rensink2007a, ref='[39]', contexts=[
    'Coming back to the transformationtool contest, these risks were exposed most in thefirst edition of the event [39].'
    ]))
DB(Citation(gorp2010a, agtive2007a, ref='[40]', contexts=[]))
DB(Citation(gorp2010a, Site('Fences',
    'http://en.wikipedia.org/wiki/Fences_(software)'), ref='[41]', contexts
    =[
    'This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, steffen2006a, ref='[42]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]']))
DB(Citation(gorp2010a, stodden2009a, ref='[43]', contexts=[
    'Apart from the technical aspects mentioned above, Stoddenanalyzes different license forms (for media as wellas software) with computational science reproducibility inmind [43].'
    , 'New licensetypes [43]']))
DB(Citation(gorp2010a, Site('Top 10 RDP Protocol Misconceptions—part 2',
    'http://blogs.msdn.com/rds/archive/2009/03/12/top-10-rdp-protocol-misconceptions-part-2.aspx'
    ), ref='[44]', contexts=[
    'The underlying protocol (Remote Desktop Protocol, or RDP)supports modern encryption methods [44].'
    ], accessed='Mar 2009'))
DB(Citation(gorp2010a, brand2007a, ref='[45]', contexts=[
    'In a special issue on experimental software engineering, van den Brand observes that “the pressure to publish is much higher than the pressure to develop good software” [45].'
    ,
    'Van den Brand confirms that, “in physics or chemistry papersabout experiments contain a lot of technical details in order tofacilitate other researchers to replay the experiments in orderto validate the results described in these papers”, and advocatesthat in software engineering, more attention should bepaid to reviewing the software artifacts that support researchcontributions [45].'
    ,
    'Van den Brand indicates that “more and more computerscientists use the open source community to distributetheir tools. In this way it is not necessary to reimplementtools, only to download and install them.” [45]. H'
    ]))
DB(Citation(gorp2010a, Site(
    'SHARE image with CPNtools and behavioral models of SHARE',
    'http://is.ieis.tue.nl/staff/pvgorp/share/?page=ConfigureNewSession&vdi=ModelsOfSHARE_v1.vdi'
    ), ref='[46]', contexts=[
    'Therefore, users are invited to connect to a SHARE demothat automatically starts the right modeling tool and loadsthe simulation model for evaluation purposes [46]'
    ,
    'By usingcitations such as [46] (cfr., discussion of Fig. 5), authors canenable readers to jump directly to the optimal environment.'
    ], accessed='Feb 2009'))
DB(Citation(gorp2010a, Site(
    'VRDP connection count bug? (wrong value of mcVRDPC lients)',
    'http://www.virtualbox.org/ticket/4655'), ref='[47]', contexts=[
    'Apart from a minor bug (see [47]) the software performedremarkably well even for users on lower bandwidth wirelessnetworks.'
    ], accessed='July 2009'))
DB(Citation(gorp2010a, Site(
    'SHARE group with basic operating system images',
    'http://is.ieis.tue.nl/staff/pvgorp/share/?page=Signup&bundlename=Operating\\%20Systems'
    ), ref='[48]', contexts=[
    'John signs up to the group “Operating Systems”[48],using his e-mail address john.doe@uni.ac.eu and a passwordof his choice.'
    ], accessed='Mar 2009'))
DB(Citation(gorp2010a, Site(
    'SHARE–Sharing Hosted Autonomous Research Environments',
    'http://is.ieis.tue.nl/staff/pvgorp/share/'), ref='[49]', contexts=[
    'More specifically, they describewhy we are applying cloud-computing technologies, how weare integrating them, and how others can use our supportiveinformation system—SHARE (Sharing Hosted AutonomousResearch Environments [49]).'
    ,
    'This article describes SHARE [49], a system that hasbeen constructed for solving such organizational problems.'
    ], accessed='2009'))
DB(Citation(gorp2010a, Site('SHARE documentation',
    'http://fmt.cs.utwente.nl/redmine/wiki/5/SHARE'), ref='[50]', contexts=
    [
    'John can now evaluate the operating systems that areavailable in SHARE by default, following the stepsdescribed in Sect. 3.1 or following the online documentation[50].S'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, gorp2008a, ref='[51]', contexts=[
    'In fact, we are also working on a UML-based techniqueto model transformation interoperability [51]'
    ]))
DB(Citation(gorp2010a, Site(
    'Call for papers: STTT special section on Graph-Based tool comparison',
    'http://www.fots.ua.ac.be/events/grabats2008/sttt-section-cfp.pdf'),
    ref='[52]', contexts=[
    'Additionally, itturned out that too much effort was required from the organizersas well as from participants when applying this approachover the Internet, for example when editing a journal [52].'
    ,
    'It should be noted that the graphbasedtools contest involved several case studies, some ofwhich could be solved in advance (offline case studies) andone of which had to be solved during the workshop (thelive contest) [52]'
    ,
    'Again,in the context of the transformation tool contest, we haveinvited all participants to investigate: (1) how to call the relevantpart of their tool with some standard inputs, (2) howto get the transformed results (and some statistics), and (3)how to pass that to a visualizer, which could be a serviceitself [52].'
    ], accessed='Nov 2008'))
DB(Citation(gorp2010a, vandewalle2009a, ref='[53]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ,
    '“Can we suppose that programssuch as MATLAB, Mathematica, or even Windows areavailable, or should we constrain ourselves to the use ofopen-source programs such as R, Octave, or SciLab in aLinux environment?” [53]'
    ,
    '“There exists a largevariety of computer platforms, and making even somesimple code work on most platforms requires a lot ofwork. We need to balance the ease of use for a readerwith the additional work to be done after development ofthe algorithms and initial code. ... ” [53]'
    ,
    '“In this tradeoff, it is also important to considerthe long-term availability of a platform. Due to changes indata formats, compilers, and research platforms, researchis often only reproducible in a limited time window.” [53]'
    ]))
DB(Citation(gorp2010a, vaquero2008a, ref='[54]', contexts=[
    '“Cloud computing” is an emerging paradigm for the provisionof computing infrastructure [54].'
    ,
    'This conforms with the definitionof cloud computing as “the user-friendly version ofgrid computing”, in which case grid computing is definedas “reduce computing costs and increase flexibility and reliabilityby using third-party operated hardware” [54].'
    ]))
DB(Citation(gorp2010a, varro2008a, ref='[55]', contexts=[
    'At the timeof writing this article (2 years after the first contest), the disadvantagesof this approach are clear: it is already impossibleto reproduce the submissions to a particular case study [55]within one man-week'
    ]))
DB(Citation(gorp2010a, Site('VMware ESXi', 'http://www.vmware.com/'), ref=
    '[56]', contexts=[
    '. Interestingly, VirtualBox can evenuse virtual machine images from other hypervisor tools suchas VMware [56].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, wang2009a, ref='[57]', contexts=[
    'Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.'
    ]))
DB(Citation(gorp2010a, Site(
    'Hwang woo-suk-wikipedia, the free encyclopedia',
    'http://en.wikipedia.org/wiki/Hwang_Woo-Suk'), ref='[58]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ], accessed='2006'))
DB(Citation(gorp2010a, winter2006a, ref='[59]', contexts=[
    'Figure 2 shows an enterprise architectural model of SHARE.Following Winter and Fischer’s terminology [59], the diagramaggregates elements from the infrastructure layer(machine and network elements) and the software layer.'
    ]))
DB(Citation(gorp2010a, zhu2006a, ref='[60]', contexts=[
    'Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].'
    ]))

from snowballing.models import *
from snowballing import dbindex
dbindex.last_citation_file = dbindex.this_file(__file__)
from ..work.y1991 import descartes1991a
from ..work.y1992 import claerbout1992a
from ..work.y1995 import buckheit1995a
from ..work.y1998 import newham1998a
from ..work.y1999 import halpin1999a
from ..work.y1999 import mylopoulos1999a
from ..work.y2002 import lerdorf2002a
from ..work.y2003 import agrawal2003a
from ..work.y2003 import angelov2003a
from ..work.y2003 import bezivin2003a
from ..work.y2003 import cuban2003a
from ..work.y2005 import barrett2005a
from ..work.y2005 import margaria2005a
from ..work.y2006 import steffen2006a
from ..work.y2006 import winter2006a
from ..work.y2006 import zhu2006a
from ..work.y2007 import biermann2007a
from ..work.y2007 import geiger2007a
from ..work.y2007 import brand2007a
from ..work.y2007 import chen2007a
from ..work.y2007 import dittner2007a
from ..work.y2007 import jensen2007a
from ..work.y2007 import piwowar2007a
from ..work.y2007 import agtive2007a
from ..work.y2007 import rensink2007a
from ..work.y2008 import decker2008a
from ..work.y2008 import gorp2008a
from ..work.y2008 import hong2008a
from ..work.y2008 import kurp2008a
from ..work.y2008 import varro2008a
from ..work.y2008 import vaquero2008a
from ..work.y2009 import buyya2009a
from ..work.y2009 import deelman2009a
from ..work.y2009 import donoho2009a
from ..work.y2009 import fomel2009a
from ..work.y2009 import jensen2009a
from ..work.y2009 import keahey2009a
from ..work.y2009 import nurmi2009a
from ..work.y2009 import stodden2009a
from ..work.y2009 import vandewalle2009a
from ..work.y2009 import wang2009a
from ..work.y2010 import bezivin2010a
from ..work.y2010 import gorp2010a
DB(Citation(gorp2010a, agrawal2003a, ref='[1]', contexts=[
    'In the graph transformation domain, GReAT [1] for examplerequires users to register for and install different partsof a tool chain manually'
    ]))
DB(Citation(gorp2010a, Site('Amazon Elastic Compute Cloud (Amazon EC2)',
    'http://aws.amazon.com/ec2/#pricing'), ref='[2]', contexts=[
    'Amazon EC2 [2]'], accessed='2009'))
DB(Citation(gorp2010a, Site('A UML profile for data modeling',
    'http://www.agiledata.org/essays/umlDataModelingProfile.html'), ref=
    '[3]', contexts=[
    'Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].'
    ], accessed='2009'))
DB(Citation(gorp2010a, angelov2003a, ref='[4]', contexts=[
    'In our ongoing work,we are investigating how this trust relationship can be supportedby electronic contracts that are based on a new licensetype [4].'
    ]))
DB(Citation(gorp2010a, barrett2005a, ref='[5]', contexts=[
    'The web server communicates with these machinesvia a secure protocol (SSH [5]).'
    ]))
DB(Citation(gorp2010a, bezivin2003a, ref='[6]', contexts=[
    'In fact, often articles are published before the underlying softwareis ready for distribution under any license (see [6] foran example from the model transformation domain).'
    ]))
DB(Citation(gorp2010a, bezivin2010a, ref='[7]', contexts=[
    'The repository has already beenmoved due to intellectual property issues with the Eclipseinitiative [7].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, biermann2007a, ref='[8]', contexts=[
    '. Even tools based on the Eclipseintegration platform often require readers to install pluginsfrom various sources (see [8] for an example from the modeltransformation domain).'
    ]))
DB(Citation(gorp2010a, buckheit1995a, ref='[9]', contexts=[
    'This may haveinspired Donoho et al. to develop the WaveLab library [9,18].'
    ,
    '. If one were interested in a figure, one would clickon it with a mouse, and a new window would instantlyappear, containing the code that the author of the articleused to create the figure. [9]'
    , 'Wavelab,Madagascar[9,19,20]']))
DB(Citation(gorp2010a, buyya2009a, ref='[10]', contexts=[
    'Buyya et al. point tovarious industrial sources to motivate the economical impactof the paradigm and derive the following running definition:“A Cloud is a type of parallel and distributed systemconsisting of a collection of inter-connected and virtualisedcomputers that are dynamically provisioned and presented asone or more unified computing resources based on servicelevelagreements established through negotiation betweenthe service provider and consumers.” [10].'
    ]))
DB(Citation(gorp2010a, chen2007a, ref='[11]', contexts=[
    'Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].'
    ]))
DB(Citation(gorp2010a, claerbout1992a, ref='[12]', contexts=[
    'Probably the most influential contribution to computationalresearch reproducibility was developed in the geophysicsdomain, by the team of Claerbout between 1990 and1995 [12].'
    ]))
DB(Citation(gorp2010a, cuban2003a, ref='[13]', contexts=[
    'WAN-Deployable As an academic research cloud,SHARE can rely on academic infrastructure, that islargely underused in most cases [13].'
    ]))
DB(Citation(gorp2010a, decker2008a, ref='[14]', contexts=[
    'At level 4, the installation of a modeling and transformationenvironment is fully automatic (or the tool runs from abrowser, as presented in [14]).'
    ]))
DB(Citation(gorp2010a, deelman2009a, ref='[15]', contexts=[
    'Executing longrunningjobs according to SLAs is a typical scenario inhigh-performance computing in general and in e-Science inparticular [15].'
    ]))
DB(Citation(gorp2010a, descartes1991a, ref='[16]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ]))
DB(Citation(gorp2010a, dittner2007a, ref='[17]', contexts=[
    'For the second edition of the contest, the organizers aimedto anticipate reproducibility problems by giving participantsaccess to virtual machines (VMs [17]) running on a localserver during the workshop. I'
    ,
    'From a platform perspective, SHARE relies on Apacheas a web container, MySQL as a database engine, and VirtualBoxas a hypervisor [17].'
    ]))
DB(Citation(gorp2010a, donoho2009a, ref='[18]', contexts=[
    'This may haveinspired Donoho et al. to develop the WaveLab library [9,18].'
    ,
    'Moreover, evenif a community adopts a standard platform (such as MATLABin the signal-processing domain [18]), we advocate thatdemonstrations should be made available via a platform suchas SHARE, because (1) results should be reproducible withminimal effort by readers from outside that community too,and (2) because of the durability concern.'
    ]))
DB(Citation(gorp2010a, Site('Madagascar—reproducible documents',
    'http://www.reproducibility.org/wiki/Reproducible_Documents'), ref=
    '[19]', contexts=[
    'Wavelab (and similar successors such as Madagascar [19]) isan online repository of research code and data, organized byresearch article.'
    , 'Wavelab,Madagascar[9,19,20]'], accessed='Mar 2010'))
DB(Citation(gorp2010a, fomel2009a, ref='[20]', contexts=[
    'Regarding durability, we support Claerbout’s observationthat every platform eventually becomes obsolete [20]. S'
    , 'Wavelab,Madagascar[9,19,20]']))
DB(Citation(gorp2010a, geiger2007a, ref='[21]', contexts=[
    'In this context, uncontrolled updatesfrom third-party components often lead to inconsistenciessome years after the related article was published (see [21]for an example from the graph-based software engineeringdomain).'
    ]))
DB(Citation(gorp2010a, halpin1999a, ref='[22]', contexts=[
    'Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].'
    ]))
DB(Citation(gorp2010a, hong2008a, ref='[23]', contexts=[
    'The third bannerintegrates with a website for collaborative bookmarkingand tagging [23].'
    ]))
DB(Citation(gorp2010a, jensen2009a, ref='[24]', contexts=[
    'The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].'
    ]))
DB(Citation(gorp2010a, jensen2007a, ref='[25]', contexts=[
    'The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].'
    ]))
DB(Citation(gorp2010a, keahey2009a, ref='[26]', contexts=[
    'As a running example, the authors dynamicallyaggregate computational resources from three different universitiesto satisfy the service level agreements (SLAs) forheavyweight biomedical computations [26].'
    , 'Nimbus [26], Eucalyptus [34], GVE [34]']))
DB(Citation(gorp2010a, Site('Wink', 'http://www.debugmode.com/wink/'), ref=
    '[27]', contexts=[
    'This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, kurp2008a, ref='[28]', contexts=[
    'Notice that thelatter property enables SHARE administrators to keep someservers shut down outside peak hours (or days), in order tosave energy or perform maintenance tasks [28].'
    ]))
DB(Citation(gorp2010a, lerdorf2002a, ref='[29]', contexts=[
    'The website is implementedin PHP [29]']))
DB(Citation(gorp2010a, margaria2005a, ref='[30]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]']))
DB(Citation(gorp2010a, mylopoulos1999a, ref='[31]', contexts=[
    'Besides these functional requirements, the system wasimplemented with the following non-functional requirements(NFRs [31]) in mind:'
    ]))
DB(Citation(gorp2010a, Site(
    'How to setup a jETI service provider (jETI server)',
    'http://jabc.cs.tu-dortmund.de/manual/index.php/JETI#Additional_Documentation'
    ), ref='[32]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]'], accessed='June 2006'))
DB(Citation(gorp2010a, newham1998a, ref='[33]', contexts=[
    'The communication between web andvirtual machine servers is realized via Bash cron jobs [33].'
    ]))
DB(Citation(gorp2010a, nurmi2009a, ref='[34]', contexts=[
    'Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.'
    , 'Nimbus [26], Eucalyptus [34], GVE [34]']))
DB(Citation(gorp2010a, Site('3TU Data Centre', 'http://datacentrum.3tu.nl/'
    ), ref='[35]', contexts=[
    'So far, the scarcest resource ishard drive space and we are working with an academic partnerto address that [35].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, Site('Open source licenses by category',
    'http://www.opensource.org/licenses/category'), ref='[36]', contexts=[
    'Open source [36]'], accessed='Mar 2010'))
DB(Citation(gorp2010a, Site('Research data! Who cares?',
    'http://w3.tue.nl/nl/diensten/bib/over/minisymposium/'), ref='[37]',
    contexts=[
    'Additionally,we wish to thank Leon Osinski for organizing an excellentworkshop related to reproducible research [37].'
    ], accessed='Sept 2009'))
DB(Citation(gorp2010a, piwowar2007a, ref='[38]', contexts=[
    'Similarly, Piwowar et al. [38] have examined the citationhistory of 85 biomedical publications'
    ]))
DB(Citation(gorp2010a, rensink2007a, ref='[39]', contexts=[
    'Coming back to the transformationtool contest, these risks were exposed most in thefirst edition of the event [39].'
    ]))
DB(Citation(gorp2010a, agtive2007a, ref='[40]', contexts=[]))
DB(Citation(gorp2010a, Site('Fences',
    'http://en.wikipedia.org/wiki/Fences_(software)'), ref='[41]', contexts
    =[
    'This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, steffen2006a, ref='[42]', contexts=[
    'Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).'
    , 'ETI, dETI, jETI[30,32,42]']))
DB(Citation(gorp2010a, stodden2009a, ref='[43]', contexts=[
    'Apart from the technical aspects mentioned above, Stoddenanalyzes different license forms (for media as wellas software) with computational science reproducibility inmind [43].'
    , 'New licensetypes [43]']))
DB(Citation(gorp2010a, Site('Top 10 RDP Protocol Misconceptions—part 2',
    'http://blogs.msdn.com/rds/archive/2009/03/12/top-10-rdp-protocol-misconceptions-part-2.aspx'
    ), ref='[44]', contexts=[
    'The underlying protocol (Remote Desktop Protocol, or RDP)supports modern encryption methods [44].'
    ], accessed='Mar 2009'))
DB(Citation(gorp2010a, brand2007a, ref='[45]', contexts=[
    'In a special issue on experimental software engineering, van den Brand observes that “the pressure to publish is much higher than the pressure to develop good software” [45].'
    ,
    'Van den Brand confirms that, “in physics or chemistry papersabout experiments contain a lot of technical details in order tofacilitate other researchers to replay the experiments in orderto validate the results described in these papers”, and advocatesthat in software engineering, more attention should bepaid to reviewing the software artifacts that support researchcontributions [45].'
    ,
    'Van den Brand indicates that “more and more computerscientists use the open source community to distributetheir tools. In this way it is not necessary to reimplementtools, only to download and install them.” [45]. H'
    ]))
DB(Citation(gorp2010a, Site(
    'SHARE image with CPNtools and behavioral models of SHARE',
    'http://is.ieis.tue.nl/staff/pvgorp/share/?page=ConfigureNewSession&vdi=ModelsOfSHARE_v1.vdi'
    ), ref='[46]', contexts=[
    'Therefore, users are invited to connect to a SHARE demothat automatically starts the right modeling tool and loadsthe simulation model for evaluation purposes [46]'
    ,
    'By usingcitations such as [46] (cfr., discussion of Fig. 5), authors canenable readers to jump directly to the optimal environment.'
    ], accessed='Feb 2009'))
DB(Citation(gorp2010a, Site(
    'VRDP connection count bug? (wrong value of mcVRDPC lients)',
    'http://www.virtualbox.org/ticket/4655'), ref='[47]', contexts=[
    'Apart from a minor bug (see [47]) the software performedremarkably well even for users on lower bandwidth wirelessnetworks.'
    ], accessed='July 2009'))
DB(Citation(gorp2010a, Site(
    'SHARE group with basic operating system images',
    'http://is.ieis.tue.nl/staff/pvgorp/share/?page=Signup&bundlename=Operating\\%20Systems'
    ), ref='[48]', contexts=[
    'John signs up to the group “Operating Systems”[48],using his e-mail address john.doe@uni.ac.eu and a passwordof his choice.'
    ], accessed='Mar 2009'))
DB(Citation(gorp2010a, Site(
    'SHARE–Sharing Hosted Autonomous Research Environments',
    'http://is.ieis.tue.nl/staff/pvgorp/share/'), ref='[49]', contexts=[
    'More specifically, they describewhy we are applying cloud-computing technologies, how weare integrating them, and how others can use our supportiveinformation system—SHARE (Sharing Hosted AutonomousResearch Environments [49]).'
    ,
    'This article describes SHARE [49], a system that hasbeen constructed for solving such organizational problems.'
    ], accessed='2009'))
DB(Citation(gorp2010a, Site('SHARE documentation',
    'http://fmt.cs.utwente.nl/redmine/wiki/5/SHARE'), ref='[50]', contexts=
    [
    'John can now evaluate the operating systems that areavailable in SHARE by default, following the stepsdescribed in Sect. 3.1 or following the online documentation[50].S'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, gorp2008a, ref='[51]', contexts=[
    'In fact, we are also working on a UML-based techniqueto model transformation interoperability [51]'
    ]))
DB(Citation(gorp2010a, Site(
    'Call for papers: STTT special section on Graph-Based tool comparison',
    'http://www.fots.ua.ac.be/events/grabats2008/sttt-section-cfp.pdf'),
    ref='[52]', contexts=[
    'Additionally, itturned out that too much effort was required from the organizersas well as from participants when applying this approachover the Internet, for example when editing a journal [52].'
    ,
    'It should be noted that the graphbasedtools contest involved several case studies, some ofwhich could be solved in advance (offline case studies) andone of which had to be solved during the workshop (thelive contest) [52]'
    ,
    'Again,in the context of the transformation tool contest, we haveinvited all participants to investigate: (1) how to call the relevantpart of their tool with some standard inputs, (2) howto get the transformed results (and some statistics), and (3)how to pass that to a visualizer, which could be a serviceitself [52].'
    ], accessed='Nov 2008'))
DB(Citation(gorp2010a, vandewalle2009a, ref='[53]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ,
    '“Can we suppose that programssuch as MATLAB, Mathematica, or even Windows areavailable, or should we constrain ourselves to the use ofopen-source programs such as R, Octave, or SciLab in aLinux environment?” [53]'
    ,
    '“There exists a largevariety of computer platforms, and making even somesimple code work on most platforms requires a lot ofwork. We need to balance the ease of use for a readerwith the additional work to be done after development ofthe algorithms and initial code. ... ” [53]'
    ,
    '“In this tradeoff, it is also important to considerthe long-term availability of a platform. Due to changes indata formats, compilers, and research platforms, researchis often only reproducible in a limited time window.” [53]'
    ]))
DB(Citation(gorp2010a, vaquero2008a, ref='[54]', contexts=[
    '“Cloud computing” is an emerging paradigm for the provisionof computing infrastructure [54].'
    ,
    'This conforms with the definitionof cloud computing as “the user-friendly version ofgrid computing”, in which case grid computing is definedas “reduce computing costs and increase flexibility and reliabilityby using third-party operated hardware” [54].'
    ]))
DB(Citation(gorp2010a, varro2008a, ref='[55]', contexts=[
    'At the timeof writing this article (2 years after the first contest), the disadvantagesof this approach are clear: it is already impossibleto reproduce the submissions to a particular case study [55]within one man-week'
    ]))
DB(Citation(gorp2010a, Site('VMware ESXi', 'http://www.vmware.com/'), ref=
    '[56]', contexts=[
    '. Interestingly, VirtualBox can evenuse virtual machine images from other hypervisor tools suchas VMware [56].'
    ], accessed='Mar 2010'))
DB(Citation(gorp2010a, wang2009a, ref='[57]', contexts=[
    'Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.'
    ]))
DB(Citation(gorp2010a, Site(
    'Hwang woo-suk-wikipedia, the free encyclopedia',
    'http://en.wikipedia.org/wiki/Hwang_Woo-Suk'), ref='[58]', contexts=[
    'Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].'
    ], accessed='2006'))
DB(Citation(gorp2010a, winter2006a, ref='[59]', contexts=[
    'Figure 2 shows an enterprise architectural model of SHARE.Following Winter and Fischer’s terminology [59], the diagramaggregates elements from the infrastructure layer(machine and network elements) and the software layer.'
    ]))
DB(Citation(gorp2010a, zhu2006a, ref='[60]', contexts=[
    'Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].'
    ]))

# coding: utf-8
from snowballing.models import *
from snowballing import dbindex
dbindex.last_citation_file = dbindex.this_file(__file__)

from ..work.y1991 import descartes1991a
from ..work.y1992 import claerbout1992a
from ..work.y1995 import buckheit1995a
from ..work.y1998 import newham1998a
from ..work.y1999 import halpin1999a
from ..work.y1999 import mylopoulos1999a
from ..work.y2002 import lerdorf2002a
from ..work.y2003 import agrawal2003a
from ..work.y2003 import angelov2003a
from ..work.y2003 import bezivin2003a
from ..work.y2003 import cuban2003a
from ..work.y2005 import barrett2005a
from ..work.y2005 import margaria2005a
from ..work.y2006 import steffen2006a
from ..work.y2006 import winter2006a
from ..work.y2006 import zhu2006a
from ..work.y2007 import biermann2007a
from ..work.y2007 import geiger2007a
from ..work.y2007 import brand2007a
from ..work.y2007 import chen2007a
from ..work.y2007 import dittner2007a
from ..work.y2007 import jensen2007a
from ..work.y2007 import piwowar2007a
from ..work.y2007 import agtive2007a
from ..work.y2007 import rensink2007a
from ..work.y2008 import decker2008a
from ..work.y2008 import gorp2008a
from ..work.y2008 import hong2008a
from ..work.y2008 import kurp2008a
from ..work.y2008 import varro2008a
from ..work.y2008 import vaquero2008a
from ..work.y2009 import buyya2009a
from ..work.y2009 import deelman2009a
from ..work.y2009 import donoho2009a
from ..work.y2009 import fomel2009a
from ..work.y2009 import jensen2009a
from ..work.y2009 import keahey2009a
from ..work.y2009 import nurmi2009a
from ..work.y2009 import stodden2009a
from ..work.y2009 import vandewalle2009a
from ..work.y2009 import wang2009a
from ..work.y2010 import bezivin2010a
from ..work.y2010 import gorp2010a


DB(Citation(
    gorp2010a, agrawal2003a, ref="[1]",
    contexts=[
        "In the graph transformation domain, GReAT [1] for examplerequires users to register for and install different partsof a tool chain manually",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Amazon Elastic Compute Cloud (Amazon EC2)", "http://aws.amazon.com/ec2/#pricing"),
    ref="[2]",
    contexts=[
        "Amazon EC2 [2]",
        
    ],
    accessed="2009",
))

DB(Citation(
    gorp2010a,
    Site("A UML profile for data modeling", "http://www.agiledata.org/essays/umlDataModelingProfile.html"),
    ref="[3]",
    contexts=[
        "Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].",
        
    ],
    accessed="2009",
))

DB(Citation(
    gorp2010a, angelov2003a, ref="[4]",
    contexts=[
        "In our ongoing work,we are investigating how this trust relationship can be supportedby electronic contracts that are based on a new licensetype [4].",
        
    ],
))

DB(Citation(
    gorp2010a, barrett2005a, ref="[5]",
    contexts=[
        "The web server communicates with these machinesvia a secure protocol (SSH [5]).",
        
    ],
))

DB(Citation(
    gorp2010a, bezivin2003a, ref="[6]",
    contexts=[
        "In fact, often articles are published before the underlying softwareis ready for distribution under any license (see [6] foran example from the model transformation domain).",
        
    ],
))

DB(Citation(
    gorp2010a, bezivin2010a, ref="[7]",
    contexts=[
        "The repository has already beenmoved due to intellectual property issues with the Eclipseinitiative [7].",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, biermann2007a, ref="[8]",
    contexts=[
        ". Even tools based on the Eclipseintegration platform often require readers to install pluginsfrom various sources (see [8] for an example from the modeltransformation domain).",
        
    ],
))

DB(Citation(
    gorp2010a, buckheit1995a, ref="[9]",
    contexts=[
        "This may haveinspired Donoho et al. to develop the WaveLab library [9,18].",
        ". If one were interested in a figure, one would clickon it with a mouse, and a new window would instantlyappear, containing the code that the author of the articleused to create the figure. [9]",
        "Wavelab,Madagascar[9,19,20]",
        
    ],
))

DB(Citation(
    gorp2010a, buyya2009a, ref="[10]",
    contexts=[
        "Buyya et al. point tovarious industrial sources to motivate the economical impactof the paradigm and derive the following running definition:“A Cloud is a type of parallel and distributed systemconsisting of a collection of inter-connected and virtualisedcomputers that are dynamically provisioned and presented asone or more unified computing resources based on servicelevelagreements established through negotiation betweenthe service provider and consumers.” [10].",
        
    ],
))

DB(Citation(
    gorp2010a, chen2007a, ref="[11]",
    contexts=[
        "Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].",
        
    ],
))

DB(Citation(
    gorp2010a, claerbout1992a, ref="[12]",
    contexts=[
        "Probably the most influential contribution to computationalresearch reproducibility was developed in the geophysicsdomain, by the team of Claerbout between 1990 and1995 [12].",
        
    ],
))

DB(Citation(
    gorp2010a, cuban2003a, ref="[13]",
    contexts=[
        "WAN-Deployable As an academic research cloud,SHARE can rely on academic infrastructure, that islargely underused in most cases [13].",
        
    ],
))

DB(Citation(
    gorp2010a, decker2008a, ref="[14]",
    contexts=[
        "At level 4, the installation of a modeling and transformationenvironment is fully automatic (or the tool runs from abrowser, as presented in [14]).",
        
    ],
))

DB(Citation(
    gorp2010a, deelman2009a, ref="[15]",
    contexts=[
        "Executing longrunningjobs according to SLAs is a typical scenario inhigh-performance computing in general and in e-Science inparticular [15].",
        
    ],
))

DB(Citation(
    gorp2010a, descartes1991a, ref="[16]",
    contexts=[
        "Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].",
        
    ],
))

DB(Citation(
    gorp2010a, dittner2007a, ref="[17]",
    contexts=[
        "For the second edition of the contest, the organizers aimedto anticipate reproducibility problems by giving participantsaccess to virtual machines (VMs [17]) running on a localserver during the workshop. I",
        "From a platform perspective, SHARE relies on Apacheas a web container, MySQL as a database engine, and VirtualBoxas a hypervisor [17].",
        
    ],
))

DB(Citation(
    gorp2010a, donoho2009a, ref="[18]",
    contexts=[
        "This may haveinspired Donoho et al. to develop the WaveLab library [9,18].",
        "Moreover, evenif a community adopts a standard platform (such as MATLABin the signal-processing domain [18]), we advocate thatdemonstrations should be made available via a platform suchas SHARE, because (1) results should be reproducible withminimal effort by readers from outside that community too,and (2) because of the durability concern.",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Madagascar—reproducible documents", "http://www.reproducibility.org/wiki/Reproducible_Documents"),
    ref="[19]",
    contexts=[
        "Wavelab (and similar successors such as Madagascar [19]) isan online repository of research code and data, organized byresearch article.",
        "Wavelab,Madagascar[9,19,20]",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, fomel2009a, ref="[20]",
    contexts=[
        "Regarding durability, we support Claerbout’s observationthat every platform eventually becomes obsolete [20]. S",
        "Wavelab,Madagascar[9,19,20]",
        
    ],
))


DB(Citation(
    gorp2010a, geiger2007a, ref="[21]",
    contexts=[
        "In this context, uncontrolled updatesfrom third-party components often lead to inconsistenciessome years after the related article was published (see [21]for an example from the graph-based software engineeringdomain).",
        
    ],
))

DB(Citation(
    gorp2010a, halpin1999a, ref="[22]",
    contexts=[
        "Figure 6 displays a class diagram that models SHARE’s datafrom a conceptual point of view: all classes in the diagramcorrespond to persistent entities [3,22].",
        
    ],
))

DB(Citation(
    gorp2010a, hong2008a, ref="[23]",
    contexts=[
        "The third bannerintegrates with a website for collaborative bookmarkingand tagging [23].",
        
    ],
))

DB(Citation(
    gorp2010a, jensen2009a, ref="[24]",
    contexts=[
        "The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].",
        
    ],
))

DB(Citation(
    gorp2010a, jensen2007a, ref="[25]",
    contexts=[
        "The model is written in the high-level colored petri-netformalism [24], using CPNtools [25].",
        
    ],
))

DB(Citation(
    gorp2010a, keahey2009a, ref="[26]",
    contexts=[
        "As a running example, the authors dynamicallyaggregate computational resources from three different universitiesto satisfy the service level agreements (SLAs) forheavyweight biomedical computations [26].",
        "Nimbus [26], Eucalyptus [34], GVE [34]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Wink", "http://www.debugmode.com/wink/"),
    ref="[27]",
    contexts=[
        "This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, kurp2008a, ref="[28]",
    contexts=[
        "Notice that thelatter property enables SHARE administrators to keep someservers shut down outside peak hours (or days), in order tosave energy or perform maintenance tasks [28].",
        
    ],
))

DB(Citation(
    gorp2010a, lerdorf2002a, ref="[29]",
    contexts=[
        "The website is implementedin PHP [29]",
        
    ],
))

DB(Citation(
    gorp2010a, margaria2005a, ref="[30]",
    contexts=[
        "Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).",
        "ETI, dETI, jETI[30,32,42]",
        
    ],
))

DB(Citation(
    gorp2010a, mylopoulos1999a, ref="[31]",
    contexts=[
        "Besides these functional requirements, the system wasimplemented with the following non-functional requirements(NFRs [31]) in mind:",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("How to setup a jETI service provider (jETI server)", "http://jabc.cs.tu-dortmund.de/manual/index.php/JETI#Additional_Documentation"),
    ref="[32]",
    contexts=[
        "Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).",
        "ETI, dETI, jETI[30,32,42]",
        
    ],
    accessed="June 2006",
))

DB(Citation(
    gorp2010a, newham1998a, ref="[33]",
    contexts=[
        "The communication between web andvirtual machine servers is realized via Bash cron jobs [33].",
        
    ],
))

DB(Citation(
    gorp2010a, nurmi2009a, ref="[34]",
    contexts=[
        "Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.",
        "Nimbus [26], Eucalyptus [34], GVE [34]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("3TU Data Centre", "http://datacentrum.3tu.nl/"),
    ref="[35]",
    contexts=[
        "So far, the scarcest resource ishard drive space and we are working with an academic partnerto address that [35].",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a,
    Site("Open source licenses by category", "http://www.opensource.org/licenses/category"),
    ref="[36]",
    contexts=[
        "Open source [36]",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a,
    Site("Research data! Who cares?", "http://w3.tue.nl/nl/diensten/bib/over/minisymposium/"),
    ref="[37]",
    contexts=[
        "Additionally,we wish to thank Leon Osinski for organizing an excellentworkshop related to reproducible research [37].",
        
    ],
    accessed="Sept 2009",
))

DB(Citation(
    gorp2010a, piwowar2007a, ref="[38]",
    contexts=[
        "Similarly, Piwowar et al. [38] have examined the citationhistory of 85 biomedical publications",
        
    ],
))

DB(Citation(
    gorp2010a, rensink2007a, ref="[39]",
    contexts=[
        "Coming back to the transformationtool contest, these risks were exposed most in thefirst edition of the event [39].",
        
    ],
))

DB(Citation(
    gorp2010a, agtive2007a, ref="[40]",
    contexts=[
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Fences", "http://en.wikipedia.org/wiki/Fences_(software)"),
    ref="[41]",
    contexts=[
        "This involves guidance on the use ofdesktop organization software (such as Fences [41]), screencapture software (such as Wink [27]) and other packagesthat are complementary to SHARE.",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, steffen2006a, ref="[42]",
    contexts=[
        "Regarding the effort concern, consider for example theamount of work that authors need to perform for adoptingheavyweight integration approaches such as the ElectronicTool Integration Platform (jETI [30,32,42]).",
        "ETI, dETI, jETI[30,32,42]",
        
    ],
))

DB(Citation(
    gorp2010a, stodden2009a, ref="[43]",
    contexts=[
        "Apart from the technical aspects mentioned above, Stoddenanalyzes different license forms (for media as wellas software) with computational science reproducibility inmind [43].",
        "New licensetypes [43]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Top 10 RDP Protocol Misconceptions—part 2", "http://blogs.msdn.com/rds/archive/2009/03/12/top-10-rdp-protocol-misconceptions-part-2.aspx"),
    ref="[44]",
    contexts=[
        "The underlying protocol (Remote Desktop Protocol, or RDP)supports modern encryption methods [44].",
        
    ],
    accessed="Mar 2009",
))

DB(Citation(
    gorp2010a, brand2007a, ref="[45]",
    contexts=[
        "In a special issue on experimental software engineering, van den Brand observes that “the pressure to publish is much higher than the pressure to develop good software” [45].",
        "Van den Brand confirms that, “in physics or chemistry papersabout experiments contain a lot of technical details in order tofacilitate other researchers to replay the experiments in orderto validate the results described in these papers”, and advocatesthat in software engineering, more attention should bepaid to reviewing the software artifacts that support researchcontributions [45].",
        "Van den Brand indicates that “more and more computerscientists use the open source community to distributetheir tools. In this way it is not necessary to reimplementtools, only to download and install them.” [45]. H",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("SHARE image with CPNtools and behavioral models of SHARE", "http://is.ieis.tue.nl/staff/pvgorp/share/?page=ConfigureNewSession&vdi=ModelsOfSHARE_v1.vdi"),
    ref="[46]",
    contexts=[
        "Therefore, users are invited to connect to a SHARE demothat automatically starts the right modeling tool and loadsthe simulation model for evaluation purposes [46]",
        "By usingcitations such as [46] (cfr., discussion of Fig. 5), authors canenable readers to jump directly to the optimal environment.",
        
    ],
    accessed="Feb 2009",
))

DB(Citation(
    gorp2010a,
    Site("VRDP connection count bug? (wrong value of mcVRDPC lients)", "http://www.virtualbox.org/ticket/4655"),
    ref="[47]",
    contexts=[
        "Apart from a minor bug (see [47]) the software performedremarkably well even for users on lower bandwidth wirelessnetworks.",
        
    ],
    accessed="July 2009",
))

DB(Citation(
    gorp2010a,
    Site("SHARE group with basic operating system images", "http://is.ieis.tue.nl/staff/pvgorp/share/?page=Signup&bundlename=Operating\%20Systems"),
    ref="[48]",
    contexts=[
        "John signs up to the group “Operating Systems”[48],using his e-mail address john.doe@uni.ac.eu and a passwordof his choice.",
        
    ],
    accessed="Mar 2009",
))

DB(Citation(
    gorp2010a,
    Site("SHARE–Sharing Hosted Autonomous Research Environments", "http://is.ieis.tue.nl/staff/pvgorp/share/"),
    ref="[49]",
    contexts=[
        "More specifically, they describewhy we are applying cloud-computing technologies, how weare integrating them, and how others can use our supportiveinformation system—SHARE (Sharing Hosted AutonomousResearch Environments [49]).",
        "This article describes SHARE [49], a system that hasbeen constructed for solving such organizational problems.",
        
    ],
    accessed="2009",
))

DB(Citation(
    gorp2010a,
    Site("SHARE documentation", "http://fmt.cs.utwente.nl/redmine/wiki/5/SHARE"),
    ref="[50]",
    contexts=[
        "John can now evaluate the operating systems that areavailable in SHARE by default, following the stepsdescribed in Sect. 3.1 or following the online documentation[50].S",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, gorp2008a, ref="[51]",
    contexts=[
        "In fact, we are also working on a UML-based techniqueto model transformation interoperability [51]",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Call for papers: STTT special section on Graph-Based tool comparison", "http://www.fots.ua.ac.be/events/grabats2008/sttt-section-cfp.pdf"),
    ref="[52]",
    contexts=[
        "Additionally, itturned out that too much effort was required from the organizersas well as from participants when applying this approachover the Internet, for example when editing a journal [52].",
        "It should be noted that the graphbasedtools contest involved several case studies, some ofwhich could be solved in advance (offline case studies) andone of which had to be solved during the workshop (thelive contest) [52]",
        "Again,in the context of the transformation tool contest, we haveinvited all participants to investigate: (1) how to call the relevantpart of their tool with some standard inputs, (2) howto get the transformed results (and some statistics), and (3)how to pass that to a visualizer, which could be a serviceitself [52].",
        
    ],
    accessed="Nov 2008",
))

DB(Citation(
    gorp2010a, vandewalle2009a, ref="[53]",
    contexts=[
        "Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].",
        "“Can we suppose that programssuch as MATLAB, Mathematica, or even Windows areavailable, or should we constrain ourselves to the use ofopen-source programs such as R, Octave, or SciLab in aLinux environment?” [53]",
        "“There exists a largevariety of computer platforms, and making even somesimple code work on most platforms requires a lot ofwork. We need to balance the ease of use for a readerwith the additional work to be done after development ofthe algorithms and initial code. ... ” [53]",
        "“In this tradeoff, it is also important to considerthe long-term availability of a platform. Due to changes indata formats, compilers, and research platforms, researchis often only reproducible in a limited time window.” [53]",
        
    ],
))

DB(Citation(
    gorp2010a, vaquero2008a, ref="[54]",
    contexts=[
        "“Cloud computing” is an emerging paradigm for the provisionof computing infrastructure [54].",
        "This conforms with the definitionof cloud computing as “the user-friendly version ofgrid computing”, in which case grid computing is definedas “reduce computing costs and increase flexibility and reliabilityby using third-party operated hardware” [54].",
        
    ],
))

DB(Citation(
    gorp2010a, varro2008a, ref="[55]",
    contexts=[
        "At the timeof writing this article (2 years after the first contest), the disadvantagesof this approach are clear: it is already impossibleto reproduce the submissions to a particular case study [55]within one man-week",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("VMware ESXi", "http://www.vmware.com/"),
    ref="[56]",
    contexts=[
        ". Interestingly, VirtualBox can evenuse virtual machine images from other hypervisor tools suchas VMware [56].",
        
    ],
    accessed="Mar 2010",
))

DB(Citation(
    gorp2010a, wang2009a, ref="[57]",
    contexts=[
        "Eucalyptus [34] and the Grid Virtualization Engine(GVE [57]) are open source cloud-computing platforms thatare similar to Nimbus but that emphasize the use of standardweb service technologies such as WSDL and BPEL more.",
        
    ],
))

DB(Citation(
    gorp2010a,
    Site("Hwang woo-suk-wikipedia, the free encyclopedia", "http://en.wikipedia.org/wiki/Hwang_Woo-Suk"),
    ref="[58]",
    contexts=[
        "Vandewalle et al. observe that although Descartes alreadystressed the importance of reproducibility in 1637 [16],fraudulent articles still slip the peer-reviewing process ofestablished journals in mature fields [53,58].",
        
    ],
    accessed="2006",
))

DB(Citation(
    gorp2010a, winter2006a, ref="[59]",
    contexts=[
        "Figure 2 shows an enterprise architectural model of SHARE.Following Winter and Fischer’s terminology [59], the diagramaggregates elements from the infrastructure layer(machine and network elements) and the software layer.",
        
    ],
))

DB(Citation(
    gorp2010a, zhu2006a, ref="[60]",
    contexts=[
        "Fortunately, this should not be an additional burden to theresearcher since the development of such stubs is increasinglyconsidered an integral part of development [11,60].",
        
    ],
))