Every reference with a DOI in the deposited reference list resolved to a known
work in Crossref or DataCite at the dated check, and none carried a publisher retraction,
withdrawal, or removal notice.
The 43 checked references that resolve
resolves10.1038/ng.295Repeatability of published microarray gene expression analyses
resolves10.1186/gb-2010-11-8-r86Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
resolves10.1186/2047-217X-1-18SOAPdenovo2: an empirically improved memory-efficient short-read
<i>de novo</i>
assembler
resolves10.1101/gr.097261.109De novo assembly of human genomes with massively parallel short read sequencing
resolves10.1073/pnas.1017351108High-quality draft assemblies of mammalian genomes from massively parallel sequence data
resolves10.4056/sigs.147362Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop
resolves10.1038/nbt1346The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
resolves10.1093/nar/gkr469BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications
resolves10.1186/2041-1480-5-14The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
resolves10.5334/jors.ayBest Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research
resolves10.1093/nar/gkr1097Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
resolves10.7717/peerj.148On the reproducibility of science: unique identification of research resources in the biomedical literature
resolves10.1007/BF02430363Designing and reporting on computational experiments with heuristic methods
resolves10.1038/ncomms3957The locust genome provides insight into swarm formation and long-distance flight
resolves10.1093/nar/gks1004MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data
resolves10.1093/nar/gkr1051The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons
resolves10.1002/minf.201200114The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing
resolves10.1093/bioinformatics/btq415ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
resolves10.14806/ej.19.B.728Bio-GraphIIn: a graph-based, integrative and semantically-enabled repository for life science experimental data
resolves10.1186/1471-2105-15-S1-S11The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
The 43 references without a DOI — listed, not checked
no DOI — not checkedNaik G. Scientists’ Elusive Goal: Reproducing Study Results. Wall Street Journal. 2011; <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://online.wsj.com/news/articles/SB10001424052970203764804577059841672541590" xlink:type="simple">http://online.wsj.com/news/articles/SB10001424052970203764804577059841672541590</ext-link></comment> [cited 15 October 2013].
no DOI — not checkedGigaScience Journal;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.gigasciencejournal.com/" xlink:type="simple">http://www.gigasciencejournal.com/</ext-link></comment>
no DOI — not checkedScientific Data;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.nature.com/sdata/" xlink:type="simple">http://www.nature.com/sdata/</ext-link></comment>
no DOI — not checkedOECD Principles and Guidelines for Access to Research Data from Public Funding;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.oecd.org/sti/sci-tech/38500813.pdf" xlink:type="simple">http://www.oecd.org/sti/sci-tech/38500813.pdf</ext-link></comment>
no DOI — not checkedBerlin Declaration on Open Access to Knowledge in the Sciences and Humanities;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://openaccess.mpg.de/" xlink:type="simple">http://openaccess.mpg.de/</ext-link></comment>
no DOI — not checkedRoyal Society—Science as an open enterprise;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://royalsociety.org/~/media/Royal_Society_Content/policy/projects/sape/2012-06-20-SAOE.pdf" xlink:type="simple">https://royalsociety.org/~/media/Royal_Society_Content/policy/projects/sape/2012-06-20-SAOE.pdf</ext-link></comment>
no DOI — not checkedResearch Data Alliance;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://rd-alliance.org/" xlink:type="simple">https://rd-alliance.org/</ext-link></comment>
no DOI — not checkedThe Future of Research Communications and e-Scholarship (Force11);. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://www.force11.org/white_paper" xlink:type="simple">https://www.force11.org/white_paper</ext-link></comment>
no DOI — not checkedNational Institutes of Health - Plan for Increasing Access to Scientific Publications and Digital Scientific Data from NIH Funded Scientific Research;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://grants.nih.gov/grants/NIH-Public-Access-Plan.pdf" xlink:type="simple">http://grants.nih.gov/grants/NIH-Public-Access-Plan.pdf</ext-link></comment>
no DOI — not checkedUsing a suite of ontologies for preserving workflow-centric research objects
no DOI — not checkedGigaDB record for SOAPdenovo2 article;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://dx.doi.org/10.5524/100044" xlink:type="simple">http://dx.doi.org/10.5524/100044</ext-link></comment>
no DOI — not checkedSOAPdenovo2 pre-publication history;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.gigasciencejournal.com/content/1/1/18/prepub" xlink:type="simple">http://www.gigasciencejournal.com/content/1/1/18/prepub</ext-link></comment>
no DOI — not checkedGenome Assembly Gold-standard Evaluations (GAGE);. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://gage.cbcb.umd.edu/" xlink:type="simple">http://gage.cbcb.umd.edu/</ext-link></comment>
no DOI — not checkedGAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. <year>2012</year>;22(3):557–567. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://dx.doi.org/10.1101/gr.131383.111" xlink:type="simple">http://dx.doi.org/10.1101/gr.131383.111</ext-link></comment>
no DOI — not checkedGigaScience Server;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://gigagalaxy.net" xlink:type="simple">http://gigagalaxy.net</ext-link></comment>
no DOI — not checkedGAGE analysis script;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://gage.cbcb.umd.edu/results/gage-paper-validation.tar.gz" xlink:type="simple">http://gage.cbcb.umd.edu/results/gage-paper-validation.tar.gz</ext-link></comment>
no DOI — not checkedOECD. Test No. 408: Repeated Dose 90-Day Oral Toxicity Study in Rodents. OECD Publishing; 2008. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http:///content/book/9789264070707-en" xlink:type="simple">/content/book/9789264070707-en</ext-link></comment>
no DOI — not checkedUpdated genome assembly of YH: the first diploid genome sequence of a Han Chinese individual (version 2, 07/2012)
no DOI — not checkedThe European Nucleotide Archive
no DOI — not checkedDatabase resources of the National Center for Biotechnology Information
no DOI — not checkedAssembly record;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/assembly/2758/" xlink:type="simple">http://www.ncbi.nlm.nih.gov/assembly/2758/</ext-link></comment>
no DOI — not checkedResource Description Framework; 2013 [cited 6 April]. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.w3.org/standards/techs/rdf" xlink:type="simple">http://www.w3.org/standards/techs/rdf</ext-link></comment>
no DOI — not checkedPROVenance Ontology (PROV-O);. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.w3.org/TR/2012/WD-prov-o-20120724/" xlink:type="simple">http://www.w3.org/TR/2012/WD-prov-o-20120724/</ext-link></comment>
no DOI — not checkedNanoMaton;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/ISA-tools/NanoMaton" xlink:type="simple">https://github.com/ISA-tools/NanoMaton</ext-link></comment>
no DOI — not checkedVandenbussche, Vatant. Linked Open Vocabularies. ERCIM news. 2014;96:21–22.
no DOI — not checkedSTATistics Ontology (STATO);. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://stato-ontology.org" xlink:type="simple">http://stato-ontology.org</ext-link></comment>
no DOI — not checkedWhy workflows break - Understanding and combating decay in Taverna workflows
no DOI — not checkedInstitute SS, Curtis+Cartwrigh. Software Preservation Benefits framework; 2010. Last accessed: December 2014. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.software.ac.uk/attach/SoftwarePreservationBenefitsFramework.pdf" xlink:type="simple">http://www.software.ac.uk/attach/SoftwarePreservationBenefitsFramework.pdf</ext-link></comment>
no DOI — not checkedZhao J, Klyne G, Gamble M, Goble CA. A Checklist-Based Approach for Quality Assessment of Scientific Information. In: Proceedings of the 3rd International Workshop on Linked Science 2013 - Supporting Reproducibility, Scientific Investigations and Experiments (LISC2013) In conjunction with the 12th International Semantic Web Conference 2013 (ISWC 2013), Sydney, Australia, October 21, 2013.; 2013.
no DOI — not checkedSOAPdenovo2 case study website;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://isa-tools.github.io/soapdenovo2/" xlink:type="simple">http://isa-tools.github.io/soapdenovo2/</ext-link></comment>
no DOI — not checkedAnderson C. The End of Theory: The Data Deluge Makes the Scientific Method Obsolete. Wired. 2008;<comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.wired.com/science/discoveries/magazine/16-07/pb_theory" xlink:type="simple">http://www.wired.com/science/discoveries/magazine/16-07/pb_theory</ext-link></comment>
no DOI — not checkedBioSharing Standards Information Resource for Life Sciences;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.biosharing.org" xlink:type="simple">http://www.biosharing.org</ext-link></comment>
no DOI — not checkedHakala J. Persistent Identifiers—an overview;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.metadaten-twr.org/2010/10/13/persistent-identifiers-an-overview/" xlink:type="simple">http://www.metadaten-twr.org/2010/10/13/persistent-identifiers-an-overview/</ext-link></comment>
no DOI — not checkedSciCrunch Resources;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://scicrunch.com/resources" xlink:type="simple">http://scicrunch.com/resources</ext-link></comment>
no DOI — not checkedBrownlee J. Clever Algorithms: Nature-Inspired Programming Recipes. Lulu Enterprises Incorporated; 2011. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://books.google.co.uk/books?id=SESWXQphCUkC" xlink:type="simple">http://books.google.co.uk/books?id=SESWXQphCUkC</ext-link></comment>
no DOI — not checkedAllen IE, Seaman CA. Superiority, Equivalence and Non-Inferiority. Quality Progress. 2007;.
no DOI — not checkedLuo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. Correction: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Correction article. <comment>Available: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://drive.google.com/file/d/0B-If8LKUjDK6YXcyelN0bkllRGc/edit" xlink:type="simple">https://drive.google.com/file/d/0B-If8LKUjDK6YXcyelN0bkllRGc/edit</ext-link></comment>
no DOI — not checkedNanopublication Schema;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://nanopub.org/nschema" xlink:type="simple">http://nanopub.org/nschema</ext-link></comment>
no DOI — not checkedRo-manager: A tool for creating and manipulating ROs to support reproducibility and reuse in sciences
no DOI — not checkedPage K, Palma R, Holubowicz P, Klyne G, Soiland-Reyes S, Cruickshank D, et al. From workflows to Research Objects: an architecture for preserving the semantics of science. In: Proceedings of the 2nd International Workshop on Linked Science; 2012.
no DOI — not checkedRO PURL;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://goo.gl/14wV3T" xlink:type="simple">http://goo.gl/14wV3T</ext-link></comment>
no DOI — not checkedDataCite;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://www.datacite.org" xlink:type="simple">https://www.datacite.org</ext-link></comment>
no DOI — not checkedDocker;. <comment>Available from: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.docker.com/" xlink:type="simple">http://www.docker.com/</ext-link></comment>
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