Biocompute Objects—A Step towards Evaluation and Validation of Biomedical Scientific Computations

References

1. 1.↵
   1. Goecks J.,
   2. Coraor N.,
   3. Nekrutenko A.,
   4. Taylor J.

   NGS Analyses by Visualization with Trackster. Nat. Biotechnol. 2012, 30 (11), 1036–1039.

   OpenUrlCrossRefPubMed
2. 2.↵
   1. Alioto T. S.,
   2. Derdak S.,
   3. Beck T. A.,
   4. Boutros P. C.,
   5. Bower L.,
   6. et al

   . A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes. bioRxiv 2014, 012997.
3. 3.↵
   1. Wilson C. A.,
   2. Simonyan V.

   FDA's Activities Supporting Regulatory Application of “Next Gen” Sequencing Technologies. PDA J. Pharm. Sci. Technol. 2014, 68 (6), 626–630.

   OpenUrlAbstract/FREE Full Text
4. 4.↵
   1. Simonyan V.,
   2. Mazumder R.

   High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes (Basel) 2014, 5 (4), 957–981.

   OpenUrl
5. 5.↵
   1. Goble C. A.,
   2. Bhagat J.,
   3. Aleksejevs S.,
   4. Cruickshank D.,
   5. Michaelides D.,
   6. et al

   . myExperiment: A Repository and Social Network for the Sharing of Bioinformatics Workflows. Nucleic Acids Res. 2010, 38 (Suppl 2), W677–W682.

   OpenUrlCrossRefPubMedWeb of Science
6. 6.↵
   1. Roure D.

   Towards Computational Research Objects. DPRMA '13 Proceedings of the 1st International Workshop on Digital Preservation of Research Methods and Artefacts. ACM: New York, NY, 2013; pp 16–19.
7. 7.↵
   1. Hettne K. M.,
   2. Dharuri H.,
   3. Zhao J.,
   4. Wolstencroft K.,
   5. Belhajjame K.,
   6. et al

   . Structuring Research Methods and Data with the Research Object Model: Genomics Workflows as a Case Study. J. Biomed. Semantics 2014, 5 (1), 41.

   OpenUrlCrossRefPubMed
8. 8.↵
   1. Wolstencroft K.,
   2. Haines R.,
   3. Fellows D.,
   4. Williams A.,
   5. Withers D.,
   6. et al

   . The Taverna Workflow Suite: Designing and Executing Workflows of Web Services on the Desktop, Web or in the Cloud. Nucleic Acids Res. 2013, 41, W557–W561.

   OpenUrlCrossRefPubMedWeb of Science
9. 9.↵
   1. Tiwari A.,
   2. Sekhar A. K.

   Workflow Based Framework for Life Science Informatics. Comput. Biol. Chem. 2007, 31 (5), 305–319.

   OpenUrlCrossRefPubMedWeb of Science
10. 10.↵
    1. Destro Bisol G.,
    2. Anagnostou P.,
    3. Capocasa M.,
    4. Bencivelli S.,
    5. Cerroni A.,
    6. et al

    . Perspectives on Open Science and Scientific Data Sharing: An Interdisciplinary Workshop. J. Anthropol. Sci. 2014, 92, 179–200.

    OpenUrl
11. 11.↵
    1. Gaudet P.,
    2. Bairoch A.,
    3. Field D.,
    4. Sansone S. A.,
    5. Taylor C.,
    6. et al

    . Towards BioDBcore: A Community-defined Information Specification for Biological Databases. Database (Oxford) 2011, baq027.
12. 12.↵
    1. Altschul S. F.,
    2. Gish W.,
    3. Miller W.,
    4. Myers E. W.,
    5. Lipman D. J.

    Basic Local Alignment Search Tool. J. Mol. Biol. 1990, 215 (3), 403–410.

    OpenUrlCrossRefPubMedWeb of Science
13. 13.↵
    1. Afgan E.,
    2. Baker D.,
    3. van den Beek M.,
    4. Blankenberg D.,
    5. Bouvier D.,
    6. et al

    . The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016, 44, W3–W10.

    OpenUrlCrossRefPubMed
14. 14.↵
    1. Lynch V. J.,
    2. Bedoya-Reina O. C.,
    3. Ratan A.,
    4. Sulak M.,
    5. Drautz-Moses D. I.,
    6. et al

    . Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Rep. 2015, 12 (2), 217–228.

    OpenUrlCrossRefPubMed
15. 15.↵
    1. Heydarian M.,
    2. Luperchio T. R.,
    3. Cutler J.,
    4. Mitchell C. J.,
    5. Kim M. S.,
    6. et al

    . Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis. J. Proteomics Bioinform. 2014, 7, 50–63.

    OpenUrlCrossRef
16. 16.↵
    1. Pond S. K.,
    2. Wadhawan S.,
    3. Chiaromonte F.,
    4. Ananda G.,
    5. Chung W. Y.,
    6. et al

    . Windshield Splatter Analysis with the Galaxy Metagenomic Pipeline. Genome Res. 2009, 19 (11), 2144–2153.

    OpenUrlAbstract/FREE Full Text
17. 17.↵
    1. Miller W.,
    2. Schuster S. C.,
    3. Welch A. J.,
    4. Ratan A.,
    5. Bedoya-Reina O. C.,
    6. et al

    . Polar and Brown Bear Genomes Reveal Ancient Admixture and Demographic Footprints of Past Climate Change. Proc. Natl Acad. Sci. U S A 2012, 109 (36), E2382–E2390.

    OpenUrlAbstract/FREE Full Text
18. 18.↵
    1. Zook J. M.,
    2. Catoe D.,
    3. McDaniel J.,
    4. Vang L.,
    5. Spies N.,
    6. et al

    . Extensive Sequencing of Seven Human Genomes To Characterize Benchmark Reference Materials. Sci. Data 2016, 3, 160025.

    OpenUrlCrossRefPubMed
19. 19.
    1. Benson D. A.,
    2. Karsch-Mizrachi I.,
    3. Lipman D. J.,
    4. Ostell J.,
    5. Wheeler D. L.

    ; GenBank. Nucleic Acids Res. 2007, 35, D21–D25.

    OpenUrlCrossRefPubMedWeb of Science
20. 20.↵
    1. Goecks J.,
    2. Nekrutenko A.,
    3. Taylor J.

    Galaxy: A Comprehensive Approach for Supporting Accessible, Reproducible, and Transparent Computational Research in the Life Sciences. Genome Biol. 2010, 11, (8), R86.

    OpenUrlCrossRefPubMed
21. 21.↵
    1. Terry S. F.

    The Global Alliance for Genomics & Health. Genet. Test. Mol. Biomarkers 2014, 18 (6), 375–376.

    OpenUrl
22. 22.↵
    1. Brownstein C. A.,
    2. Beggs A. H.,
    3. Homer N.,
    4. Merriman B.,
    5. Yu T. W.,
    6. et al

    . An International Effort towards Developing Standards for Best Practices in Analysis, Interpretation and Reporting of Clinical Genome Sequencing Results in the CLARITY Challenge. Genome Biol. 2014, 15 (1), R53.

    OpenUrlCrossRefPubMed