References

Boland, M. R., Karczewski, K. J., Tatonetti, N. P. 2017. Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing. PLoS Computational Biology. 13 (1): e1005278. [10.1371/journal.pcbi.1005278] [id:Boland2017]

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C. P., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., Vingron, M. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.. Nature genetics. 29 (4): 365--71. [10.1038/ng1201-365] [id:Brazma2001]

Buneman, P., Khanna, S., Tan, W.-C. 2000. Data Provenance: Some Basic Issues. Lecture Notes in Computer Science: Foundations of Software Technology and Theoretical Computer Science. 1974 : 87--93. [10.1007/3-540-44450-5_6] [id:Buneman2000]

Chavan, V., Penev, L. 2011. The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics. 12 (Suppl 15): S2. [10.1186/1471-2105-12-S15-S2] [id:Chavan2011]

Cock, P. J. A., Fields, C. J., Goto, N., Heuer, M. L., Rice, P. M. 2009. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research. 38 (6): 1767--1771. [10.1093/nar/gkp1137] [id:Cock2009]

Gewin, V. 2016. Data sharing: An open mind on open data. Nature. 529 (7584): 117--119. [10.1038/nj7584-117a] [id:Gewin2016]

Goodman, S. N., Fanelli, D., Ioannidis, J. P. A. 2016. What does research reproducibility mean?. Science Translational Medicine. 8 (341): 341ps12--341ps12. [10.1126/scitranslmed.aaf5027] [id:Goodman2016]

Hart, E. M., Barmby, P., LeBauer, D., Michonneau, F., Mount, S., Mulrooney, P., Poisot, T., Woo, K. H., Zimmerman, N. B., Hollister, J. W. 2016. Ten Simple Rules for Digital Data Storage. PLoS Computational Biology. 12 (10): e1005097. [10.1371/journal.pcbi.1005097] [id:Hart2016]

Hoehndorf, R., Alshahrani, M., Gkoutos, G. V., Gosline, G., Groom, Q., Hamann, T., Kattge, J., de Oliveira, S. M., Schmidt, M., Sierra, S., Smets, E., Vos, R. A., Weiland, C. 2016. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Journal of Biomedical Semantics. 7 (1): 65. [10.1186/s13326-016-0107-8] [id:Hoehndorf2016]

Lariviere, V., Kiermer, V., MacCallum, C. J., McNutt, M., Patterson, M., Pulverer, B., Swaminathan, S., Taylor, S., Curry, S. 2016. A simple proposal for the publication of journal citation distributions. bioRxiv. 062109. [10.1101/062109] [id:Lariviere2016]

List, M., Ebert, P., Albrecht, F. 2017. Ten Simple Rules for Developing Usable Software in Computational Biology. PLoS Computational Biology. 13 (1): e1005265. [10.1371/journal.pcbi.1005265] [id:List2017]

Malone, J., Stevens, R., Jupp, S., Hancocks, T., Parkinson, H., Brooksbank, C. 2016. Ten Simple Rules for Selecting a Bio-ontology. PLoS Computational Biology. 12 (2): e1004743. [10.1371/journal.pcbi.1004743] [id:Malone2016]

Markowetz, F. 2017. All biology is computational biology. PLoS Biology. 15 (3): e2002050. [10.1371/journal.pbio.2002050] [id:Markowetz2017]

Michener, W. K. 2015. Ten Simple Rules for Creating a Good Data Management Plan. PLoS Computational Biology. 11 (10): e1004525. [10.1371/journal.pcbi.1004525] [id:Michener2015]

Mobley, A., Linder, S. K., Braeuer, R., Ellis, L. M., Zwelling, L. 2013. A Survey on Data Reproducibility in Cancer Research Provides Insights into Our Limited Ability to Translate Findings from the Laboratory to the Clinic. PLoS ONE. 8 (5): e63221. [10.1371/journal.pone.0063221] [id:Mobley2013]

Noble, W. S. 2009. A quick guide to organizing computational biology projects. PLoS Computational Biology. 5 (7): e1000424. [10.1371/journal.pcbi.1000424] [id:Noble2009]

Nosek, B. A., Alter, G., Banks, G. C., Borsboom, D., Bowman, S. D., Breckler, S. J., Buck, S., Chambers, C. D., Chin, G., Christensen, G., Contestabile, M., Dafoe, A., Eich, E., Freese, J., Glennerster, R., Goroff, D., Green, D. P., Hesse, B., Humphreys, M., Ishiyama, J., Karlan, D., Kraut, A., Lupia, A., Mabry, P., Madon, T., Malhotra, N., Mayo-Wilson, E., McNutt, M., Miguel, E., Paluck, E. L., Simonsohn, U., Soderberg, C., Spellman, B. A., Turitto, J., VandenBos, G., Vazire, S., Wagenmakers, E. J., Wilson, R., Yarkoni, T. 2015. Promoting an open research culture. Science. 348 (6242): 1422--1425. [10.1126/science.aab2374] [id:Nosek2015]

Pepe, A., Cantiello, M., Nicholson, J. 2017. The arXiv of the future will not look like the arXiv. Authorea preprint. [10.22541/au.149693987.70506124] [id:Pepe2017]

Perez-Riverol, Y., Gatto, L., Wang, R., Sachsenberg, T., Uszkoreit, J., Leprevost, F., Fufezan, C., Ternent, T., Eglen, S. J., Katz, D. S., Pollard, T. J., Konovalov, A., Flight, R. M., Blin, K., Vizcaino, J. A. 2016. Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Computational Biology. 12 (7): e1004947. [10.1371/journal.pcbi.1004947] [id:Perez2016]

Piwowar, H. A., Vision, T. J. 2013. Data reuse and the open data citation advantage. PeerJ. 1 : e175. [10.7717/peerj.175] [id:Piwowar2013]

Pond, S. K., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W. Y., Taylor, J., Nekrutenko, A. 2009. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research. 19 (11): 2144--2153. [10.1101/gr.094508.109] [id:Pond2009]

Sandve, G. K., Nekrutenko, A., Taylor, J., Hovig, E. 2013. Ten Simple Rules for Reproducible Computational Research. PLoS Computational Biology. 9 (10): e1003285. [10.1371/journal.pcbi.1003285] [id:Sandve2013]

Taschuk, M., Wilson, G. 2017. Ten simple rules for making research software more robust. PLoS Computational Biology. 13 (4): e1005412. [10.1371/journal.pcbi.1005412] [id:Taschuk2017]

Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P.-A., Julian, R. K., Jones, A. R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E. W., Dunn, M. J., Heck, A. J. R., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, A. A., Patterson, S. D., Ping, P., Seymour, S. L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T. M., Whitelegge, J. P., Wilkins, M. R., Xenarios, I., Yates, J. R., Hermjakob, H. 2007. The minimum information about a proteomics experiment (MIAPE).. Nature biotechnology. 25 (8): 887--93. [10.1038/nbt1329] [id:Taylor2007]

Weinberger, C. J., Evans, J. A., Allesina, S. 2015. Ten simple (Empirical) rules for writing science. PLoS Computational Biology. 11 (4): e1004205. [10.1371/journal.pcbi.1004205] [id:Weinberger2015]

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., {da Silva Santos}, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M, Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A., Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., {'t Hoen}, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S.-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J., Mons, B. 2016. The FAIR Guiding Principles for scientific data management and stewardship.. Scientific data. 3 : 160018. [10.1038/sdata.2016.18] [id:Wilkinson2016]

Zhang, W. 2014. Ten Simple Rules for Writing Research Papers. PLoS Computational Biology. 10 (1): e1003453. [10.1371/journal.pcbi.1003453] [id:Zhang2014]

Ziemann, M., Eren, Y., El-Osta, A. 2016. Gene name errors are widespread in the scientific literature. Genome Biology. 17 (1): 177. [10.1186/s13059-016-1044-7] [id:Ziemann2016]

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