Bioconda: sustainable and comprehensive software distribution for the life sciences
| العنوان: | Bioconda: sustainable and comprehensive software distribution for the life sciences |
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| المؤلفون: | Dale R., Gruning B., Sjodin A., Rowe J., Chapman B. A., Tomkins-Tinch C. H., Valieris R., Batut B., Caprez A., Cokelaer T., Yusuf D., Beauchamp K. A., Brinda K., Wollmann T., Corguille G. L., Ryan D., Bretaudeau A., Hoogstrate Y., Pedersen B. S., Heeringen S., Raden M., Luna-Valero S., Soranzo N., Smet M. D., Kuster G. V., Kirchner R., Pantano L., Charlop-Powers Z., Thornton K., Martin M., Beek M. D., Maticzka D., Miladi M., Will S., Gravouil K., Unneberg P., Brueffer C., Blank C., Piro V. C., Wolff J., Antao T., Gladman S., Shlyakhter I., Hollander M., Mabon P., Shen W., Boekel J., Holtgrewe M., Bouvier D., de Ruiter J. R., Cabral J., Choudhary S., Harding N., Kleinkauf R., Enns E., Eggenhofer F., Brown J., Cock P. J. A., Timm H., Thomas C., Zhang X. -O., Chambers M., Turaga N., Seiler E., Brislawn C., Pruesse E., Fallmann J., Kelleher J., Nguyen H., Parsons L., Fang Z., Stovner E. B., Stoler N., Ye S., Wohlers I., Farouni R., Freeberg M., Johnson J. E., Bargull M., Kensche P. R., Webster T. H., Eppley J. M., Stahl C., Rose A. S., Reynolds A., Wang L. -B., Garnier X., Dirmeier S., Knudsen M., Taylor J., Srivastava A., Rai V., Agren R., Junge A., Guimera R. V., Khan A., Schmeier S., He G., Pinello L., Hagglund E., Mikheyev A. S., Preussner J., Waters N. R., Li W., Capellades J., Chande A. T., Pirola Y., Hiltemann S., Bendall M. L., Singh S., Dunn W. A., Drouin A., Domenico T. D., Bruijn I., Larson D. E., Chicco D., Grassi E., Gonnella G., B J., Wang L., Giacomoni F., Clarke E., Blankenberg D., Tran C., Patro R., Laurent S., Gopez M., Sennblad B., Baaijens J. A., Ewels P., Wright P. R., Enache O. M., Roger P., Dampier W., Koppstein D., Devisetty U. K., Rausch T., Cornwell M., Salatino A. E., Seiler J., Jung M., Kornobis E., Cumbo F., Stocker B. K., Moskalenko O., Bogema D. R., Workentine M. L., Newhouse S. J., Leprevost F. D. V., Arvai K., Koster J. |
| المساهمون: | Albert-Ludwigs-Universität Freiburg, National Institutes of Health [Bethesda] (NIH), Swedish Defence Research Agency [Stockholm] (FOI), Umeå University, Harvard T.H. Chan School of Public Health, New York University [Abu Dhabi], NYU System (NYU), Harvard University [Cambridge], Hospital Camargo Sao Paulo, Partenaires INRAE, University of Duisburg-Essen, This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health (R.D.), the Netherlands Organisation for Scientific Research (NWO) (VENI grant 016.Veni.173.076 to J.K.), the German Research Foundation (SFB 876 to J.K.), and the NYU Abu Dhabi Research Institute for the NYU Abu Dhabi Center for Genomics and Systems Biology, program number CGSB1 (grant to J.R. and A. Yousif)., We thank all contributors, the conda-forge team, and Anaconda Inc. for excellent cooperation. Further, we thank Travis CI (https://travis-ci.comTest) and Circle CI (https://circleci.comTest) for providing free Linux and macOS computing capacity. Finally, we thank ELIXIR (https://www.elixir-europe.orgTest) for constant support and donation of staff., Etienne Kornobis (Epigenetic Regulation Unit, Institut Pasteur, Paris, France) fait partie de Bioconda Team, Bioinformatics Group, Department of Computer Science, University of Freiburg [Freiburg], Laboratory of Cellular and Developmental Biology (LCDB), NIDDK, NIH, Department of Organismic and Evolutionary Biology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Umea Plant Science Center (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Harvard University, Universität Duisburg-Essen = University of Duisburg-Essen [Essen], Dale, R, Gruning, B, Sjodin, A, Rowe, J, Chapman, B, Tomkins-Tinch, C, Valieris, R, Batut, B, Caprez, A, Cokelaer, T, Yusuf, D, Beauchamp, K, Brinda, K, Wollmann, T, Corguille, G, Ryan, D, Bretaudeau, A, Hoogstrate, Y, Pedersen, B, Heeringen, S, Raden, M, Luna-Valero, S, Soranzo, N, Smet, M, Kuster, G, Kirchner, R, Pantano, L, Charlop-Powers, Z, Thornton, K, Martin, M, Beek, M, Maticzka, D, Miladi, M, Will, S, Gravouil, K, Unneberg, P, Brueffer, C, Blank, C, Piro, V, Wolff, J, Antao, T, Gladman, S, Shlyakhter, I, Hollander, M, Mabon, P, Shen, W, Boekel, J, Holtgrewe, M, Bouvier, D, de Ruiter, J, Cabral, J, Choudhary, S, Harding, N, Kleinkauf, R, Enns, E, Eggenhofer, F, Brown, J, Cock, P, Timm, H, Thomas, C, Zhang, X, Chambers, M, Turaga, N, Seiler, E, Brislawn, C, Pruesse, E, Fallmann, J, Kelleher, J, Nguyen, H, Parsons, L, Fang, Z, Stovner, E, Stoler, N, Ye, S, Wohlers, I, Farouni, R, Freeberg, M, Johnson, J, Bargull, M, Kensche, P, Webster, T, Eppley, J, Stahl, C, Rose, A, Reynolds, A, Wang, L, Garnier, X, Dirmeier, S, Knudsen, M, Taylor, J, Srivastava, A, Rai, V, Agren, R, Junge, A, Guimera, R, Khan, A, Schmeier, S, He, G, Pinello, L, Hagglund, E, Mikheyev, A, Preussner, J, Waters, N, Li, W, Capellades, J, Chande, A, Pirola, Y, Hiltemann, S, Bendall, M, Singh, S, Dunn, W, Drouin, A, Domenico, T, Bruijn, I, Larson, D, Chicco, D, Grassi, E, Gonnella, G, B, J, Giacomoni, F, Clarke, E, Blankenberg, D, Tran, C, Patro, R, Laurent, S, Gopez, M, Sennblad, B, Baaijens, J, Ewels, P, Wright, P, Enache, O, Roger, P, Dampier, W, Koppstein, D, Devisetty, U, Rausch, T, Cornwell, M, Salatino, A, Seiler, J, Jung, M, Kornobis, E, Cumbo, F, Stocker, B, Moskalenko, O, Bogema, D, Workentine, M, Newhouse, S, Leprevost, F, Arvai, K, Koster, J, Urology, Pathology |
| المصدر: | Nature Methods Nature Methods, Nature Publishing Group, 2018, 15 (7), pp.475-476. ⟨10.1038/s41592-018-0046-7⟩ Nature Methods, Nature Publishing Group, 2018, 15 (7), pp.475-476 Nature Methods, 2018, 15 (7), pp.475-476. ⟨10.1038/s41592-018-0046-7⟩ Nature Methods, 15(7), 475-476. Nature Publishing Group |
| بيانات النشر: | HAL CCSD, 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Medizin, computer.software_genre, Biochemistry, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Software system, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Social software engineering, Database, business.industry, Software development, INF/01 - INFORMATICA, Computational Biology, Cell Biology, Software distribution, 030104 developmental biology, Software construction, [SDE]Environmental Sciences, Package development process, Backporting, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Software, 030217 neurology & neurosurgery, Biotechnology |
| الوصف: | International audience; We present Bioconda (https://bioconda.github.ioTest), a distribution of bioinformatics software for the lightweight, multi- platform and language-agnostic package manager Conda. Currently, Bioconda o ers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bio- conda improves analysis reproducibility by allowing users to de ne isolated environments with de ned software versions, all of which are easily installed and managed without administrative privileges. |
| اللغة: | English |
| تدمد: | 1548-7091 1548-7105 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::183f2a9d867a8a3bf8cb7ac58bc6740eTest https://hal-pasteur.archives-ouvertes.fr/pasteur-02926292Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....183f2a9d867a8a3bf8cb7ac58bc6740e |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15487091 15487105 |
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