A Framework for the Interoperability of Cloud Platforms: Towards FAIR Data in SAFE Environments

Autor: Robert L. Grossman, Rebecca R. Boyles, Brandi N. Davis-Dusenbery, Amanda Haddock, Allison P. Heath, Brian D. O’Connor, Adam C. Resnick, Deanne M. Taylor, Stan Ahalt

Publikováno v: Scientific Data, Vol 11, Iss 1, Pp 1-8 (2024)

As the number of cloud platforms supporting scientific research grows, there is an increasing need to support interoperability between two or more cloud platforms. A well accepted core concept is to make data in cloud platforms Findable, Accessible,

Externí odkaz: https://doaj.org/article/a36aa7d60b3e414aa2ca10b14b3b4a81

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

Autor: Michael C. Schatz, Anthony A. Philippakis, Enis Afgan, Eric Banks, Vincent J. Carey, Robert J. Carroll, Alessandro Culotti, Kyle Ellrott, Jeremy Goecks, Robert L. Grossman, Ira M. Hall, Kasper D. Hansen, Jonathan Lawson, Jeffrey T. Leek, Anne O’Donnell Luria, Stephen Mosher, Martin Morgan, Anton Nekrutenko, Brian D. O’Connor, Kevin Osborn, Benedict Paten, Candace Patterson, Frederick J. Tan, Casey Overby Taylor, Jennifer Vessio, Levi Waldron, Ting Wang, Kristin Wuichet, Alexander Baumann, Andrew Rula, Anton Kovalsy, Clare Bernard, Derek Caetano-Anollés, Geraldine A. Van der Auwera, Justin Canas, Kaan Yuksel, Kate Herman, M. Morgan Taylor, Marianie Simeon, Michael Baumann, Qi Wang, Robert Title, Ruchi Munshi, Sushma Chaluvadi, Valerie Reeves, William Disman, Salin Thomas, Allie Hajian, Elizabeth Kiernan, Namrata Gupta, Trish Vosburg, Ludwig Geistlinger, Marcel Ramos, Sehyun Oh, Dave Rogers, Frances McDade, Mim Hastie, Nitesh Turaga, Alexander Ostrovsky, Alexandru Mahmoud, Dannon Baker, Dave Clements, Katherine E.L. Cox, Keith Suderman, Nataliya Kucher, Sergey Golitsynskiy, Samantha Zarate, Sarah J. Wheelan, Kai Kammers, Ana Stevens, Carolyn Hutter, Christopher Wellington, Elena M. Ghanaim, Ken L. Wiley, Jr., Shurjo K. Sen, Valentina Di Francesco, Deni s Yuen, Brian Walsh, Luke Sargent, Vahid Jalili, John Chilton, Lori Shepherd, B.J. Stubbs, Ash O’Farrell, Benton A. Vizzier, Jr., Charles Overbeck, Charles Reid, David Charles Steinberg, Elizabeth A. Sheets, Julian Lucas, Lon Blauvelt, Louise Cabansay, Noah Warren, Brian Hannafious, Tim Harris, Radhika Reddy, Eric Torstenson, M. Katie Banasiewicz, Haley J. Abel, Jason Walker

Publikováno v: Cell Genomics, Vol 2, Iss 1, Pp 100085- (2022)

Summary: The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, managemen

Externí odkaz: https://doaj.org/article/95ac1623e901491c821d128f529da364

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

Autor: Shakuntala Baichoo, Yassine Souilmi, Sumir Panji, Gerrit Botha, Ayton Meintjes, Scott Hazelhurst, Hocine Bendou, Eugene de Beste, Phelelani T. Mpangase, Oussema Souiai, Mustafa Alghali, Long Yi, Brian D. O’Connor, Michael Crusoe, Don Armstrong, Shaun Aron, Fourie Joubert, Azza E. Ahmed, Mamana Mbiyavanga, Peter van Heusden, Lerato E. Magosi, Jennie Zermeno, Liudmila Sergeevna Mainzer, Faisal M. Fadlelmola, C. Victor Jongeneel, Nicola Mulder

Publikováno v: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-13 (2018)

Abstract Background The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research consortium fun

Externí odkaz: https://doaj.org/article/b9386fe4dced4b938ad6c01dba73df71

Correction: U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line.

Autor: Michael James Clark, Nils Homer, Brian D O'Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, Stanley F Nelson

Publikováno v: PLoS Genetics, Vol 14, Iss 5, p e1007392 (2018)

[This corrects the article DOI: 10.1371/journal.pgen.1000832.].

Externí odkaz: https://doaj.org/article/73af865225ee49c598b02cb89e808d4d

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

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Zechen, Chong, Oliver, Drechsel, Lewis Jonathan Dursi, Roland, Eils, Shadrielle M, G Espiritu, Robert, S Fulton, Shengjie, Gao, Josep L, L Gelpi, Mark, B Gerstein, Santiago, Gonzalez, Ivo, G Gut, Faraz, Hach, Michael, C Heinold, Jonathan, Hinton, Taobo, Hu, Vincent, Huang, Huang, Yi, Barbara, Hutter, David, R Jones, Jongsun, Jung, Natalie, Jäger, Hyung-Lae, Kim, Kortine, Kleinheinz, Sushant, Kumar, Yogesh, Kumar, Christopher, M Lalansingh, Ivica, Letunic, Dimitri, Livitz, Eric, Z Ma, Yosef, E Maruvka, R Jay Mashl, Andrew, Menzies, Ana, Milovanovic, Morten Muhlig Nielsen, Stephan, Ossowski, Nagarajan, Paramasivam, Jakob Skou Pedersen, Marc, D Perry, Montserrat, Puiggròs, Keiran, M Raine, Esther, Rheinbay, Romina, Royo, S Cenk Sahinalp, Iman, Sarrafi, Matthias, Schlesner, Jared, T Simpson, Lucy, Stebbings, Miranda, D Stobbe, Jon, W Teague, Grace, Tiao, David, Torrents, Jeremiah, A Wala, Jiayin, Wang, Sebastian, M Waszak, Joachim, Weischenfeldt, Michael, C Wendl, Johannes, Werner, 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Publikováno v: Nature Communications, 11(1):4748. Nature Publishing Group
Nature communications, 11(1):4748. Nature Publishing Group
Nature communications, 11 (1
NATURE COMMUNICATIONS
Nature Communications, 11 (1)
Nature Communications, Vol 11, Iss 1, Pp 1-27 (2020)
Bailey, M H, Meyerson, W U, Dursi, L J, Wang, L B, Dong, G, Liang, W W, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, M H, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, Weischenfeldt, J, Brunak, S, Ding, L, Favero, F, MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium 2020, ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ', Nature Communications, vol. 11, no. 1, 4748 . https://doi.org/10.1038/s41467-020-18151-y
Bailey, Matthew H; Meyerson, William U; Dursi, Lewis Jonathan; Wang, Liang-Bo; Dong, Guanlan; Liang, Wen-Wei; Weerasinghe, Amila; Li, Shantao; Kelso, Sean; Saksena, Gordon; Ellrott, Kyle; Wendl, Michael C; Wheeler, David A; Getz, Gad; Simpson, Jared T; Gerstein, Mark B; Ding, Li (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11(1), p. 4748. Springer Nature 10.1038/s41467-020-18151-y
Nature communications, vol 11, iss 1
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RUO. Repositorio Institucional de la Universidad de Oviedo
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Nature Communications
Dipòsit Digital de la UB
Universidad de Barcelona
Nature Communications, 11, 1
Recercat. Dipósit de la Recerca de Catalunya
Digital.CSIC. Repositorio Institucional del CSIC
Nature Communications, 11
RUO: Repositorio Institucional de la Universidad de Oviedo
Universidad de Oviedo (UNIOVI)
Bailey, M H, Meyerson, W U, Dursi, L J, Wang, L B, Dong, G, Liang, W W, Weerasinghe, A, Li, S, Kelso, S, Akbani, R, Anur, P, Bailey, M H, Buchanan, A, Chiotti, K, Covington, K, Creason, A, Ding, L, MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium 2020, ' Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples ', Nature Communications, vol. 11, no. 1, 4748 . https://doi.org/10.1038/s41467-020-18151-y
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)

MC3 Working Group: Rehan Akbani21, Pavana Anur22, Matthew H. Bailey1,2,3, Alex Buchanan9, Kami Chiotti9, Kyle Covington12,23, Allison Creason9, Li Ding1,2,3,20, Kyle Ellrott9, Yu Fan21, Steven Foltz1,2, Gad Getz8,14,15,16, Walker Hale12, David Haussl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79caf69aa08507159a37977adcb4937b
https://www.bib.irb.hr/1104730