Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers

PLoS Computational Biology

Volumn 13, Issue 5, 2017, Pages

  Grüning, Björn A ^a   Rasche, Eric ^b   Rebolledo Jaramillo, Boris ^c   Eberhard, Carl ^d   Houwaart, Torsten ^a   Chilton, John ^e   Coraor, Nate ^e   Backofen, Rolf ^a   Taylor, James ^d   Nekrutenko, Anton ^e  

^a UNIVERSITY OF FREIBURG   (Germany)

^b TEXAS A AND M UNIVERSITY   (United States)

^c UNIVERSIDAD DEL DESARROLLO   (Chile)

^d JOHNS HOPKINS UNIVERSITY   (United States)

^e PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX DATA; DATA SEQUENCING; ENTRY BARRIERS; HYBRID PLATFORM; PRIMARY DATA;

DATA ANALYSIS; HUMAN; PUBLICATION; SCIENTIST; BIOLOGY; HIGH THROUGHPUT SEQUENCING; MEDICAL RESEARCH; ORGANIZATION AND MANAGEMENT; PERSONNEL; PROCEDURES; SOFTWARE;

BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RESEARCH PERSONNEL; SOFTWARE;

EID: 85020102727     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1005425     Document Type: Article

References (21)

1. Fleury V, Gouyet JF, Leonetti M, Branching in Nature. Dynamics and Morphogenesis of Branching Structures, from Cell to River Networks. Springer Science & Business Media; 2013. Available from: http://books.google.com/books?id=WKXyCAAAQBAJ&pg=PR6&dq=intitle:branching+in+nature&hl=&cd=1&source=gbs_api.
2. van der Walt S, Colbert SC, Varoquaux G, The NumPy Array: A Structure for Efficient Numerical Computation. Comput Sci Eng. 2011;13(2):22–30.
3. Jones E, Oliphant T, Peterson P. SciPy: Open source scientific tools for Python, 2001-2008b;. Available from: https://www.scipy.org/
4. Hunter JD, Matplotlib: A 2D Graphics Environment. Comput Sci Eng. 2007;9(3):90–95.
5. Sloggett C, Goonasekera N, Afgan E, BioBlend: automating pipeline analyses within Galaxy and CloudMan. Bioinformatics. 2013;29(13):1685–1686. doi: 10.1093/bioinformatics/btt199 23630176
6. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP, GenePattern 2.0. Nat Genet. 2006;38(5):500–501. doi: 10.1038/ng0506-500 16642009
7. Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, et al. Mobyle: a new full web bioinformatics framework. Bioinformatics. 2009;25(22):3005. doi: 10.1093/bioinformatics/btp493 19689959
8. Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, et al. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci. 2011;2:34. doi: 10.3389/fpls.2011.00034 22645531
9. Goecks J, Nekrutenko A, Taylor J, Galaxy TeamGalaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86. doi: 10.1186/gb-2010-11-8-r86 20738864
10. Qu K, Garamszegi S, Wu F, Thorvaldsdóttir H, Liefeld T, Ocana M, et al. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016;13(3):245–247. doi: 10.1038/nmeth.3732 26780094
11. Pérez F, Granger BE, IPython: A System for Interactive Scientific Computing. Comput Sci Eng. 2007;9(3):21–29.
12. Gandrud, C. Reproducible Research with R and R Studio. 2013;.
13. Ide N, Pustejovsky J, Cieri C, Nyberg E, DiPersio D, Shi C, Murakami Y, Lin D, et al. In: The Language Application Grid. Cham: Springer International Publishing; 2016. p. 51–70. Available from: https://link.springer.com/chapter/10.1007/978-3-319-31468-6_4
14. Rebolledo Jaramillo B, Su MSW, Stoler N, McElhoe JA, Dickins B, Blankenberg D, et al. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proc Natl Acad Sci USA. 2014;111(43):15474–15479. doi: 10.1073/pnas.1409328111 25313049
15. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 2013;.
16. Schurch NJ, Schofield P, Gierlin′ski M, Cole C, Sherstnev A, Singh V, et al. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?RNA. 2016;22(6):839–851. doi: 10.1261/rna.053959.115 27022035
17. Kim D, Langmead B, Salzberg SL, HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; p. 1–6.
18. Anders S, Pyl PT, Huber W, HTSeq–A Python framework to work with high-throughput sequencing data. Bioinformatics. 2014;31(2):btu638–169.
19. Love MI, Huber W, Anders S, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):1.
20. Cree LM, Samuels DC, de Sousa Lopes SC, Rajasimha HK, Wonnapinij P, Mann JR, et al. A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Nat Genet. 2008;40(2):249–254. doi: 10.1038/ng.2007.63 18223651
21. Blankenberg Daniel, Kuster Von, Gregory Bouvier, Emil Baker, Dannon Afgan, Enis Stoler, Nicholas et al. Dissemination of scientific software with Galaxy ToolShed. Genome Biology. 2014;15(2):403. doi: 10.1186/gb4161 25001293