ISAC's Gating-ML 2.0 data exchange standard for gating description

Cytometry Part A

Volumn 87, Issue 7, 2015, Pages 683-687

  Spidlen, Josef ^a   Moore, Wayne ^b,m   Brinkman, Ryan ^a   Almarode, Jay ^d   Anderson, Ernie ^e   Blenman, Kim ^f   Bray, Chris ^g   Martin Buscher ^h   Cavenaugh, James ⁱ   Goldberg, Michael ⁱ   Hyun, Bill ^j   Kripal, David ^k   Krouse, Kevin ^k   Leif, Robert ^l   Novo, David ⁿ   Parks, David ^m   Treister, Adam ^k   Wood, James ^o   Zordan, Michael ^p  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^d Amron Neuroscience   (United States)

^e BECKMAN COULTER INC   (United States)

^f YALE UNIVERSITY   (United States)

^g Verity Software House Inc   (United States)

^h Miltenyi Biotechnology   (Germany)

ⁱ BD BIOSCIENCES   (United States)

^j UNIVERSITY OF CALIFORNIA   (United States)

^k University of California ^*  (United States)

^l Newport University   (United States)

^m STANFORD UNIVERSITY   (United States)

ⁿ De Novo Software   (United States)

^o WAKE FOREST UNIVERSITY   (United States)

^p Sony Biotechnology   (United States)

more..

Author keywords

Bioinformatics; Data standard; File format; Flow cytometry; Gating

Indexed keywords

BIOLOGY; FLOW CYTOMETRY; PROCEDURES; REPRODUCIBILITY; SOFTWARE; STANDARD; STANDARDS;

COMPUTATIONAL BIOLOGY; FLOW CYTOMETRY; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84932196277     PISSN: 15524922     EISSN: 15524930     Source Type: Journal    
DOI: 10.1002/cyto.a.22690     Document Type: Article

References (13)

1. Data File Standards Committee of the Society for Analytical Cytology. Data file standard for flow cytometry. Cytometry 1990;11:323-332.
2. Seamer LC, Bagwell CB, Barden L, Redelman D, Salzman GC, Wood JC, Murphy RF. Proposed new data file standard for flow cytometry, version FCS 3.0. Cytometry 1997;28:118-122.
3. Spidlen J, Moore W, Parks D, Goldberg M, Bray C, Bierre P, Gorombey P, Hyun B, Hubbard M, Lange S, et al. Data file standard for flow cytometry, version FCS 3.1. Cytometry A 2010;77A:97-100.
4. Spidlen J, Leif RC, Moore W, Roederer M, Brinkman RR; for the Advancement of Cytometry Data Standards Task Force IS. Gating-ML: XML-based gating descriptions in flow cytometry. Cytometry A 2008A;73:1151-1157.
5. World Wide Web Consortium (W3C). XML Schema 1.0 (W3C Recommendation). 2004. URL: http://www.w3.org/TR/xmlschema-1/. Accessed June 10, 2014.
6. Parks DR, Roederer M, Moore WA. A new "logicle" display method avoids deceptive effects of logarithmic scaling for low signals and compensated data. Cytometry A 2006;69A:541-551.
7. Stanford University-Office of Technology Licensing. An Improved Method for Visualization of Multidimensional Data ("Logicle"). 2004. URL: http://techfinder.stanford.edu/technology_detail.php?ID=23438. Accessed June 10, 2014.
8. Spidlen J, Gopalakrishnan N, Hahne F, Ellis B, Gentleman R, Dalphin M, LeMeur N, Purcell B. flowUtils-Utilities for flow cytometry. 2014. URL: http://www.bioconductor.org/packages/devel/bioc/html/flowUtils.html. Accessed October 30, 2014.
9. FlowRepository Development Team. Gating-ML 2.0 support in FlowRepository. 2014. URL: http://flowrepository.org/gating-ml-2-support. Accessed June 10, 2014.
10. Finck R. Gating-ML support in MATLAB. 2014. URL: http://www.mathworks.com/matlabcentral/fileexchange/46106-gating-ml. Accessed June 10, 2014.
11. Spidlen J. GPArc-GenePattern Archive, ApplyGatingML2 module. 2014. URL: http://tinyurl.com/GatingML2GPArc. Accessed June 10, 2014.
12. International Society for Advancement of Cytometry Data Standards Task Force. Archival Cytometry Standard (ACS). 2010. URL: http://flowcyt.sf.net/acs/ACS.v1.0.101013.pdf. Accessed June 10, 2014.
13. Spidlen J, Bray C, ISAC Data Standards Task Force, Brinkman RR. ISAC's classification results file format (CLR). Cytometry A 2015;87A:86-88.