OpenBEB: Open biological experiment browser for correlative measurements

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Ramakrishnan, Chandrasekhar ^a,b   Bieri, Andrej ^a   Sauter, Nora ^a   Roizard, Sophie ^c   Ringler, Philippe ^a   Müller, Shirley A ^a   Goldie, Kenneth N ^a   Enimanev, Kaloyan ^b   Stahlberg, Henning ^a   Rinn, Bernd ^a,b   Braun, Thomas ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

^b ETH ZURICH   (Switzerland)

^c EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER ARCHITECTURE; COMPUTER PROGRAMMING; DATA ACQUISITION; INFORMATION MANAGEMENT; METADATA; MOLECULAR BIOLOGY;

BIOLOGICAL EXPERIMENTS; COMPLEMENTARY TECHNIQUES; DATA MANAGEMENT TOOLS; DEPLOYMENT MECHANISMS; HIGH-THROUGHPUT APPROACHES; INTERACTION NETWORKS; NEW EXPERIMENTAL METHOD; SCIENTIFIC COMMUNITY;

EXPERIMENTS;

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; LABORATORY AUTOMATION; METHODOLOGY; SYSTEMS BIOLOGY;

AUTOMATION, LABORATORY; COMPUTER SIMULATION; SOFTWARE DESIGN; SYSTEMS BIOLOGY;

EID: 84897943633     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-84     Document Type: Article

References (10)

1. Aderem A. Systems biology: its practice and challenges. Cell 2005, 121:511-513. 10.1016/j.cell.2005.04.020, 15907465.
2. Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S-cerevisiae reveals the architecture of biological noise. Nature 2006, 441:840-846. 10.1038/nature04785, 16699522.
3. Allan C, Burel JM, Moore J, Blackburn C, Linkert M, Loynton S, MacDonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. OMERO: flexible, model-driven data management for experimental biology. Nat Methods 2012, 9:245-253. 10.1038/nmeth.1896, 3437820, 22373911.
4. Suloway C, Pulokas J, Fellmann D, Cheng A, Guerra F, Quispe J, Stagg S, Potter CS, Carragher B. Automated molecular microscopy: the new Leginon system. J Struct Bio 2005, 151:41-60.
5. Kislinger T, Rahman K, Radulovic D, Cox B, Rossant J, Emili A. PRISM, a generic large scale proteomic investigation strategy for mammals. Mol Cell Proteomics 2003, 2:96-106. 10.1074/mcp.M200074-MCP200, 12644571.
6. Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmstrom L, Aebersold R, Rinn B. openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinforma 2011, 12:468.
7. ZIP File Format Specification. http://www.pkware.com/documents/casestudies/APPNOTE.TXT.
8. Kemmerling S, Ziegler J, Schweighauser G, Arnold SA, Giss D, Müller SA, Ringler P, Goldie KN, Goedecke N, Hierlemann A, Stahlberg H, Braun T. Connecting μ-fluidics to electron microscopy. J Struct Biol 2012, 177:128-134. 10.1016/j.jsb.2011.11.001, 22094535.
9. Engel A. Chapter 9 - Scanning transmission electron microscopy: biological applications. Advances in Imaging and Electron Physics 2009, 159:357-386. Amsterdam: Elsevier Inc, Hawkes PW.
10. Kemmerling S, Arnold SA, Bircher BA, Sauter N, Escobedo C, Dernick G, Hierlemann A, Stahlberg H, Braun T. Single-cell lysis for visual analysis by electron microscopy. J Struct Biol 2013, 183:467-473. 10.1016/j.jsb.2013.06.012, 23816812.