-
1
-
-
49949099664
-
Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges
-
Stein LD. Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges. Nat Rev Genet 2008, 678-88.
-
(2008)
Nat Rev Genet
, pp. 678-688
-
-
Stein, L.D.1
-
4
-
-
79951493627
-
On the future of genomics data
-
Kahn SD. On the future of genomics data. Science 2011, 728-9.
-
(2011)
Science
, pp. 728-729
-
-
Kahn, S.D.1
-
5
-
-
67649595544
-
MIMAS 3.0 is a Multiomics Information Management and Annotation System
-
Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M. MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics 2009, 151.
-
(2009)
BMC Bioinformatics
, pp. 151
-
-
Gattiker, A.1
Hermida, L.2
Liechti, R.3
Xenarios, I.4
Collin, O.5
Rougemont, J.6
Primig, M.7
-
6
-
-
54849436647
-
MiMiR - an integrated platform for microarray data sharing, mining and analysis
-
10.1186/1471-2105-9-379, 2572073, 18801157
-
Tomlinson C, Thimma M, Alexandrakis S, Castillo T, Dennis JL, Brooks A, Bradley T, Turnbull C, Blaveri E, Barton G, et al. MiMiR - an integrated platform for microarray data sharing, mining and analysis. BMC Bioinformatics 2008, 9:379. 10.1186/1471-2105-9-379, 2572073, 18801157.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 379
-
-
Tomlinson, C.1
Thimma, M.2
Alexandrakis, S.3
Castillo, T.4
Dennis, J.L.5
Brooks, A.6
Bradley, T.7
Turnbull, C.8
Blaveri, E.9
Barton, G.10
-
7
-
-
77956486125
-
Next generation tools for genomic data generation, distribution, and visualization
-
10.1186/1471-2105-11-455, 2944281, 20828407
-
Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ. Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinformatics 2010, 11:455. 10.1186/1471-2105-11-455, 2944281, 20828407.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 455
-
-
Nix, D.A.1
Di Sera, T.L.2
Dalley, B.K.3
Milash, B.A.4
Cundick, R.M.5
Quinn, K.S.6
Courdy, S.J.7
-
8
-
-
78650616537
-
BiologicalNetworks 2.0 an integrative view of genome biology data
-
Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M. BiologicalNetworks 2.0 an integrative view of genome biology data. BMC Bioinformatics 2010, 610.
-
(2010)
BMC Bioinformatics
, pp. 610
-
-
Kozhenkov, S.1
Dubinina, Y.2
Sedova, M.3
Gupta, A.4
Ponomarenko, J.5
Baitaluk, M.6
-
9
-
-
30744438115
-
Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High throughput Biological Experiments
-
Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, States D, Hanash S, Paulovich A, McIntosh MW. Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High throughput Biological Experiments. J Proteome Research 2006, 5:112-121.
-
(2006)
J Proteome Research
, vol.5
, pp. 112-121
-
-
Rauch, A.1
Bellew, M.2
Eng, J.3
Fitzgibbon, M.4
Holzman, T.5
Hussey, P.6
Igra, M.7
Maclean, B.8
Lin, C.W.9
Detter, A.10
Fang, R.11
Faca, V.12
Gafken, P.13
Zhang, H.14
Whiteaker, J.15
States, D.16
Hanash, S.17
Paulovich, A.18
McIntosh, M.W.19
-
10
-
-
33645461851
-
PRISM: A data management system for high-throughput proteomics
-
10.1002/pmic.200500500, 16470653
-
Kiebel GR, Auberry KJ, Jaitly N, Clark DA, Monroe ME, Peterson ES, Tolic N, Anderson GA, Smith RD. PRISM: A data management system for high-throughput proteomics. Proteomics 2006, 6:1783-1790. 10.1002/pmic.200500500, 16470653.
-
(2006)
Proteomics
, vol.6
, pp. 1783-1790
-
-
Kiebel, G.R.1
Auberry, K.J.2
Jaitly, N.3
Clark, D.A.4
Monroe, M.E.5
Peterson, E.S.6
Tolic, N.7
Anderson, G.A.8
Smith, R.D.9
-
11
-
-
33645801199
-
2DDB - a bioinformatics solution for analysis of quantitative proteomics data
-
10.1186/1471-2105-7-158, 1435938, 16549013
-
Malmström L, Marko-Varga G, Westergren-Thorsson G, Laurell T, Malmström J. 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. BMC Bioinformatics 2006, 7:158. 10.1186/1471-2105-7-158, 1435938, 16549013.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 158
-
-
Malmström, L.1
Marko-Varga, G.2
Westergren-Thorsson, G.3
Laurell, T.4
Malmström, J.5
-
12
-
-
77951958243
-
CPFP: a central proteomics facilities pipeline
-
10.1093/bioinformatics/btq081, 20189941
-
Trudgian DC, Thomas B, McGowan SJ, Kessler BM, Salek M, Acuto O. CPFP: a central proteomics facilities pipeline. Bioinformatics 2010, 26:1131-2. 10.1093/bioinformatics/btq081, 20189941.
-
(2010)
Bioinformatics
, vol.26
, pp. 1131-1132
-
-
Trudgian, D.C.1
Thomas, B.2
McGowan, S.J.3
Kessler, B.M.4
Salek, M.5
Acuto, O.6
-
13
-
-
77954720730
-
MASPECTRAS 2: An integration and analysis platform for proteomic data
-
10.1002/pmic.201000075, 20455215
-
Ubaida Mohien C, Hartler J, Breitwieser F, Rix U, Remsing Rix L, Winter GE, Thallinger GG, Bennett KL, Superti-Furga G, Trajanoski Z, Colinge J. MASPECTRAS 2: An integration and analysis platform for proteomic data. Proteomics 2010, 10:2719-22. 10.1002/pmic.201000075, 20455215.
-
(2010)
Proteomics
, vol.10
, pp. 2719-2722
-
-
Ubaida Mohien, C.1
Hartler, J.2
Breitwieser, F.3
Rix, U.4
Remsing Rix, L.5
Winter, G.E.6
Thallinger, G.G.7
Bennett, K.L.8
Superti-Furga, G.9
Trajanoski, Z.10
Colinge, J.11
-
14
-
-
77957947158
-
ProHits: integrated software for mass spectrometry-based interaction proteomics
-
Liu G, Zhang J, Larsen B, Stark C, Breitkreutz A, Lin ZY, Breitkreutz BJ, Ding Y, Colwill K, Pasculescu A, Pawson T, Wrana JL, Nesvizhskii AI, Raught B, Tyers M, Gingras AC. ProHits: integrated software for mass spectrometry-based interaction proteomics. Nat Biotechnol 2010, 10:1015-7.
-
(2010)
Nat Biotechnol
, vol.10
, pp. 1015-1017
-
-
Liu, G.1
Zhang, J.2
Larsen, B.3
Stark, C.4
Breitkreutz, A.5
Lin, Z.Y.6
Breitkreutz, B.J.7
Ding, Y.8
Colwill, K.9
Pasculescu, A.10
Pawson, T.11
Wrana, J.L.12
Nesvizhskii, A.I.13
Raught, B.14
Tyers, M.15
Gingras, A.C.16
-
15
-
-
77955801615
-
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
10.1186/gb-2010-11-8-r86, 2945788, 20738864, Galaxy Team
-
Goecks J, Nekrutenko A, Taylor J, . Galaxy Team Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11:R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864, Galaxy Team.
-
(2010)
Genome Biol
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
16
-
-
84888284166
-
KNIME
-
KNIME. , http://www.knime.org/
-
-
-
-
17
-
-
10244255212
-
Taverna, an exemplar platform for integrating bioinformatics workflows across loosely coupled sites and thechnologies that share common semantics
-
10.1093/bioinformatics/bth361, 15201187
-
Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P. Taverna, an exemplar platform for integrating bioinformatics workflows across loosely coupled sites and thechnologies that share common semantics. Bioinformatics 2004, 20:3045-3054. 10.1093/bioinformatics/bth361, 15201187.
-
(2004)
Bioinformatics
, vol.20
, pp. 3045-3054
-
-
Oinn, T.1
Addis, M.2
Ferris, J.3
Marvin, D.4
Senger, M.5
Greenwood, M.6
Carver, T.7
Glover, K.8
Pocock, M.R.9
Wipat, A.10
Li, P.11
-
18
-
-
5444235762
-
Kepler: An Extensible System for Design and Execution of Scientific Workflows
-
Global Grid Forum 10
-
Altintas I, Berkley C, Jaeger E, Jones M, Ludäscher B, Mock S. Kepler: An Extensible System for Design and Execution of Scientific Workflows. Proceedings of the The Future of Grid Data Environments 2004, Global Grid Forum 10.
-
(2004)
Proceedings of the The Future of Grid Data Environments
-
-
Altintas, I.1
Berkley, C.2
Jaeger, E.3
Jones, M.4
Ludäscher, B.5
Mock, S.6
-
19
-
-
33244457031
-
Multi-Grid, Multi-User Workflows in the P-GRADE Grid Portal
-
Kacsuk P, Sipos G. Multi-Grid, Multi-User Workflows in the P-GRADE Grid Portal. J Grid Comp 2005, 3:221-238.
-
(2005)
J Grid Comp
, vol.3
, pp. 221-238
-
-
Kacsuk, P.1
Sipos, G.2
-
20
-
-
33846706581
-
TOPP-the OpenMS proteomics pipeline
-
10.1093/bioinformatics/btl299, 17237091
-
Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M. TOPP-the OpenMS proteomics pipeline. Bioinformatics 2007, 23:e191-7. 10.1093/bioinformatics/btl299, 17237091.
-
(2007)
Bioinformatics
, vol.23
-
-
Kohlbacher, O.1
Reinert, K.2
Gröpl, C.3
Lange, E.4
Pfeifer, N.5
Schulz-Trieglaff, O.6
Sturm, M.7
-
22
-
-
33746704351
-
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology
-
10.1186/1471-2105-7-286, 1524999, 16756676
-
Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 2006, 7:286. 10.1186/1471-2105-7-286, 1524999, 16756676.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 286
-
-
Marzolf, B.1
Deutsch, E.W.2
Moss, P.3
Campbell, D.4
Johnson, M.H.5
Galitski, T.6
-
23
-
-
80053638965
-
Life sciences data and application integration with B-fabric
-
Türker C, Akal F, Schlapbach R. Life sciences data and application integration with B-fabric. J Integr Bioinform 2011, 8:159.
-
(2011)
J Integr Bioinform
, vol.8
, pp. 159
-
-
Türker, C.1
Akal, F.2
Schlapbach, R.3
-
24
-
-
80053057733
-
The SEEK: a platform for sharing data and models in systems biology
-
Wolstencroft K, Owen S, du Preez F, Krebs O, Mueller W, Goble C, Snoep JL. The SEEK: a platform for sharing data and models in systems biology. Methods Enzymol 2011, 500:629-55.
-
(2011)
Methods Enzymol
, vol.500
, pp. 629-655
-
-
Wolstencroft, K.1
Owen, S.2
du Preez, F.3
Krebs, O.4
Mueller, W.5
Goble, C.6
Snoep, J.L.7
-
25
-
-
77958070752
-
Towards a comprehensive open source platform for management and analysis of High Content Screening data
-
Kozak K, Bauch A, Csucs G, Pylak T, Rinn B. Towards a comprehensive open source platform for management and analysis of High Content Screening data. Eur Pharmaceut Rev 2010, 4:34-39.
-
(2010)
Eur Pharmaceut Rev
, vol.4
, pp. 34-39
-
-
Kozak, K.1
Bauch, A.2
Csucs, G.3
Pylak, T.4
Rinn, B.5
-
26
-
-
0002630778
-
Persistence and loose coupling in living systems
-
Glassman RB. Persistence and loose coupling in living systems. Behavioral Science 1973, 18:83-98.
-
(1973)
Behavioral Science
, vol.18
, pp. 83-98
-
-
Glassman, R.B.1
-
27
-
-
0003885424
-
Software Engineering: A Practitioner's Approach
-
ISBN 0-071-26782-4
-
Pressman RS. Software Engineering: A Practitioner's Approach. McGraw-Hill Higher Education 1982, ISBN 0-071-26782-4.
-
(1982)
McGraw-Hill Higher Education
-
-
Pressman, R.S.1
-
28
-
-
35348910886
-
Guidelines for the effective use of entity-attribute-value modeling for biomedical databases
-
10.1016/j.ijmedinf.2006.09.023, 2110957, 17098467
-
Donu V, Nadkarni P. Guidelines for the effective use of entity-attribute-value modeling for biomedical databases. Int J Med Inform 2007, 76(11-12):769-779. 10.1016/j.ijmedinf.2006.09.023, 2110957, 17098467.
-
(2007)
Int J Med Inform
, vol.76
, Issue.11-12
, pp. 769-779
-
-
Donu, V.1
Nadkarni, P.2
-
29
-
-
0014797273
-
A Relational Model of Data for Large Shared Data Banks
-
Codd EF. A Relational Model of Data for Large Shared Data Banks. Comm ACM 1970, 13(6):377-387.
-
(1970)
Comm ACM
, vol.13
, Issue.6
, pp. 377-387
-
-
Codd, E.F.1
-
30
-
-
84888284195
-
CIFEX
-
CIFEX. , https://wiki-bsse.ethz.ch/display/CFX/Home
-
-
-
-
31
-
-
84888281043
-
Atlassian
-
Atlassian. , http://www.atlassian.com/software/crowd
-
-
-
-
32
-
-
84888279072
-
SRF
-
SRF. , http://srf.sourceforge.net
-
-
-
-
33
-
-
84888276852
-
Demo instance
-
Demo instance. , http://openbis-demo.ethz.ch
-
-
-
-
34
-
-
78751595020
-
Polycomb preferentially targets stalled promoters of coding and noncoding trascripts
-
Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R. Polycomb preferentially targets stalled promoters of coding and noncoding trascripts. Genome Res 2011, (2):216-26.
-
(2011)
Genome Res
, Issue.2
, pp. 216-226
-
-
Enderle, D.1
Beisel, C.2
Stadler, M.B.3
Gerstung, M.4
Athri, P.5
Paro, R.6
-
35
-
-
78751590899
-
Silencing chromatin: comparing modes and mechanisms
-
Beisel C, Paro R. Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet 2011, (2):123-35.
-
(2011)
Nat Rev Genet
, Issue.2
, pp. 123-135
-
-
Beisel, C.1
Paro, R.2
-
36
-
-
84870647022
-
UCSC Genome Browser
-
UCSC Genome Browser. , http://genome.ucsc.edu/cgi-bin/hgGateway
-
-
-
-
37
-
-
8344284323
-
A common open representation of mass spectrometry data and its application to proteomics research
-
Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotech 2004, 22:1459-1466.
-
(2004)
Nat Biotech
, vol.22
, pp. 1459-1466
-
-
Pedrioli, P.G.A.1
Eng, J.K.2
Hubley, R.3
Vogelzang, M.4
Deutsch, E.W.5
Raught, B.6
Pratt, B.7
Nilsson, E.8
Angeletti, R.H.9
Apweiler, R.10
Cheung, K.11
Costello, C.E.12
Hermjakob, H.13
Huang, S.14
Julian, R.K.15
Kapp, E.16
McComb, M.E.17
Oliver, S.G.18
Omenn, G.19
Paton, N.W.20
Simpson, R.21
Smith, R.22
Taylor, C.F.23
Zhu, W.24
Aebersold, R.25
more..
-
38
-
-
84888280415
-
Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry based proteomics
-
Malmstrom J, Karlsson C, Nordenfelt P, Ossola R, Weisser H, Quandt A, Hansson K, Aebersold R, Malmstrom L, Bjorck L. Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry based proteomics. J Biol Chem 2011,
-
(2011)
J Biol Chem
-
-
Malmstrom, J.1
Karlsson, C.2
Nordenfelt, P.3
Ossola, R.4
Weisser, H.5
Quandt, A.6
Hansson, K.7
Aebersold, R.8
Malmstrom, L.9
Bjorck, L.10
-
39
-
-
0031027334
-
Relative Contributions of Hyaluronic Acid Capsule and M Protein to Virulence in a Mucoid Strain of the Group A Streptococcus
-
174557, 8975893
-
Moses AE. Relative Contributions of Hyaluronic Acid Capsule and M Protein to Virulence in a Mucoid Strain of the Group A Streptococcus. Infect Immun 1997, 65:64-71. 174557, 8975893.
-
(1997)
Infect Immun
, vol.65
, pp. 64-71
-
-
Moses, A.E.1
-
40
-
-
84888282940
-
OpenBIS Documentation and Download Site
-
openBIS Documentation and Download Site. , https://wiki-bsse.ethz.ch/display/bis/Home
-
-
-
-
41
-
-
84888281295
-
GEO
-
GEO. , http://www.ncbi.nlm.nih.gov/geo/
-
-
-
-
42
-
-
33746930864
-
A uniform proteomics MS/MS analysis platform utilizing open XML file formats
-
Keller A, Eng J, Zhang N, Li XJ, Aebersold R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol Syst Biol 2005, 1:1-8.
-
(2005)
Mol Syst Biol
, vol.1
, pp. 1-8
-
-
Keller, A.1
Eng, J.2
Zhang, N.3
Li, X.J.4
Aebersold, R.5
-
43
-
-
84888276400
-
PeptideAtlas
-
PeptideAtlas. , http://www.peptideatlas.org
-
-
-
|