-
1
-
-
77955506280
-
What Do I Want from the Publisher of the Future?
-
doi:10.1371/journal.pcbi.1000787
-
Bourne PE (2010) What Do I Want from the Publisher of the Future? PLoS Comput Biol 6(5): e1000787. doi:10.1371/journal.pcbi.1000787.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.5
-
-
Bourne, P.E.1
-
2
-
-
47149093812
-
Examining the Challenges of Scientific Workflows
-
doi: http://dx.doi.org/10.1109/MC.2007.421
-
Gil Y, Deelman E, Ellisman M, Fahringer T, Fox G, et al (2007) Examining the Challenges of Scientific Workflows, IEEE Computer, vol. 40, no. 12, pp. 24-32, doi: http://dx.doi.org/10.1109/MC.2007.421.
-
(2007)
IEEE Computer
, vol.40
, Issue.12
, pp. 24-32
-
-
Gil, Y.1
Deelman, E.2
Ellisman, M.3
Fahringer, T.4
Fox, G.5
-
3
-
-
34548103735
-
Workflows for e-Science
-
1st Edition., 181 illus.
-
Taylor IJ, Deelman E, Gannon DB, Shields M (Eds.) (2007) Workflows for e-Science. Scientific Workflows for Grids, 1st Edition., XXII, 530 p. 181 illus.
-
(2007)
Scientific Workflows for Grids
, vol.22
, pp. 530
-
-
Taylor, I.J.1
Deelman, E.2
Gannon, D.B.3
Shields, M.4
-
4
-
-
78649661569
-
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
-
doi:10.1371/journal.pcbi.1000976
-
Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, et al. (2010) The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Comput Biol 6(11): e1000976. doi:10.1371/journal.pcbi.1000976.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.11
-
-
Kinnings, S.L.1
Xie, L.2
Fung, K.H.3
Jackson, R.M.4
Xie, L.5
-
5
-
-
67349196123
-
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
-
Doi: doi: 10.1038/nmeth.1333. Available from
-
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R et al (2009). A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nature Methods, 6(6):423-30. Doi: doi: 10.1038/nmeth.1333. Available from http://www.nature.com/nmeth/journal/v6/n6/full/nmeth.1333.html.
-
(2009)
Nature Methods
, vol.6
, Issue.6
, pp. 423-430
-
-
Bell, A.W.1
Deutsch, E.W.2
Au, C.E.3
Kearney, R.E.4
Beavis, R.5
-
6
-
-
59149088407
-
Repeatability of Published Microarray Gene Expression Analyses
-
doi: 10.1038/ng.295. Available from
-
Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X et al. (2009). Repeatability of Published Microarray Gene Expression Analyses. Nature Genetics, 41(2):149-55. doi: 10.1038/ng.295. Available from http://www.nature.com/ng/ journal/v41/n2/full/ng.295.html.
-
(2009)
Nature Genetics
, vol.41
, Issue.2
, pp. 149-155
-
-
Ioannidis, J.P.1
Allison, D.B.2
Ball, C.A.3
Coulibaly, I.4
Cui, X.5
-
7
-
-
79955753954
-
Case Studies in Reproducibility
-
doi: 10.1093/bib/bbq084. Available
-
Hothorn T, Leisch F (2011). Case Studies in Reproducibility. Briefings in Bioinformatics, 12(3). doi: 10.1093/bib/bbq084. Available: http://bib. oxfordjournals.org/content/12/3/288.
-
(2011)
Briefings in Bioinformatics
, vol.12
, Issue.3
-
-
Hothorn, T.1
Leisch, F.2
-
8
-
-
77951163222
-
Deriving Chemosensitivity from Cell Lines: Forensic Bioinformatics and Reproducible Research in High-Throughput Biology
-
doi: 10.1214/09-AOAS291. Available from
-
Baggerly KA, Coombes KR (2009) Deriving Chemosensitivity from Cell Lines: Forensic Bioinformatics and Reproducible Research in High-Throughput Biology. Annals of Applied Statistics, 3(4) 1309-1334. doi: 10.1214/09-AOAS291. Available from http://projecteuclid.org/DPubS?service = UI&version = 1.0&verb = Display&handle = euclid.aoas/1267453942.
-
(2009)
Annals of Applied Statistics
, vol.3
, Issue.4
, pp. 1309-1334
-
-
Baggerly, K.A.1
Coombes, K.R.2
-
10
-
-
80855164967
-
Retracted Science and the retracted index
-
doi:10.1128/IAI.05661-11
-
Fang CF, Casadevall A (2011). Retracted Science and the retracted index. Infection and Immunity. doi:10.1128/IAI.05661-11.
-
(2011)
Infection and Immunity
-
-
Fang, C.F.1
Casadevall, A.2
-
11
-
-
84945508858
-
Illuminating the Black Box
-
Editorial. Available: Accessed 2013 October 15
-
Nature Editorial. Illuminating the Black Box (2006). Nature, 442(7098). Available: http://www.nature.com/nature/journal/v442/n7098/full/442001a.html. Accessed 2013 October 15.
-
(2006)
Nature
, vol.442
, Issue.7098
-
-
-
12
-
-
84858376519
-
Scientists' Elusive Goal: Reproducing Study Results
-
Website. Available: Accessed 2013 October 15
-
Naik G (2011) Scientists' Elusive Goal: Reproducing Study Results. The Wall Street Journal Website. Available: http://online.wsj.com/news/articles/ SB10001424052970203764804577059841672541590 Accessed 2013 October 15.
-
(2011)
The Wall Street Journal
-
-
Naik, G.1
-
13
-
-
85053483930
-
Electronic documents give reproducible research a new meaning
-
Expanded Abstracts, 92: Society of Exploration Geophysics, Available from
-
Claerbout J, Karrenbach M (1992). Electronic documents give reproducible research a new meaning. 62nd Annual International Meeting of the Society of Exploration Geophysics., Expanded Abstracts, 92: Society of Exploration Geophysics, 601-604. Available from http://sepwww.stanford.edu/doku.php?id= sep:research:reproducible:seg92.
-
(1992)
62nd Annual International Meeting of the Society of Exploration Geophysics
, pp. 601-604
-
-
Claerbout, J.1
Karrenbach, M.2
-
14
-
-
23844508989
-
Making Scientific computations reproducible
-
Available from
-
Schwab M, Karrenbach N, Claerbout J (2000). Making Scientific computations reproducible. Computing in Science & Engineering, 2(6), pp.61-67. Available from http://sep.stanford.edu/lib/exe/fetch.php?id= sep%3Aresearch%3Areproducible&cache=cache&media=sep:research: reproducible:cip.pdf.
-
(2000)
Computing in Science & Engineering
, vol.2
, Issue.6
, pp. 61-67
-
-
Schwab, M.1
Karrenbach, N.2
Claerbout, J.3
-
15
-
-
85032750960
-
What, why and how of reproducible research in signal processing
-
Vandewalle P, Kovačević J, Vetterli M (2009) What, why and how of reproducible research in signal processing. IEEE Signal Processing 26(3) pp. 37-47. doi: http://dx.doi.org/10.1109/MSP.2009.932122.
-
(2009)
IEEE Signal Processing
, vol.26
, Issue.3
, pp. 37-47
-
-
Vandewalle, P.1
Kovačević, J.2
Vetterli, M.3
-
17
-
-
43249117418
-
The repeatability experiment of SIGMOD 2008
-
Available from
-
Manolescu I, Afanasiev L, Arion A, Dittrich J, Manegold S et al (2008). The repeatability experiment of SIGMOD 2008 ACM SIGMOD Record 37(1). Available from http://portal.acm.org/citation.cfm?id = 1374780.1374791&coll = &dl =&idx = J689h = newsletter&WantType=Newsletters&title= ACM%20SIGMOD%20Recor.
-
(2008)
ACM SIGMOD Record
, vol.37
, Issue.1
-
-
Manolescu, I.1
Afanasiev, L.2
Arion, A.3
Dittrich, J.4
Manegold, S.5
-
18
-
-
80053402117
-
Repeatability and workability evaluation of SIGMOD 2011
-
Bonnet P, Manegold S, Bjørling M, Cao W, Gonzalez J et al (2011). Repeatability and workability evaluation of SIGMOD 2011. SIGMOD Record 40(2): 45-48.
-
(2011)
SIGMOD Record
, vol.40
, Issue.2
, pp. 45-48
-
-
Bonnet, P.1
Manegold, S.2
Bjørling, M.3
Cao, W.4
Gonzalez, J.5
-
19
-
-
84896731534
-
RepliCHI SIG - From a panel to a new submission venue for replication
-
DOI:10.1145/2212360.2212419
-
Wilson ML, Mackay W, Hovy E, Chi MS, Bernstein JN (2012). RepliCHI SIG - from a panel to a new submission venue for replication. ACM SIGCHI. DOI:10.1145/2212360.2212419.
-
(2012)
ACM SIGCHI
-
-
Wilson, M.L.1
Mackay, W.2
Hovy, E.3
Chi, M.S.4
Bernstein, J.N.5
-
20
-
-
70149102312
-
Reproducible research and Biostatistics
-
Diggle PJ, Zeger SL (2009) Reproducible research and Biostatistics. Biostatistics 10(3).
-
(2009)
Biostatistics
, vol.10
, Issue.3
-
-
Diggle, P.J.1
Zeger, S.L.2
-
21
-
-
84896720264
-
-
website. Available: Accessed 2013 October 15
-
Beyond the PDF website. Available: http://sites.google.com/site/ beyondthepdf. Accessed 2013 October 15.
-
Beyond the PDF
-
-
-
22
-
-
84896740074
-
Improving Future Research Communication and e-Scholarship
-
Available: Accessed 2013 October 23
-
Bourne PE, Clark T, Dale R Waard A, Herman I et al (2013) "Improving Future Research Communication and e-Scholarship". The FORCE 11 Manifesto. Available: http://www.force11.org/white-paper. Accessed 2013 October 23.
-
(2013)
The FORCE 11 Manifesto
-
-
Bourne, P.E.1
Clark, T.2
Dale, R.3
Waard, A.4
Herman, I.5
-
23
-
-
58149122709
-
The Legal Framework for Reproducible Research in the Sciences: Licensing and Copyright
-
Stodden V (2009). The Legal Framework for Reproducible Research in the Sciences: Licensing and Copyright. IEEE Computing in Science and Engineering, 11(1).
-
(2009)
IEEE Computing in Science and Engineering
, vol.11
, Issue.1
-
-
Stodden, V.1
-
24
-
-
77956632782
-
Transparency and reproducibility in data analysis: The Prostate Cancer Prevention Trial
-
Baker SG, Drake AK, Pinsky P, Parnes HL, Kramer BS (2010) Transparency and reproducibility in data analysis: the Prostate Cancer Prevention Trial. Biostatistics, 11(3).
-
(2010)
Biostatistics
, vol.11
, Issue.3
-
-
Baker, S.G.1
Drake, A.K.2
Pinsky, P.3
Parnes, H.L.4
Kramer, B.S.5
-
25
-
-
84861052984
-
Replication studies: Bad copy
-
doi:10.1038/485298a
-
Yong E (2012) Replication studies: Bad copy. Nature 485, 298-300. doi:10.1038/485298a.
-
(2012)
Nature
, vol.485
, pp. 298-300
-
-
Yong, E.1
-
27
-
-
0242529706
-
Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis
-
Proceedings of Computational Statistics. In Härdle W, Rönz B (editors). doi: 10.1007/978-3-642-57489-4-89
-
Leisch F (2002) Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis. Proceedings of Computational Statistics. In Härdle W, Rönz B (editors). Compstat, Proceedings in Computational Statistics. pp. 575-580. doi: 10.1007/978-3-642-57489-4-89
-
(2002)
Compstat, Proceedings in Computational Statistics
, pp. 575-580
-
-
Leisch, F.1
-
28
-
-
84857959137
-
Caching code chunks in dynamic documents: The weaver package
-
Available
-
Falcon S (2007) Caching code chunks in dynamic documents: The weaver package. Computational Statistics, (24)2. Available: http://www.springerlink. com/content/55411257n1473414/.
-
(2007)
Computational Statistics
, Issue.24
, pp. 2
-
-
Falcon, S.1
-
29
-
-
75649122581
-
Accessible Reproducible Research
-
Available
-
Mesirov JP (2010) Accessible Reproducible Research. Science, 327:415. Available: http://www.sciencemag.org/cgi/rapidpdf/327/5964/415?ijkey =WzYHd6g6IBNeQ&keytype = ref&siteid = sci.
-
(2010)
Science
, vol.327
, pp. 415
-
-
Mesirov, J.P.1
-
31
-
-
79953183568
-
Special Issue on The third provenance challenge on using the open provenance model for interoperability
-
Simmhan Y, Groth P, Moreau L (Eds) (2011). Special Issue on The third provenance challenge on using the open provenance model for interoperability. Future Generation Computer Systems, 27(6).
-
(2011)
Future Generation Computer Systems
, vol.27
, Issue.6
-
-
Simmhan, Y.1
Groth, P.2
Moreau, L.3
-
32
-
-
79953210348
-
The Open Provenance Model Core Specification
-
v1.1. Preprint available from
-
Moreau L, Clifford B, Freire J, Futrelle J, Gil Y et al. (2011) The Open Provenance Model Core Specification (v1.1). Future Generation Computer Systems, 27(6). Preprint available from http://www.bibbase.org/cache/www.isi.edu--7Egil- publications.bib/moreau-etal-fgcs11.html.
-
(2011)
Future Generation Computer Systems
, vol.27
, Issue.6
-
-
Moreau, L.1
Clifford, B.2
Freire, J.3
Futrelle, J.4
Gil, Y.5
-
33
-
-
0033954256
-
The Protein Data Bank
-
2000 Available
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN et al (2000). The Protein Data Bank. Nucleic Acid Research 2000 28(1), 235-242. Available: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472/?tool =pubmed.
-
(2000)
Nucleic Acid Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
-
34
-
-
9144244232
-
MODBASE, a database of annotated comparative protein structure models and associated resources
-
Available from
-
Pieper U, Webb BM, Barkan DY, Schneidman-Duhovny D, Schlessinger A, et al. (2011). MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research 32(Database issue):D217-22. Available from: http://salilab.org/pdf/Pieper-NucleicAcidsRes- 2010.pdf.
-
(2011)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISSUE
-
-
Pieper, U.1
Webb, B.M.2
Barkan, D.Y.3
Schneidman-Duhovny, D.4
Schlessinger, A.5
-
35
-
-
84896737962
-
-
website. Available: Accessed 2013 October 15
-
TB-Drugome website. Available: http://funsite.sdsc.edu/drugome/TB. Accessed 2013 October 15.
-
TB-Drugome
-
-
-
36
-
-
84896726611
-
-
website. Available: Accessed 2013 October 15
-
Wings Drugome website. Available: http://www.wings-workflows.org/drugome. Accessed 2013 October 15.
-
Wings Drugome
-
-
-
37
-
-
79960253596
-
A Semantic Framework for Automatic Generation of Computational Workflows Using Distributed Data and Component Catalogs
-
Gil Y, Gonzalez-Calero PA, Kim J, Moody J, Ratnakar V (2011). A Semantic Framework for Automatic Generation of Computational Workflows Using Distributed Data and Component Catalogs. Journal of Experimental and Theoretical Artificial Intelligence, 23(4).
-
(2011)
Journal of Experimental and Theoretical Artificial Intelligence
, vol.23
, Issue.4
-
-
Gil, Y.1
Gonzalez-Calero, P.A.2
Kim, J.3
Moody, J.4
Ratnakar, V.5
-
38
-
-
79951861831
-
Wings: Intelligent Workflow-Based Design of Computational Experiments
-
Gil Y, Ratnakar V, Kim J, Gonzalez-Calero PA, Groth P et al (2011). Wings: Intelligent Workflow-Based Design of Computational Experiments. IEEE Intelligent Systems, 26(1).
-
(2011)
IEEE Intelligent Systems
, vol.26
, Issue.1
-
-
Gil, Y.1
Ratnakar, V.2
Kim, J.3
Gonzalez-Calero, P.A.4
Groth, P.5
-
39
-
-
84896695958
-
-
website. Available from: Accessed on October 15, 2013
-
Wings workflow management system website. Available from: http://www.wings-workflows.org. Accessed on October 15, 2013.
-
Wings Workflow Management System
-
-
-
40
-
-
48249123880
-
Computational Biology Resources Lack Persistence and Usability
-
Veretnik S, Fink JL, Bourne PE (2008). Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136
-
(2008)
PLoS Comp. Biol.
, vol.4
, Issue.7
-
-
Veretnik, S.1
Fink, J.L.2
Bourne, P.E.3
-
41
-
-
84864205983
-
Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach
-
Rocca RA, Magoon G, Reynolds DF, Krahn T, Tilroe VO et al. (2012) Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach. PLoS ONE 7(7).
-
(2012)
PLoS ONE
, vol.7
, Issue.7
-
-
Rocca, R.A.1
Magoon, G.2
Reynolds, D.F.3
Krahn, T.4
Tilroe, V.O.5
-
42
-
-
44449139387
-
Detecting Evolutionary Linkages Across Fold and Functional Space with Sequence Order Independent Profile-profile Alignments
-
Xie L, Bourne PE (2008) Detecting Evolutionary Linkages Across Fold and Functional Space with Sequence Order Independent Profile-profile Alignments. Proc. Nat. Acad. Sci. (USA), 105(14) 5441-5446.
-
(2008)
Proc. Nat. Acad. Sci. (USA)
, vol.105
, Issue.14
, pp. 5441-5446
-
-
Xie, L.1
Bourne, P.E.2
-
43
-
-
78449284386
-
Precalculated Protein Structure Alignments at the RCSB PDB website
-
doi:10.1093/bioinformatics/btq572. Available
-
Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C et al (2010) Precalculated Protein Structure Alignments at the RCSB PDB website. Bioinformatics, doi:10.1093/bioinformatics/btq572. Available: http://bioinformatics. oxfordjournals.org/content/early/2010/10/10/bioinformatics.btq572.abstract. html?ijkey= zAIg7fpd9Bhgni4&keytype = ref.
-
(2010)
Bioinformatics
-
-
Prlic, A.1
Bliven, S.2
Rose, P.W.3
Bluhm, W.F.4
Bizon, C.5
-
44
-
-
84855187626
-
Improving molecular docking through eHiTS' tunable scoring function
-
Available
-
Ravitz O, Zsoldos Z, Simon A (2011). Improving molecular docking through eHiTS' tunable scoring function. Journal of ComputerAided Molecular Design. Available: http://www.ncbi.nlm.nih.gov/pubmed/22076470.
-
(2011)
Journal of ComputerAided Molecular Design
-
-
Ravitz, O.1
Zsoldos, Z.2
Simon, A.3
-
46
-
-
84896694908
-
-
website. Available: Accessed 2013 October 15
-
W3C Provenance Working Group website. Available: http://www.w3.org/2011/ prov/wiki/Main-Page. Accessed 2013 October 15.
-
-
-
-
47
-
-
84896710098
-
-
Website. Available: Accessed 2013 October 15
-
OPMW Website. Available: http://www.opmw.org. Accessed 2013 October 15.
-
-
-
-
49
-
-
85046448768
-
Linked Data: Evolving the Web into a Global Data Space
-
Morgan and Claypool Publishers
-
Heath T, Bizer C (2011). Linked Data: Evolving the Web into a Global Data Space. Morgan and Claypool Publishers, Synthesis Lectures on the Semantic Web. 136 p.
-
(2011)
Synthesis Lectures on the Semantic Web
, pp. 136
-
-
Heath, T.1
Bizer, C.2
-
50
-
-
84857953041
-
A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data
-
doi: 10.1145/2110497.2110504
-
Garijo D, Gil Y (2011). A New Approach for Publishing Workflows: Abstractions, Standards, and Linked Data. Proceedings of the Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS'11), held in conjunction with SC 2011, Seattle, Washington. pp. 47-56 doi: 10.1145/2110497.2110504, http://doi.acm.org/10.1145/2110497.2110504.
-
(2011)
Proceedings of the Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS'11), Held in Conjunction with SC 2011, Seattle, Washington
, pp. 47-56
-
-
Garijo, D.1
Gil, Y.2
-
52
-
-
84896710142
-
-
Available: Accessed 2013 October 15
-
FigShare data repository. Available: http://figshare.com/. Accessed 2013 October 15.
-
FigShare Data Repository
-
-
-
53
-
-
84877272579
-
Enhancing reproducibility
-
doi:10.1038/nmeth.2471
-
Nature Methods (2013). Enhancing reproducibility., 10, 367. doi:10.1038/nmeth.2471.
-
(2013)
Nature Methods
, vol.10
, pp. 367
-
-
-
54
-
-
84896721973
-
Reporting Checklist for Life Sciences Articles
-
Website Available: Accessed 2013 October 15
-
Nature Website(2013). Reporting Checklist for Life Sciences Articles, Nature. Available: http://www.nature.com/authors/policies/checklist.pdf. Accessed 2013 October 15.
-
(2013)
Nature
-
-
-
55
-
-
84883739411
-
-
Executive Order, Available: Accessed 2013 October 15
-
Obama B (2013). Making Open and Machine Readable the New Default for Government Information. Executive Order, The White House. Available: http://www.whitehouse.gov/the-press-office/2013/05/09/executive-order-making- open-and-machine-readable-new-default-government. Accessed 2013 October 15.
-
(2013)
Making Open and Machine Readable the New Default for Government Information
-
-
Obama, B.1
-
56
-
-
84896718603
-
Increasing Public Access to the Results of Scientific Research
-
Available: Accessed 2013 October 23
-
Holdren J (2013). Increasing Public Access to the Results of Scientific Research. Memorandum of the US Office of Science and Technology. Available: https://petitions.whitehouse.gov/response/increasing-public-access-results- scientificresearch. Accessed 2013 October 23.
-
(2013)
Memorandum of the US Office of Science and Technology
-
-
Holdren, J.1
-
57
-
-
33646855259
-
-
website. Available: Accessed 2013 October 15
-
Pipeline Pilot website. Available: http://accelrys.com/products/pipeline- pilot. Accessed 2013 October 15.
-
Pipeline Pilot
-
-
-
58
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Galaxy Team doi:10.1186/gb-2010-11-8-r86
-
Goecks J, Nekrutenko A, Taylor J, Galaxy Team (2010) Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 11 (8). doi:10.1186/gb-2010-11-8-r86.
-
(2010)
Genome Biology
, vol.11
, Issue.8
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
59
-
-
84896735876
-
-
Website. Available from: Accessed on October 15, 2013
-
Knime Website. Available from: http://www.knime.org. Accessed on October 15, 2013.
-
-
-
|