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updated Brunn reference

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1 parent e44c25e commit dfa6ba5e2a6a6205d6b50329e4776d62c3a11fae @jonalv jonalv committed May 20, 2011
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  1. +60 −54 paper.bib
  2. BIN paper.pdf
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@@ -2,13 +2,30 @@
%% http://bibdesk.sourceforge.net/
-%% Created for Geoffrey Hutchison at 2011-05-13 15:34:28 -0400
+%% Created for Jonathan Alvarsson at 2011-05-20 11:58:06 +0200
%% Saved with string encoding Unicode (UTF-8)
+@article{Alvarsson:2011fk,
+ Abstract = {BACKGROUND:Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expensive, and heavyweight and there is a need for a extensible lightweight open system for handling plate design, and validation and preparation of data.RESULTS:A Bioclipse plugin consisting of a client part and a relational database was constructed. A multiple-step plate layout point-and-click interface was implemented inside Bioclipse. The system contains a data validation step, where outliers can be removed, and finally a plate report with all relevant calculated data, including dose-response curves. CONCLUSIONS:Brunn is capable of handling the data from microplate assays. It can create dose-response curves and calculate IC50 values. Using a system of this sort facilitates work in the laboratory. Being able to reuse already constructed plates and plate layouts by starting out from an earlier step in the plate layout design process saves time and cuts down on error sources.},
+ Author = {Alvarsson, Jonathan and Andersson, Claes and Spjuth, Ola and Larsson, Rolf and Wikberg, Jarl},
+ Date-Added = {2011-05-20 11:57:25 +0200},
+ Date-Modified = {2011-05-20 11:57:34 +0200},
+ Doi = {10.1186/1471-2105-12-179},
+ Issn = {1471-2105},
+ Journal = {BMC Bioinformatics},
+ Number = {1},
+ Pages = {179},
+ Title = {Brunn: An open source laboratory information system for microplates with a graphical plate layout design process},
+ Url = {http://www.biomedcentral.com/1471-2105/12/179},
+ Volume = {12},
+ Year = {2011},
+ Bdsk-Url-1 = {http://www.biomedcentral.com/1471-2105/12/179},
+ Bdsk-Url-2 = {http://dx.doi.org/10.1186/1471-2105-12-179}}
+
@article{Munos:2006vn,
Abstract = {The low number of novel therapeutics approved by the US FDA in recent years continues to cause great concern about productivity and declining innovation. Can open-source drug research and development, using principles pioneered by the highly successful open-source software movement, help revive the industry?},
Author = {Munos, Bernard},
@@ -99,14 +116,6 @@ @article{Lonie2011
Year = {2011},
Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cpc.2010.07.048}}
-@article{Alvarsson:2011fk,
- Author = {Alvarsson, Jonathan and Andersson, Claes and Spjuth, Ola and Larsson, Rolf and Wikberg, Jarl E S},
- Date-Added = {2011-05-12 16:38:45 +0200},
- Date-Modified = {2011-05-12 16:43:59 +0200},
- Journal = {BMC Bioinformatics},
- Title = {Brunn: An open source laboratory information system for microplates with a graphical plate layout design process},
- Year = {Accepted}}
-
@article{Wagener:2009uq,
Abstract = {Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use.},
Author = {Wagener, Johannes and Spjuth, Ola and Willighagen, Egon L and Wikberg, Jarl E S},
@@ -528,51 +537,49 @@ @article{Frenking
Bdsk-Url-1 = {http://dx.doi.org/10.1021/j100023a009}}
@article{Rappe:1992um,
-author = {A. K. Rapp\'e and C. J. Casewit and K. S. Colwell and W. A. Goddard III and W. M. Skiff},
-title = {UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations},
-journal = {Journal of the American Chemical Society},
-year = {1992},
-Volume = {114},
-Number = {25},
-Pages = {10024-10035},
-}
-
-@Article{NWChem,
- Author = "M. Valiev and E. J. Bylaska and N. Govind and K. Kowalski and T. P. Straatsma and H. J. J. {van Dam} and D. Wang and J. Nieplocha and E. Apra and T. L. Windus and W. A. {de Jong}",
- Title = "NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations",
- Journal = "Comput. Phys. Commun.",
- Volume = "181",
- Number = "9",
- Pages = "1477–1489",
- doi = "10.1016/j.cpc.2010.04.018",
- year = 2010
-}
-
-@Article {smsd,
-author = {Rahman, S.A. and Bashton, M. and Holliday, G.L. an Schrader, R. and Thornton, J.M.},
-title = { Small Molecule Subgraph Detector ({SMSD}) Toolkit},
-journal = {J.~Cheminf.},
-year = {2009},
-volume = {1},
-issue = {12}}
-
-@Article{orchem,
-author = {Rijnbeek, M. and Steinbeck, C.},
-title = {{OrChem} - An Open Source Chemistry Search Engine for Oracle},
-journal = {J.~Cheminf.},
-year = {2009},
-volume = {1},
-issue = {17}}
-
-@Article{padel,
-author = {Yap, C.W.},
-title = {{PaDEL}-Descriptor: An open source software to calculate molecular descriptors and fingerprints},
-journal = {J.~Comp.~Chem.},
-year = {2011},
-volume = {32},
-issue = {7},
-pages = {1466--1474}}
+ Author = {A. K. Rapp\'e and C. J. Casewit and K. S. Colwell and W. A. Goddard III and W. M. Skiff},
+ Journal = {Journal of the American Chemical Society},
+ Number = {25},
+ Pages = {10024-10035},
+ Title = {UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations},
+ Volume = {114},
+ Year = {1992}}
+
+@article{NWChem,
+ Author = {M. Valiev and E. J. Bylaska and N. Govind and K. Kowalski and T. P. Straatsma and H. J. J. {van Dam} and D. Wang and J. Nieplocha and E. Apra and T. L. Windus and W. A. {de Jong}},
+ Doi = {10.1016/j.cpc.2010.04.018},
+ Journal = {Comput. Phys. Commun.},
+ Number = {9},
+ Pages = {1477--1489},
+ Title = {NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations},
+ Volume = {181},
+ Year = 2010,
+ Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cpc.2010.04.018}}
+
+@article{smsd,
+ Author = {Rahman, S.A. and Bashton, M. and Holliday, G.L. an Schrader, R. and Thornton, J.M.},
+ Issue = {12},
+ Journal = {J.~Cheminf.},
+ Title = {Small Molecule Subgraph Detector ({SMSD}) Toolkit},
+ Volume = {1},
+ Year = {2009}}
+@article{orchem,
+ Author = {Rijnbeek, M. and Steinbeck, C.},
+ Issue = {17},
+ Journal = {J.~Cheminf.},
+ Title = {{OrChem} - An Open Source Chemistry Search Engine for Oracle},
+ Volume = {1},
+ Year = {2009}}
+
+@article{padel,
+ Author = {Yap, C.W.},
+ Issue = {7},
+ Journal = {J.~Comp.~Chem.},
+ Pages = {1466--1474},
+ Title = {{PaDEL}-Descriptor: An open source software to calculate molecular descriptors and fingerprints},
+ Volume = {32},
+ Year = {2011}}
@article{Dong:2007aa,
Author = {Dong, X. and Gilbert, K. and Guha, R. and Heiland, R. and Kim, J. and Pierce, M. and Fox, G. and Wild, D.J.},
@@ -582,4 +589,3 @@ @article{Dong:2007aa
Title = {A Web Service Infrastructure for Chemoinformatics},
Volume = {47},
Year = {2007}}
-
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