[rkward-cvs] SF.net SVN: rkward:[3575] branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/ sources.bib
sjar at users.sourceforge.net
sjar at users.sourceforge.net
Wed May 18 20:34:53 UTC 2011
Revision: 3575
http://rkward.svn.sourceforge.net/rkward/?rev=3575&view=rev
Author: sjar
Date: 2011-05-18 20:34:53 +0000 (Wed, 18 May 2011)
Log Message:
-----------
+ some citations added
Note: Jabref changed the file automatically in other placer (again)
Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib 2011-05-18 20:31:34 UTC (rev 3574)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/sources.bib 2011-05-18 20:34:53 UTC (rev 3575)
@@ -57,7 +57,8 @@
@ARTICLE{Almiron2009,
author = {Marcelo G. Almiron and E. S. Almeida and M. N. Miranda},
- title = {The reliability of statistical functions in four software packages freely used in numerical computation},
+ title = {The reliability of statistical functions in four software packages
+ freely used in numerical computation},
journal = {Brazilian Journal of Probability and Statistics},
year = {2009},
volume = {23},
@@ -67,7 +68,8 @@
}
@ARTICLE{Almiron2010,
- author = {Marcelo G. Almiron and Bruno Lopes and Alyson L. C. Oliveira and Antonio C. Medeiros and Alejandro C. Frery},
+ author = {Marcelo G. Almiron and Bruno Lopes and Alyson L. C. Oliveira and
+ Antonio C. Medeiros and Alejandro C. Frery},
title = {On the Numerical Accuracy of Spreadsheets},
journal = {Journal of Statistical Software},
year = {2010},
@@ -84,7 +86,8 @@
}
@BOOK{RossiB2010,
- title = {Download Patterns and Releases in Open Source Software Projects: A Perfect Symbiosis?},
+ title = {Download Patterns and Releases in Open Source Software Projects:
+ A Perfect Symbiosis?},
publisher = {Springer Boston},
year = {2010},
editor = {Springer Boston},
@@ -94,7 +97,21 @@
comment = {ISSN 1868-4238, ISBN 978-3-642-13243-8},
doi = {10.1007/978-3-642-13244-5_20},
owner = {tux},
- review = {Software usage by end-users is one of the factors used to evaluate the success of software projects. In the context of open source software, there is no single and non-controversial measure of usage, though. Still, one of the most used and readily available measure is data about projects downloads. Nevertheless, download counts and averages do not convey as much information as the patterns in the original downloads time series. In this research, we propose a method to increase the expressiveness of mere download rates by considering download patterns against software releases. We apply experimentally our method to the most downloaded projects of SourceForge’s history crawled through the FLOSSMole repository. Findings show that projects with similar usage can have indeed different levels of sensitivity to releases, revealing different behaviors of users. Future research will develop further the pattern recognition approach to automatically categorize open source projects according to their download patterns.},
+ review = {Software usage by end-users is one of the factors used to evaluate
+ the success of software projects. In the context of open source software,
+ there is no single and non-controversial measure of usage, though.
+ Still, one of the most used and readily available measure is data
+ about projects downloads. Nevertheless, download counts and averages
+ do not convey as much information as the patterns in the original
+ downloads time series. In this research, we propose a method to increase
+ the expressiveness of mere download rates by considering download
+ patterns against software releases. We apply experimentally our method
+ to the most downloaded projects of SourceForge’s history crawled
+ through the FLOSSMole repository. Findings show that projects with
+ similar usage can have indeed different levels of sensitivity to
+ releases, revealing different behaviors of users. Future research
+ will develop further the pattern recognition approach to automatically
+ categorize open source projects according to their download patterns.},
timestamp = {2010.07.01}
}
@@ -218,7 +235,8 @@
@ARTICLE{Fox2005,
author = {John Fox},
- title = {The \proglang{R} Commander: A Basic-Statistics Graphical User Interface to \proglang{R}},
+ title = {The \proglang{R} Commander: A Basic-Statistics Graphical User Interface
+ to \proglang{R}},
journal = {Journal of Statistical Software},
year = {2005},
volume = {14},
@@ -236,7 +254,12 @@
@MANUAL{Rcmdr2010,
title = {\pkg{Rcmdr}: \proglang{R} Commander},
- author = {John Fox and with contributions from Liviu Andronic and Michael Ash and Theophilius Boye and Stefano Calza and Andy Chang and Philippe Grosjean and Richard Heiberger and G. Jay Kerns and Renaud Lancelot and Matthieu Lesnoff and Uwe Ligges and Samir Messad and Martin Maechler and Robert Muenchen and Duncan Murdoch and Erich Neuwirth and Dan Putler and Brian Ripley and Miroslav Ristic and and Peter Wolf.},
+ author = {John Fox and with contributions from Liviu Andronic and Michael Ash
+ and Theophilius Boye and Stefano Calza and Andy Chang and Philippe
+ Grosjean and Richard Heiberger and G. Jay Kerns and Renaud Lancelot
+ and Matthieu Lesnoff and Uwe Ligges and Samir Messad and Martin Maechler
+ and Robert Muenchen and Duncan Murdoch and Erich Neuwirth and Dan
+ Putler and Brian Ripley and Miroslav Ristic and and Peter Wolf.},
year = {2010},
note = {\proglang{R} package version 1.6-2},
owner = {tux},
@@ -254,14 +277,28 @@
}
@ARTICLE{Gentleman2004,
- author = {Robert Gentleman and Vincent Carey and Douglas Bates and Ben Bolstad and Marcel Dettling and Sandrine Dudoit and Byron Ellis and Laurent Gautier and Yongchao Ge and Jeff Gentry and Kurt Hornik and Torsten Hothorn and Wolfgang Huber and Stefano Iacus and Rafael Irizarry and Friedrich Leisch and Cheng Li and Martin Maechler and Anthony Rossini and Gunther Sawitzki and Colin Smith and Gordon Smyth and Luke Tierney and Jean Yang and Jianhua Zhang},
- title = {Bioconductor: open software development for computational biology and bioinformatics},
+ author = {Robert Gentleman and Vincent Carey and Douglas Bates and Ben Bolstad
+ and Marcel Dettling and Sandrine Dudoit and Byron Ellis and Laurent
+ Gautier and Yongchao Ge and Jeff Gentry and Kurt Hornik and Torsten
+ Hothorn and Wolfgang Huber and Stefano Iacus and Rafael Irizarry
+ and Friedrich Leisch and Cheng Li and Martin Maechler and Anthony
+ Rossini and Gunther Sawitzki and Colin Smith and Gordon Smyth and
+ Luke Tierney and Jean Yang and Jianhua Zhang},
+ title = {Bioconductor: open software development for computational biology
+ and bioinformatics},
journal = {Genome Biology},
year = {2004},
volume = {5},
pages = {R80},
number = {10},
- abstract = {The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.},
+ abstract = {The Bioconductor project is an initiative for the collaborative creation
+ of extensible software for computational biology and bioinformatics.
+ The goals of the project include: fostering collaborative development
+ and widespread use of innovative software, reducing barriers to entry
+ into interdisciplinary scientific research, and promoting the achievement
+ of remote reproducibility of research results. We describe details
+ of our aims and methods, identify current challenges, compare Bioconductor
+ to other open bioinformatics projects, and provide working examples.},
doi = {10.1186/gb-2004-5-10-r80},
issn = {1465-6906},
pubmedid = {15461798},
@@ -324,6 +361,23 @@
url = {http://cran.r-project.org/doc/html/interface98-paper/paper_2.html}
}
+ at ARTICLE{Jarvis2010,
+ author = {Jarvis, Stuart},
+ title = {KDE 4 on windows},
+ journal = {Linux J.},
+ year = {2010},
+ volume = {2010},
+ month = {February},
+ acmid = {1723010},
+ address = {Seattle, WA, USA},
+ articleno = {1},
+ issn = {1075-3583},
+ issue = {190},
+ issue_date = {February 2010},
+ publisher = {Specialized Systems Consultants, Inc.},
+ url = {http://portal.acm.org/citation.cfm?id=1723009.1723010}
+}
+
@ARTICLE{Karatzoglou2004,
author = {Alexandros Karatzoglou and Alexandros Smola and Kurt Hornik and Achim
Zeileis},
@@ -348,7 +402,17 @@
title = {Multi-Platform Document-Oriented GUIs},
year = {2010},
abstract = {In recent years, increasing complexity of graphical user interfaces
- (GUIs) of applications has led to problems in GUI management, since there is no single layout to fulfill every user’s needs. GUI editors have been developed to enhance end-user options but they commonly fail to preserve personalized GUIs. This paper presents an extension to the GUI editor built into the Auckland Layout Model (ALM) that can permanently store user-defined GUI layouts and reproduce them on different platforms. A novel technique called the document-oriented approach has been exploited to empower end-user customization, which allows GUI layouts to be dynamically edited, saved using a standardized XML-based GUI description language, and loaded in a platform-independent manner.},
+ (GUIs) of applications has led to problems in GUI management, since
+ there is no single layout to fulfill every user’s needs. GUI editors
+ have been developed to enhance end-user options but they commonly
+ fail to preserve personalized GUIs. This paper presents an extension
+ to the GUI editor built into the Auckland Layout Model (ALM) that
+ can permanently store user-defined GUI layouts and reproduce them
+ on different platforms. A novel technique called the document-oriented
+ approach has been exploited to empower end-user customization, which
+ allows GUI layouts to be dynamically edited, saved using a standardized
+ XML-based GUI description language, and loaded in a platform-independent
+ manner.},
institution = {CiteSeerX - Scientific Literature Digital Library and Search Engine
[http://citeseerx.ist.psu.edu/oai2] (United States)},
keywords = {GUI customization, platform-independent GUIs, ALM},
@@ -381,7 +445,8 @@
@ARTICLE{Lecoutre2003,
author = {E Lecoutre},
- title = {The \pkg{R2HTML} Package - Formatting HTML output on the fly or by using a template scheme},
+ title = {The \pkg{R2HTML} Package - Formatting HTML output on the fly or by
+ using a template scheme},
journal = {\proglang{R} News},
year = {2003},
volume = {3},
@@ -400,7 +465,9 @@
year = {2002},
pages = {575–580},
eid = {Physica Verlag, Heidelberg},
- abstract = {. (2002) Sweave: dynamic generation of statistical reports using literate data analysis. In Hardle,W. and Ronz,B. (eds.) Proceedings in Computational Statistics. Physica Verlag, Heidelberg, pp. 575–580.},
+ abstract = {. (2002) Sweave: dynamic generation of statistical reports using literate
+ data analysis. In Hardle,W. and Ronz,B. (eds.) Proceedings in Computational
+ Statistics. Physica Verlag, Heidelberg, pp. 575–580.},
owner = {tux},
timestamp = {2010.07.01}
}
@@ -451,7 +518,8 @@
@ARTICLE{Newton2007,
author = {Richard Newton and Lorenz Wernisch},
- title = {{Rwui}: A Web Application to Create User Friendly Web Interfaces for \proglang{R} Scripts},
+ title = {{Rwui}: A Web Application to Create User Friendly Web Interfaces
+ for \proglang{R} Scripts},
journal = {\proglang{R} News},
year = {2007},
volume = {7},
@@ -462,6 +530,17 @@
url = {http://CRAN.R-project.org/doc/Rnews/}
}
+ at MISC{perens1999,
+ author = {Bruce Perens},
+ title = {Open Sources: Voices from the Open Source Revolution},
+ howpublished = {http://oreilly.com/catalog/opensources/book/perens.html},
+ month = mar,
+ year = {1999},
+ shorttitle = {Open Sources},
+ type = {{Text.Article}},
+ url = {http://oreilly.com/catalog/opensources/book/perens.html}
+}
+
@MANUAL{Plate2009,
title = {\pkg{trackObjs}: Track Objects},
author = {Tony Plate},
@@ -482,15 +561,67 @@
url = {http://www.statistiklabor.de/}
}
+ at ARTICLE{Roediger2011,
+ author = {R\"{o}diger, Stefan and Ruhland, Mirko and Schmidt, Carsten and Schr\"{o}der,
+ Christian and Grossmann, Kai and B\"{o}hm, Alexander and Nitschke,
+ J\"{o}rg and Berger, Ingo and Schimke, Ingolf and Schierack, Peter},
+ title = {Fluorescence Dye Adsorption Assay to Quantify Carboxyl Groups on
+ the Surface of Poly(methyl methacrylate) Microbeads},
+ journal = {Analytical Chemistry},
+ year = {2011},
+ volume = {83},
+ pages = {3379-3385},
+ number = {9},
+ abstract = { Microbead-based assays have evolved into powerful tools for the multiplex
+ detection of biomolecules. Analytes are captured by DNA or protein
+ capture molecules which are coupled on microbead surfaces. A homogeneous
+ carboxylation of microbeads is essential for the optimal and reproducible
+ coupling of capture molecules and thus a prerequisite for an optimal
+ multiplex microbead-based assay performance. We developed a simple
+ fluorescence dye adsorption assay for the description of microbead
+ carboxylation and for the prediction of coupling successes of capture
+ molecules. Using the fluorescence dye SYTO-62 it is possible to quantify
+ the degree of carboxylation of poly(methyl methacrylate) (PMMA) microbeads
+ within 1 h in a multiplex format by fluorescence microscopy or flow
+ cytometry. Compared to conventional bulk assays which only provide
+ an average degree of carboxylation the main advantage of the SYTO-62
+ assay is the single microbead analysis and therefore the description
+ of the qualitative distribution of carboxylation in microbead populations.
+ The SYTO-62 assay is sensitive enough to even determine weak carboxylation.
+ Also, the quality of microbeads can be evaluated. To our knowledge
+ this is the first report which applies a reversible noncovalent fluorescent
+ dye adsorption assay to quantify the degree of carboxylation on surfaces.
+ },
+ doi = {10.1021/ac103277s},
+ eprint = {http://pubs.acs.org/doi/pdf/10.1021/ac103277s},
+ url = {http://pubs.acs.org/doi/abs/10.1021/ac103277s}
+}
+
@ARTICLE{RaffelsbergerW2008,
- author = {Raffelsberger, Wolfgang and Krause, Yannick and Moulinier, Luc and Kieffer, David and Morand, Anne-Laure and Brino, Laurent and Poch, Olivier},
- title = {{\pkg{RReportGenerator}: automatic reports from routine statistical analysis using \proglang{R}}},
+ author = {Raffelsberger, Wolfgang and Krause, Yannick and Moulinier, Luc and
+ Kieffer, David and Morand, Anne-Laure and Brino, Laurent and Poch,
+ Olivier},
+ title = {{\pkg{RReportGenerator}: automatic reports from routine statistical
+ analysis using \proglang{R}}},
journal = {Bioinformatics},
year = {2008},
volume = {24},
pages = {276-278},
number = {2},
- abstract = {Summary: With the establishment of high-throughput (HT) screening methods there is an increasing need for automatic analysis methods. Here we present RReportGenerator, a user-friendly portal for automatic routine analysis using the statistical platform R and Bioconductor. RReportGenerator is designed to analyze data using predefined analysis scenarios via a graphical user interface (GUI). A report in pdf format combining text, figures and tables is automatically generated and results may be exported. To demonstrate suitable analysis tasks we provide direct web access to a collection of analysis scenarios for summarizing data from transfected cell arrays (TCA), segmentation of CGH data, and microarray quality control and normalization.Availability: RReportGenerator, a user manual and a collection of analysis scenarios are available under a GNU public license on http://www-bio3d-igbmc.u-strasbg.fr/~wraffContact: wolfgang.raffelsberger at igbmc.u-strasbg.fr},
+ abstract = {Summary: With the establishment of high-throughput (HT) screening
+ methods there is an increasing need for automatic analysis methods.
+ Here we present RReportGenerator, a user-friendly portal for automatic
+ routine analysis using the statistical platform R and Bioconductor.
+ RReportGenerator is designed to analyze data using predefined analysis
+ scenarios via a graphical user interface (GUI). A report in pdf format
+ combining text, figures and tables is automatically generated and
+ results may be exported. To demonstrate suitable analysis tasks we
+ provide direct web access to a collection of analysis scenarios for
+ summarizing data from transfected cell arrays (TCA), segmentation
+ of CGH data, and microarray quality control and normalization.Availability:
+ RReportGenerator, a user manual and a collection of analysis scenarios
+ are available under a GNU public license on http://www-bio3d-igbmc.u-strasbg.fr/~wraffContact:
+ wolfgang.raffelsberger at igbmc.u-strasbg.fr},
doi = {10.1093/bioinformatics/btm556},
eprint = {http://bioinformatics.oxfordjournals.org/content/24/2/276.full.pdf+html},
url = {http://bioinformatics.oxfordjournals.org/content/24/2/276.abstract}
@@ -537,7 +668,8 @@
@ARTICLE{Rizopoulos2006,
author = {Dimitris Rizopoulos},
- title = {\pkg{ltm}: An \proglang{R} package for Latent Variable Modelling and Item Response Theory Analyses},
+ title = {\pkg{ltm}: An \proglang{R} package for Latent Variable Modelling
+ and Item Response Theory Analyses},
journal = {Journal of Statistical Software},
year = {2006},
volume = {17},
@@ -546,36 +678,52 @@
url = {http://www.jstatsoft.org/v17/i05/}
}
- at ARTICLE{Roediger2011,
- author = {R\"{o}diger, Stefan and Ruhland, Mirko and Schmidt, Carsten and Schr\"{o}der, Christian and Grossmann, Kai and B\"{o}hm, Alexander and Nitschke, J\"{o}rg and Berger, Ingo and Schimke, Ingolf and Schierack, Peter},
- title = {Fluorescence Dye Adsorption Assay to Quantify Carboxyl Groups on the Surface of Poly(methyl methacrylate) Microbeads},
- journal = {Analytical Chemistry},
- year = {2011},
- volume = {83},
- pages = {3379-3385},
- number = {9},
- abstract = { Microbead-based assays have evolved into powerful tools for the multiplex detection of biomolecules. Analytes are captured by DNA or protein capture molecules which are coupled on microbead surfaces. A homogeneous carboxylation of microbeads is essential for the optimal and reproducible coupling of capture molecules and thus a prerequisite for an optimal multiplex microbead-based assay performance. We developed a simple fluorescence dye adsorption assay for the description of microbead carboxylation and for the prediction of coupling successes of capture molecules. Using the fluorescence dye SYTO-62 it is possible to quantify the degree of carboxylation of poly(methyl methacrylate) (PMMA) microbeads within 1 h in a multiplex format by fluorescence microscopy or flow cytometry. Compared to conventional bulk assays which only provide an average degree of carboxylation the main advantage of the SYTO-62 assay is the single microbead analysis and therefore the description of the qualitative distribution of carboxylation in microbead populations. The SYTO-62 assay is sensitive enough to even determine weak carboxylation. Also, the quality of microbeads can be evaluated. To our knowledge this is the first report which applies a reversible noncovalent fluorescent dye adsorption assay to quantify the degree of carboxylation on surfaces.
- },
- doi = {10.1021/ac103277s},
- eprint = {http://pubs.acs.org/doi/pdf/10.1021/ac103277s},
- url = {http://pubs.acs.org/doi/abs/10.1021/ac103277s}
-}
-
@ARTICLE{Rugg-Gunn2010,
author = {Rugg-Gunn, Peter J. and Cox, Brian J. and Ralston, Amy and Rossant,
Janet},
- title = {Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo},
+ title = {Distinct histone modifications in stem cell lines and tissue lineages
+ from the early mouse embryo},
journal = {Proceedings of the National Academy of Sciences},
year = {2010},
volume = {107},
pages = {10783-10790},
number = {24},
- abstract = {A unique property of the mammalian embryo is that stem cells can be derived from its early tissue lineages. These lineages will give rise to the fetus as well as essential extraembryonic tissues. Understanding how chromatin regulation participates in establishment of these lineages in the embryo and their derived stem cells provides insight that will critically inform our understanding of embryogenesis and stem cell biology. Here, we compare the genomewide location of active and repressive histone modifications in embryonic stem cells, trophoblast stem cells, and extraembryonic endoderm stem cells from the mouse. Our results show that the active modification H3K4me3 has a similar role in the three stem cell types, but the repressive modification H3K27me3 varies in abundance and genomewide distribution. Thus, alternative mechanisms mediate transcriptional repression in stem cells from the embryo. In addition, using carrier chromatin immunoprecipitation we show that bivalent histone domains seen in embryonic stem cells exist in pluripotent cells of the early embryo. However, the epigenetic status of extraembryonic progenitor cells in the embryo did not entirely reflect the extraembryonic stem cell lines. These studies indicate that histone modification mechanisms may differ between early embryo lineages and emphasize the importance of examining in vivo and in vitro progenitor cells.},
+ abstract = {A unique property of the mammalian embryo is that stem cells can be
+ derived from its early tissue lineages. These lineages will give
+ rise to the fetus as well as essential extraembryonic tissues. Understanding
+ how chromatin regulation participates in establishment of these lineages
+ in the embryo and their derived stem cells provides insight that
+ will critically inform our understanding of embryogenesis and stem
+ cell biology. Here, we compare the genomewide location of active
+ and repressive histone modifications in embryonic stem cells, trophoblast
+ stem cells, and extraembryonic endoderm stem cells from the mouse.
+ Our results show that the active modification H3K4me3 has a similar
+ role in the three stem cell types, but the repressive modification
+ H3K27me3 varies in abundance and genomewide distribution. Thus, alternative
+ mechanisms mediate transcriptional repression in stem cells from
+ the embryo. In addition, using carrier chromatin immunoprecipitation
+ we show that bivalent histone domains seen in embryonic stem cells
+ exist in pluripotent cells of the early embryo. However, the epigenetic
+ status of extraembryonic progenitor cells in the embryo did not entirely
+ reflect the extraembryonic stem cell lines. These studies indicate
+ that histone modification mechanisms may differ between early embryo
+ lineages and emphasize the importance of examining in vivo and in
+ vitro progenitor cells.},
doi = {10.1073/pnas.0914507107},
eprint = {http://www.pnas.org/content/107/24/10783.full.pdf+html},
url = {http://www.pnas.org/content/107/24/10783.abstract}
}
+ at BOOK{Sarkar2008,
+ title = {\pkg{Lattice}: Multivariate Data Visualization with \proglang{R}},
+ publisher = {Springer},
+ year = {2008},
+ author = {Deepayan Sarkar},
+ address = {New York},
+ note = {ISBN 978-0-387-75968-5},
+ url = {http://lmdvr.r-forge.r-project.org}
+}
+
@MANUAL{TeachingDemos2010,
title = {\pkg{TeachingDemos}: Demonstrations for teaching and learning},
author = {Greg Snow},
@@ -609,14 +757,37 @@
}
@ARTICLE{Visne2009,
- author = {Visne, Ilhami and Dilaveroglu, Erkan and Vierlinger, Klemens and Lauss, Martin and Yildiz, Ahmet and Weinhaeusel, Andreas and Noehammer, Christa and Leisch, Friedrich and Kriegner, Albert},
+ author = {Visne, Ilhami and Dilaveroglu, Erkan and Vierlinger, Klemens and
+ Lauss, Martin and Yildiz, Ahmet and Weinhaeusel, Andreas and Noehammer,
+ Christa and Leisch, Friedrich and Kriegner, Albert},
title = {\pkg{RGG}: A general GUI Framework for \proglang{R} scripts},
journal = {BMC Bioinformatics},
year = {2009},
volume = {10},
pages = {74},
number = {1},
- abstract = {BACKGROUND:R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required.RESULTS:We have developed a software tool called R GUI Generator (RGG) which enables the easy generation of Graphical User Interfaces (GUIs) for the programming language R by adding a few Extensible Markup Language (XML) - tags. RGG consists of an XML-based GUI definition language and a Java-based GUI engine. GUIs are generated in runtime from defined GUI tags that are embedded into the R script. User-GUI input is returned to the R code and replaces the XML-tags. RGG files can be developed using any text editor. The current version of RGG is available as a stand-alone software (RGGRunner) and as a plug-in for JGR.CONCLUSION:RGG is a general GUI framework for R that has the potential to introduce R statistics (R packages, built-in functions and scripts) to users with limited programming skills and helps to bridge the gap between R developers and GUI-dependent users. RGG aims to abstract the GUI development from individual GUI toolkits by using an XML-based GUI definition language. Thus RGG can be easily integrated in any software. The RGG project further includes the development of a web-based repository for RGG-GUIs. RGG is an open source project licensed under the Lesser General Public License (LGPL) and can be downloaded freely at http://rgg.r-forge.r-project.org},
+ abstract = {BACKGROUND:R is the leading open source statistics software with a
+ vast number of biostatistical and bioinformatical analysis packages.
+ To exploit the advantages of R, extensive scripting/programming skills
+ are required.RESULTS:We have developed a software tool called R GUI
+ Generator (RGG) which enables the easy generation of Graphical User
+ Interfaces (GUIs) for the programming language R by adding a few
+ Extensible Markup Language (XML) - tags. RGG consists of an XML-based
+ GUI definition language and a Java-based GUI engine. GUIs are generated
+ in runtime from defined GUI tags that are embedded into the R script.
+ User-GUI input is returned to the R code and replaces the XML-tags.
+ RGG files can be developed using any text editor. The current version
+ of RGG is available as a stand-alone software (RGGRunner) and as
+ a plug-in for JGR.CONCLUSION:RGG is a general GUI framework for R
+ that has the potential to introduce R statistics (R packages, built-in
+ functions and scripts) to users with limited programming skills and
+ helps to bridge the gap between R developers and GUI-dependent users.
+ RGG aims to abstract the GUI development from individual GUI toolkits
+ by using an XML-based GUI definition language. Thus RGG can be easily
+ integrated in any software. The RGG project further includes the
+ development of a web-based repository for RGG-GUIs. RGG is an open
+ source project licensed under the Lesser General Public License (LGPL)
+ and can be downloaded freely at http://rgg.r-forge.r-project.org},
doi = {10.1186/1471-2105-10-74},
issn = {1471-2105},
owner = {tux},
@@ -628,13 +799,14 @@
@ARTICLE{Yang2011,
author = {Ling Yang and Jun Liu and Mu Liu and Meirui Qian and Minzhou Zhang
and Huajun Hu},
- title = {Identification of fatty acid synthase from the Pacific white shrimp, Litopenaeus vannamei and its specific expression profiles during white spot syndrome virus infection},
+ title = {Identification of fatty acid synthase from the Pacific white shrimp,
+ Litopenaeus vannamei and its specific expression profiles during
+ white spot syndrome virus infection},
journal = {Fish \& Shellfish Immunology},
year = {2011},
volume = {30},
pages = {744 - 749},
number = {2},
- abstract = {},
doi = {DOI: 10.1016/j.fsi.2010.12.026},
issn = {1050-4648},
keywords = {Fatty acid synthase},
@@ -669,14 +841,16 @@
journal = {ACM},
year = {2005},
pages = {67-72},
- comment = {Open Source Application Spaces: Fifth Workshop on Open Source Software Engineering (5-WOSSE)},
+ comment = {Open Source Application Spaces: Fifth Workshop on Open Source Software
+ Engineering (5-WOSSE)},
owner = {tux},
timestamp = {2010.07.01}
}
@ARTICLE{Zou2009,
author = {Zou, Wei and Tolstikov, Vladimir V.},
- title = {Pattern Recognition and Pathway Analysis with Genetic Algorithms in Mass Spectrometry Based Metabolomics},
+ title = {Pattern Recognition and Pathway Analysis with Genetic Algorithms
+ in Mass Spectrometry Based Metabolomics},
journal = {Algorithms},
year = {2009},
volume = {2},
@@ -689,13 +863,34 @@
@ARTICLE{Zou2008,
author = {Zou, Wei and Tolstikov, Vladimir V.},
- title = {Probing genetic algorithms for feature selection in comprehensive metabolic profiling approach},
+ title = {Probing genetic algorithms for feature selection in comprehensive
+ metabolic profiling approach},
journal = {Rapid Communications in Mass Spectrometry},
year = {2008},
volume = {22},
pages = {1312--1324},
number = {8},
- abstract = {Abstract Six different clones of 1-year-old loblolly pine (Pinus taeda L.) seedlings grown under standardized conditions in a green house were used for sample preparation and further analysis. Three independent and complementary analytical techniques for metabolic profiling were applied in the present study: hydrophilic interaction chromatography (HILIC-LC/ESI-MS), reversed-phase liquid chromatography (RP-LC/ESI-MS), and gas chromatography all coupled to mass spectrometry (GC/TOF-MS). Unsupervised methods, such as principle component analysis (PCA) and clustering, and supervised methods, such as classification, were used for data mining. Genetic algorithms (GA), a multivariate approach, was probed for selection of the smallest subsets of potentially discriminative classifiers. From more than 2000 peaks found in total, small subsets were selected by GA as highly potential classifiers allowing discrimination among six investigated genotypes. Annotated GC/TOF-MS data allowed the generation of a small subset of identified metabolites. LC/ESI-MS data and small subsets require further annotation. The present study demonstrated that combination of comprehensive metabolic profiling and advanced data mining techniques provides a powerful metabolomic approach for biomarker discovery among small molecules. Utilizing GA for feature selection allowed the generation of small subsets of potent classifiers. Copyright © 2008 John Wiley & Sons, Ltd.},
+ abstract = {Abstract Six different clones of 1-year-old loblolly pine (Pinus taeda
+ L.) seedlings grown under standardized conditions in a green house
+ were used for sample preparation and further analysis. Three independent
+ and complementary analytical techniques for metabolic profiling were
+ applied in the present study: hydrophilic interaction chromatography
+ (HILIC-LC/ESI-MS), reversed-phase liquid chromatography (RP-LC/ESI-MS),
+ and gas chromatography all coupled to mass spectrometry (GC/TOF-MS).
+ Unsupervised methods, such as principle component analysis (PCA)
+ and clustering, and supervised methods, such as classification, were
+ used for data mining. Genetic algorithms (GA), a multivariate approach,
+ was probed for selection of the smallest subsets of potentially discriminative
+ classifiers. From more than 2000 peaks found in total, small subsets
+ were selected by GA as highly potential classifiers allowing discrimination
+ among six investigated genotypes. Annotated GC/TOF-MS data allowed
+ the generation of a small subset of identified metabolites. LC/ESI-MS
+ data and small subsets require further annotation. The present study
+ demonstrated that combination of comprehensive metabolic profiling
+ and advanced data mining techniques provides a powerful metabolomic
+ approach for biomarker discovery among small molecules. Utilizing
+ GA for feature selection allowed the generation of small subsets
+ of potent classifiers. Copyright © 2008 John Wiley & Sons, Ltd.},
doi = {10.1002/rcm.3507},
issn = {1097-0231},
publisher = {John Wiley \& Sons, Ltd.},
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