ReportingTools and gene annotation
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Ugo Borello ▴ 340
@ugo-borello-5753
Last seen 3.3 years ago
France
Good morning, I am using ReportingTools with DESeq2 and I am not able to add the gene annotation to my final report. I have ensembl gene id as identifiers and not entrez id! I followed Jason's suggestions as described here: http://article.gmane.org/gmane.science.biology.informatics.conductor/5 1995/m atch= But the add.anns() functions doesn't work in my hands. > mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl") > add.anns <- function(df, mart, ...) + { + nm <- rownames(df) + anns <- getBM( + attributes = c("ensembl_gene_id", "external_gene_id", "description"), + filters = "ensembl_gene_id", values = nm, mart = mart) + anns <- anns[match(nm, anns[, 1]), ] + colnames(anns) <- c("ID", "Gene Symbol", "Gene Description") + df <- cbind(anns, df[, 2:nrow(df)]) + rownames(df) <- nm + df + } > publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = list(add.anns, modifyReportDF), mart = mart) ## dds is the DESeqDataSet object Show Traceback Rerun with Debug Error in `[.data.frame`(df, , 2:nrow(df)) : undefined columns selected I also tried this: > publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = list(add.anns, modifyReportDF), mart = mart, df= counts(dds)) # dds is the DESeqDataSet object Show Traceback Rerun with Debug Error in df[, 2:nrow(df)] : subscript out of bounds What am I doing wrong? Is there a simple way of adding my annotation to the HTML report? ENSEMBL ENTREZID SYMBOL GENENAME 1 ENSMUSG00000000001 14679 Gnai guanine nucleotide binding protein (G protein), alpha inhibiting 3 2 ENSMUSG00000000028 12544 Cdc45 cell division cycle 45 3 ENSMUSG00000000031 NA NA NA 4 ENSMUSG00000000037 107815 Scml2 sex comb on midleg-like 2 (Drosophila) 5 ENSMUSG00000000049 11818 Apoh apolipoprotein H 6 ENSMUSG00000000056 67608 Narf nuclear prelamin A recognition factor Thank you Ugo > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ReportingTools_2.2.0 knitr_1.5 org.Mm.eg.db_2.10.1 RSQLite_0.11.4 DBI_0.2-7 [6] AnnotationDbi_1.24.0 Biobase_2.22.0 DESeq2_1.2.9 RcppArmadillo_0.4.000.2 Rcpp_0.10.6 [11] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0 biomaRt_2.18.0 loaded via a namespace (and not attached): [1] annotate_1.40.0 AnnotationForge_1.4.4 Biostrings_2.30.1 biovizBase_1.10.7 bitops_1.0-6 [6] BSgenome_1.30.0 Category_2.28.0 cluster_1.14.4 colorspace_1.2-4 dichromat_2.0-0 [11] digest_0.6.4 edgeR_3.4.2 evaluate_0.5.1 formatR_0.10 Formula_1.1-1 [16] genefilter_1.44.0 GenomicFeatures_1.14.2 ggbio_1.10.10 ggplot2_0.9.3.1 GO.db_2.10.1 [21] GOstats_2.28.0 graph_1.40.1 grid_3.0.2 gridExtra_0.9.1 GSEABase_1.24.0 [26] gtable_0.1.2 Hmisc_3.14-0 hwriter_1.3 labeling_0.2 lattice_0.20-24 [31] latticeExtra_0.6-26 limma_3.18.10 locfit_1.5-9.1 MASS_7.3-29 Matrix_1.1-2 [36] munsell_0.4.2 PFAM.db_2.10.1 plyr_1.8 proto_0.3-10 R.methodsS3_1.6.1 [41] R.oo_1.17.0 R.utils_1.28.4 RBGL_1.38.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 [46] reshape2_1.2.2 Rsamtools_1.14.2 rtracklayer_1.22.3 scales_0.2.3 splines_3.0.2 [51] stats4_3.0.2 stringr_0.6.2 survival_2.37-7 tools_3.0.2 VariantAnnotation_1.8.10 [56] XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.8.0
Annotation GO cycle ReportingTools DESeq2 Annotation GO cycle ReportingTools DESeq2 • 1.1k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Hi Ugo, On 2/10/2014 6:02 AM, Ugo Borello wrote: > Good morning, > I am using ReportingTools with DESeq2 and I am not able to add the gene > annotation to my final report. > I have ensembl gene id as identifiers and not entrez id! > > I followed Jason's suggestions as described here: > > http://article.gmane.org/gmane.science.biology.informatics.conductor /51995/m > atch= > > But the add.anns() functions doesn't work in my hands. > >> mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl") >> add.anns <- function(df, mart, ...) > + { > + nm <- rownames(df) > + anns <- getBM( > + attributes = c("ensembl_gene_id", "external_gene_id", "description"), > + filters = "ensembl_gene_id", values = nm, mart = mart) > + anns <- anns[match(nm, anns[, 1]), ] > + colnames(anns) <- c("ID", "Gene Symbol", "Gene Description") > + df <- cbind(anns, df[, 2:nrow(df)]) Note that in the line above you are subsetting 'df' by column, using the number of rows. I am not sure if you want to eliminate the first column here (as you are using the rownames to annotate, so I don't know what the first column contains). But it is simpler to eliminate the first column than to keep the 2:ncol(columns): df <- cbind(anns, df[,-1]) Best, Jim > + rownames(df) <- nm > + df > + } >> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = > list(add.anns, modifyReportDF), mart = mart) ## dds is the DESeqDataSet > object > > Show Traceback > Rerun with Debug > Error in `[.data.frame`(df, , 2:nrow(df)) : undefined columns selected > > I also tried this: >> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = > list(add.anns, modifyReportDF), mart = mart, df= counts(dds)) # dds is the > DESeqDataSet object > > Show Traceback > Rerun with Debug > Error in df[, 2:nrow(df)] : subscript out of bounds > > > What am I doing wrong? > > Is there a simple way of adding my annotation to the HTML report? > > ENSEMBL ENTREZID SYMBOL GENENAME > 1 ENSMUSG00000000001 14679 Gnai guanine nucleotide binding protein > (G protein), alpha inhibiting 3 > 2 ENSMUSG00000000028 12544 Cdc45 cell division cycle 45 > 3 ENSMUSG00000000031 NA NA NA > 4 ENSMUSG00000000037 107815 Scml2 sex comb on midleg-like 2 (Drosophila) > 5 ENSMUSG00000000049 11818 Apoh apolipoprotein H > 6 ENSMUSG00000000056 67608 Narf nuclear prelamin A recognition > factor > > > Thank you > > Ugo > > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] ReportingTools_2.2.0 knitr_1.5 org.Mm.eg.db_2.10.1 > RSQLite_0.11.4 DBI_0.2-7 > [6] AnnotationDbi_1.24.0 Biobase_2.22.0 DESeq2_1.2.9 > RcppArmadillo_0.4.000.2 Rcpp_0.10.6 > [11] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 > BiocGenerics_0.8.0 biomaRt_2.18.0 > > loaded via a namespace (and not attached): > [1] annotate_1.40.0 AnnotationForge_1.4.4 Biostrings_2.30.1 > biovizBase_1.10.7 bitops_1.0-6 > [6] BSgenome_1.30.0 Category_2.28.0 cluster_1.14.4 > colorspace_1.2-4 dichromat_2.0-0 > [11] digest_0.6.4 edgeR_3.4.2 evaluate_0.5.1 > formatR_0.10 Formula_1.1-1 > [16] genefilter_1.44.0 GenomicFeatures_1.14.2 ggbio_1.10.10 > ggplot2_0.9.3.1 GO.db_2.10.1 > [21] GOstats_2.28.0 graph_1.40.1 grid_3.0.2 > gridExtra_0.9.1 GSEABase_1.24.0 > [26] gtable_0.1.2 Hmisc_3.14-0 hwriter_1.3 > labeling_0.2 lattice_0.20-24 > [31] latticeExtra_0.6-26 limma_3.18.10 locfit_1.5-9.1 > MASS_7.3-29 Matrix_1.1-2 > [36] munsell_0.4.2 PFAM.db_2.10.1 plyr_1.8 > proto_0.3-10 R.methodsS3_1.6.1 > [41] R.oo_1.17.0 R.utils_1.28.4 RBGL_1.38.0 > RColorBrewer_1.0-5 RCurl_1.95-4.1 > [46] reshape2_1.2.2 Rsamtools_1.14.2 rtracklayer_1.22.3 > scales_0.2.3 splines_3.0.2 > [51] stats4_3.0.2 stringr_0.6.2 survival_2.37-7 > tools_3.0.2 VariantAnnotation_1.8.10 > [56] XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.8.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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On Mon, Feb 10, 2014 at 7:28 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Ugo, > > > On 2/10/2014 6:02 AM, Ugo Borello wrote: > >> Good morning, >> I am using ReportingTools with DESeq2 and I am not able to add the gene >> annotation to my final report. >> I have ensembl gene id as identifiers and not entrez id! >> >> I followed Jason's suggestions as described here: >> >> http://article.gmane.org/gmane.science.biology. >> informatics.conductor/51995/m >> atch= >> >> But the add.anns() functions doesn't work in my hands. >> >> mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl") >>> add.anns <- function(df, mart, ...) >>> >> + { >> + nm <- rownames(df) >> + anns <- getBM( >> + attributes = c("ensembl_gene_id", "external_gene_id", >> "description"), >> + filters = "ensembl_gene_id", values = nm, mart = mart) >> + anns <- anns[match(nm, anns[, 1]), ] >> + colnames(anns) <- c("ID", "Gene Symbol", "Gene Description") >> + df <- cbind(anns, df[, 2:nrow(df)]) >> > > Note that in the line above you are subsetting 'df' by column, using the > number of rows. I am not sure if you want to eliminate the first column > here (as you are using the rownames to annotate, so I don't know what the > first column contains). But it is simpler to eliminate the first column > than to keep the 2:ncol(columns): > > df <- cbind(anns, df[,-1]) > > To be safe you'll want df <- cbind(anns, df[,-1,drop=FALSE]) Best, > > Jim > > + rownames(df) <- nm >> + df >> + } >> >>> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = >>> >> list(add.anns, modifyReportDF), mart = mart) ## dds is the DESeqDataSet >> object >> >> Show Traceback >> Rerun with Debug >> Error in `[.data.frame`(df, , 2:nrow(df)) : undefined columns selected >> >> I also tried this: >> >>> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = >>> >> list(add.anns, modifyReportDF), mart = mart, df= counts(dds)) # dds is >> the >> DESeqDataSet object >> >> Show Traceback >> Rerun with Debug >> Error in df[, 2:nrow(df)] : subscript out of bounds >> >> >> What am I doing wrong? >> >> Is there a simple way of adding my annotation to the HTML report? >> >> ENSEMBL ENTREZID SYMBOL GENENAME >> 1 ENSMUSG00000000001 14679 Gnai guanine nucleotide binding >> protein >> (G protein), alpha inhibiting 3 >> 2 ENSMUSG00000000028 12544 Cdc45 cell division cycle 45 >> 3 ENSMUSG00000000031 NA NA NA >> 4 ENSMUSG00000000037 107815 Scml2 sex comb on midleg-like 2 >> (Drosophila) >> 5 ENSMUSG00000000049 11818 Apoh apolipoprotein H >> 6 ENSMUSG00000000056 67608 Narf nuclear prelamin A recognition >> factor >> >> >> Thank you >> >> Ugo >> >> >> sessionInfo() >>> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] ReportingTools_2.2.0 knitr_1.5 org.Mm.eg.db_2.10.1 >> RSQLite_0.11.4 DBI_0.2-7 >> [6] AnnotationDbi_1.24.0 Biobase_2.22.0 DESeq2_1.2.9 >> RcppArmadillo_0.4.000.2 Rcpp_0.10.6 >> [11] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 >> BiocGenerics_0.8.0 biomaRt_2.18.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.40.0 AnnotationForge_1.4.4 Biostrings_2.30.1 >> biovizBase_1.10.7 bitops_1.0-6 >> [6] BSgenome_1.30.0 Category_2.28.0 cluster_1.14.4 >> colorspace_1.2-4 dichromat_2.0-0 >> [11] digest_0.6.4 edgeR_3.4.2 evaluate_0.5.1 >> formatR_0.10 Formula_1.1-1 >> [16] genefilter_1.44.0 GenomicFeatures_1.14.2 ggbio_1.10.10 >> ggplot2_0.9.3.1 GO.db_2.10.1 >> [21] GOstats_2.28.0 graph_1.40.1 grid_3.0.2 >> gridExtra_0.9.1 GSEABase_1.24.0 >> [26] gtable_0.1.2 Hmisc_3.14-0 hwriter_1.3 >> labeling_0.2 lattice_0.20-24 >> [31] latticeExtra_0.6-26 limma_3.18.10 locfit_1.5-9.1 >> MASS_7.3-29 Matrix_1.1-2 >> [36] munsell_0.4.2 PFAM.db_2.10.1 plyr_1.8 >> proto_0.3-10 R.methodsS3_1.6.1 >> [41] R.oo_1.17.0 R.utils_1.28.4 RBGL_1.38.0 >> RColorBrewer_1.0-5 RCurl_1.95-4.1 >> [46] reshape2_1.2.2 Rsamtools_1.14.2 rtracklayer_1.22.3 >> scales_0.2.3 splines_3.0.2 >> [51] stats4_3.0.2 stringr_0.6.2 survival_2.37-7 >> tools_3.0.2 VariantAnnotation_1.8.10 >> [56] XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.8.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]
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It worked. I have now a very nice and useful report; I ma so happy. Thank yo very very much, Ugo From: Michael Lawrence <lawrence.michael@gene.com> Date: Mon, 10 Feb 2014 09:12:16 -0800 To: "James W. MacDonald" <jmacdon@uw.edu> Cc: Ugo Borello <ugo.borello@inserm.fr>, "bioconductor@r-project.org" <bioconductor@r-project.org> Subject: Re: [BioC] ReportingTools and gene annotation On Mon, Feb 10, 2014 at 7:28 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Ugo, > > > On 2/10/2014 6:02 AM, Ugo Borello wrote: >> Good morning, >> I am using ReportingTools with DESeq2 and I am not able to add the gene >> annotation to my final report. >> I have ensembl gene id as identifiers and not entrez id! >> >> I followed Jason's suggestions as described here: >> >> http://article.gmane.org/gmane.science.biology.informatics.conducto r/51995/m >> <http: article.gmane.org="" gmane.science.biology.informatics.conduct="" or="" 51995="" m="">> > >> atch= >> >> But the add.anns() functions doesn't work in my hands. >> >>> mart <- useMart("ensembl",dataset="mmusculus_gene_ensembl") >>> add.anns <- function(df, mart, ...) >> + { >> + � nm <- rownames(df) >> + � anns <- getBM( >> + � � attributes = c("ensembl_gene_id", "external_gene_id", "description"), >> + � � filters = "ensembl_gene_id", values = nm, mart = mart) >> + � anns <- anns[match(nm, anns[, 1]), ] >> + � colnames(anns) <- c("ID", "Gene Symbol", "Gene Description") >> + � df <- cbind(anns, df[, 2:nrow(df)]) > > Note that in the line above you are subsetting 'df' by column, using the > number of rows. I am not sure if you want to eliminate the first column here > (as you are using the rownames to annotate, so I don't know what the first > column contains). But it is simpler to eliminate the first column than to keep > the 2:ncol(columns): > > df <- cbind(anns, df[,-1]) > To be safe you'll want� df <- cbind(anns, df[,-1,drop=FALSE]) > Best, > > Jim > >> + � rownames(df) <- nm >> + � df >> + } >>> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = >> list(add.anns, modifyReportDF), mart = mart) � �## dds is the DESeqDataSet >> object >> >> � Show Traceback >> � Rerun with Debug >> � Error in `[.data.frame`(df, , 2:nrow(df)) : undefined columns selected >> >> I also tried this: >>> publish(dds, des2Report, factor= colData(dds)$condition, .modifyDF = >> list(add.anns, modifyReportDF), mart = mart, df= counts(dds)) �# dds is the >> DESeqDataSet object >> >> � Show Traceback >> � Rerun with Debug >> � Error in df[, 2:nrow(df)] : subscript out of bounds >> >> >> What am I doing wrong? >> >> Is there a simple way of adding my annotation to the HTML report? >> >> � ENSEMBL � � � � � � � � � � � � �ENTREZID SYMBOL � � GENENAME >> 1 ENSMUSG00000000001 � �14679 � Gnai � � guanine nucleotide binding protein >> (G protein), alpha inhibiting 3 >> 2 ENSMUSG00000000028 � �12544 �Cdc45 � cell division cycle 45 >> 3 ENSMUSG00000000031 � � � NA � � NA � � �NA >> 4 ENSMUSG00000000037 � 107815 �Scml2 �sex comb on midleg-like 2 (Drosophila) >> 5 ENSMUSG00000000049 � �11818 � Apoh � �apolipoprotein H >> 6 ENSMUSG00000000056 � �67608 � Narf � � nuclear prelamin A recognition >> factor >> >> >> Thank you >> >> Ugo >> >> >>> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel �stats � � graphics �grDevices utils � � datasets �methods >> base >> >> other attached packages: >> � [1] ReportingTools_2.2.0 � �knitr_1.5 � � � � � � � org.Mm.eg.db_2.10.1 >> RSQLite_0.11.4 � � � � �DBI_0.2-7 >> � [6] AnnotationDbi_1.24.0 � �Biobase_2.22.0 � � � � �DESeq2_1.2.9 >> RcppArmadillo_0.4.000.2 Rcpp_0.10.6 >> [11] GenomicRanges_1.14.4 � �XVector_0.2.0 � � � � � IRanges_1.20.6 >> BiocGenerics_0.8.0 � � �biomaRt_2.18.0 >> >> loaded via a namespace (and not attached): >> � [1] annotate_1.40.0 � � � � �AnnotationForge_1.4.4 � �Biostrings_2.30.1 >> biovizBase_1.10.7 � � � �bitops_1.0-6 >> � [6] BSgenome_1.30.0 � � � � �Category_2.28.0 � � � � �cluster_1.14.4 >> colorspace_1.2-4 � � � � dichromat_2.0-0 >> [11] digest_0.6.4 � � � � � � edgeR_3.4.2 � � � � � � �evaluate_0.5.1 >> formatR_0.10 � � � � � � Formula_1.1-1 >> [16] genefilter_1.44.0 � � � �GenomicFeatures_1.14.2 � ggbio_1.10.10 >> ggplot2_0.9.3.1 � � � � �GO.db_2.10.1 >> [21] GOstats_2.28.0 � � � � � graph_1.40.1 � � � � � � grid_3.0.2 >> gridExtra_0.9.1 � � � � �GSEABase_1.24.0 >> [26] gtable_0.1.2 � � � � � � Hmisc_3.14-0 � � � � � � hwriter_1.3 >> labeling_0.2 � � � � � � lattice_0.20-24 >> [31] latticeExtra_0.6-26 � � �limma_3.18.10 � � � � � �locfit_1.5-9.1 >> MASS_7.3-29 � � � � � � �Matrix_1.1-2 >> [36] munsell_0.4.2 � � � � � �PFAM.db_2.10.1 � � � � � plyr_1.8 >> proto_0.3-10 � � � � � � R.methodsS3_1.6.1 >> [41] R.oo_1.17.0 � � � � � � �R.utils_1.28.4 � � � � � RBGL_1.38.0 >> RColorBrewer_1.0-5 � � � RCurl_1.95-4.1 >> [46] reshape2_1.2.2 � � � � � Rsamtools_1.14.2 � � � � rtracklayer_1.22.3 >> scales_0.2.3 � � � � � � splines_3.0.2 >> [51] stats4_3.0.2 � � � � � � stringr_0.6.2 � � � � � �survival_2.37-7 >> tools_3.0.2 � � � � � � �VariantAnnotation_1.8.10 >> [56] XML_3.95-0.2 � � � � � � xtable_1.7-1 � � � � � � zlibbioc_1.8.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> [[alternative HTML version deleted]]
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