From 9c38326caf196f09add931f0030a96db0c0c7aec Mon Sep 17 00:00:00 2001 From: Michael Barton Date: Mon, 17 Aug 2015 15:41:38 -0700 Subject: [PATCH 1/7] Update dictionary Signed-off-by: Michael Barton --- aspell.en.pws | 306 +++++++++++++++++++++++++------------------------- 1 file changed, 153 insertions(+), 153 deletions(-) diff --git a/aspell.en.pws b/aspell.en.pws index 5bd9d2d0..25211c2f 100644 --- a/aspell.en.pws +++ b/aspell.en.pws @@ -1,11 +1,150 @@ personal_ws-1.1 en 508 -absorbance ABySS +AI +API +ASM +ATPase ActiveRecord +Archaea +Arginine +Asparagine +Aspartate +Assemblathon +BBSRC +BMC +BioPerl +BioRuby +BioStar +Bioboxes +CLI +CMP +COGs +CRISPR +CSS +CSV +Complementation +Connotea +Cornu +Daltons +Debian +Denormalisation +DockerHub +Dockerfile +Doudoroff +EMBL +EMR +Entner +Erlang +Eubacteria +FBA +Folate +FriendFeed +GC +GFF +GMP +Gemfile +GenBank +Glycerolipid +Google +Heizer +HubMed +IEEE +Illumina +Inkscape +Inositol +Interoperability +Isoleucine +JGI's +JSON +JavaScript +KBp +KEGG +Kbp +Kmer +Kwalify +LaTeX +Loess +MAFFT +MATLAB +MBp +MCA +MOMA +Makefile +Makefiles +Mannan +Mbp +Meraculous +Metagenomics +Multivatiate +MySQL +NADH +NADPH +NCBI +NKU +NRPS +Nunn +ORF +ORFs +ORM +OSX +OTU +OTUs +Orthology +PAML +PCR +PHP +PLoS +PVD +Pentose +Phosphatidate +Phosphatidyl +Phosphatidylcholine +Phosphatidylethanolamine +Phosphatidylserine +Phospholipid +Phosphorylation +Pilus +Ploidy +Precedings +Procfile +Prokaryotes +Proteomics +Pseudomonad +Pseudomonads +Pseudomonas +PubMed +Pyruvate +RAxML +README +RSS +RSpec +Replicons +Ronn +Roraima +RubyGems +SBW +SGD +SOLiD +SQL +SVN +Saccharomyces +Shoulda +Spearman +Spearman's +Sterol +Taskfile +Threonine +Trehalose +Ubuntu +Valine +Wellcome +Wikipedia +YPD +Zymosterol +absorbance adaptated aeruginosa agglomerative -AI al aldolase amino @@ -13,38 +152,25 @@ amplicon amplicons ancova anova -API arb -Archaea archaeal arg -Arginine artefactually -ASM asn -Asparagine -Aspartate -Assemblathon assemblathons -ATPase barcode barcodes bashrc bayanus -BBSRC benchmarked benchmarking biobox -Bioboxes bioboxes bioinformatician bioinformaticians bioinformatics biomolecular biomolecules -BioPerl -BioRuby -BioStar biosynthesis biosynthetic biosynthetically @@ -55,7 +181,6 @@ blogger bloggers blogging blogs -BMC bowtie bp castellii @@ -73,66 +198,46 @@ chemoheterotrophic chemostat circos citeulike -CLI clojure clustalw -CMP codeml codon codons -COGs coli commensal -Complementation complementation -Connotea contig contigs coreutil coreutils -Cornu -CRISPR -CSS -CSV curation cyanobacterium cys -Daltons dAMP dCMP +dGMP +dN +dS +dTMP de -Debian decomplected dehydrogenase dehydrogenases dendrogram dendrograms -Denormalisation deplexed deplexing -dGMP diauxic dinucleotide discontiguous dispensability -dN dnaml -Dockerfile -DockerHub -Doudoroff downvote -dS -dTMP efflux -EMBL -EMR -Entner epistatic equilibria -Erlang essentiality et -Eubacteria eukaryotes eukaryotic evaluator @@ -143,16 +248,10 @@ extremophiles facultive fasta fastq -FBA fermentative fluorescens -Folate -FriendFeed friendfeed functionalisation -GC -Gemfile -GenBank genomer genomic genomics @@ -161,7 +260,6 @@ genotypic geochemical geochemically geomicrobiology -GFF gigabase gigabases github @@ -170,11 +268,8 @@ glu glutamic glutamine gly -Glycerolipid glycolysis glycolytic -GMP -Google gzipped hadoop haploinsufficiency @@ -182,7 +277,6 @@ haploinsufficient haploproficiency haploproficient haplotype -Heizer hemizygotes hemizygous heteroscedastic @@ -197,66 +291,42 @@ homopolymer homopolymers homopolymorphic homozygote -HubMed humic hyperthermophile hyperthermophiles -IEEE +iPod ile -Illumina img indels indices -Inkscape -Inositol -Interoperability interoperable intraspecies intron -iPod irreproducible isoenzymes -Isoleucine isomerase -JavaScript jgi -JGI's -JSON kb -KBp -Kbp -KEGG kilobase kilobases kinase kluyveri -Kmer kmer kmers kudriavzevii -Kwalify -LaTeX leu leucine -Loess loess login lys -MAFFT -Makefile +mRNA +mRNAs makefile -Makefiles makefiles -Mannan -MATLAB -MBp -Mbp -MCA mcl megabase megabases megablast -Meraculous mesophile mesophiles metabolome @@ -266,7 +336,6 @@ metadata metagenome metagenomes metagenomic -Metagenomics metagenomics microarray microbiome @@ -277,73 +346,44 @@ misassembly mmol mmols modularised -MOMA monoploid mothur -mRNA -mRNAs multi multimeric -Multivatiate mutualism -MySQL -NADH -NADPH -NCBI newbler -NKU novo -NRPS nucleotide nucleotides nucmer -Nunn oligonucleotide oligonucleotides omic online operon oppourtunisitic -ORF -ORFs -ORM ortholog orthologous orthologs -Orthology orthoquartzite -OSX -OTU -OTUs overfit overfitting -PAML paradoxus parallelisation paralog paralogs parameterised pathogenicity -PCR pdf -Pentose peptide peptone phaseolicola phe phenotypes phenotypic -Phosphatidate -Phosphatidyl -Phosphatidylcholine -Phosphatidylethanolamine -Phosphatidylserine phosphoketolase -Phospholipid -Phosphorylation photoautotrophic photoautotrophs -PHP phylip phylogenetic phylogenetically @@ -352,22 +392,16 @@ phylogenies phylogenomic phylogenomics pili -Pilus plasmid plasmids -Ploidy -PLoS plugin png polymorphisms polynucleotides powerpoint practices -Precedings priori -Procfile programmatically -Prokaryotes prokaryotic proline promer @@ -375,30 +409,23 @@ protegens proteome proteomes proteomic -Proteomics proteomics proven pseudogenes -Pseudomonad -Pseudomonads -Pseudomonas -PubMed putida -PVD pyochelin pyochelins pyoverdine pyoverdines pyrosequencing -Pyruvate quantile quantisation +rDNA +rRNA +rRNAs rakefile rakefiles -RAxML rcoffee -rDNA -README readonly readseq redox @@ -406,54 +433,37 @@ relaxase relaxases replicase replicases -Replicons reproducibility reproducibly resequencing ribosomal ribosome -Ronn -Roraima -rRNA -rRNAs -RSpec -RSS -RubyGems rubygems -Saccharomyces -SBW scaffolded scaffolder screenshot screenshots ser serine -SGD -Shoulda siderophore siderophores silico silva -SOLiD -Spearman -Spearman's speciation -SQL -Sterol stoichiometric stoichiometries stoichiometry stutzeri subtilis svd -SVN synomous synteny synthase synthases syringae +tRNA +tRNAs tandemly -Taskfile taxa terabases tetramer @@ -462,7 +472,6 @@ tetranucleotide tetranucleotides tfasty thr -Threonine topoisomerase topoisomerases tranfer @@ -470,21 +479,16 @@ transcriptome transcriptomic translocate translocating -Trehalose triose -tRNA -tRNAs trp tryptophan turbidostat typhi tyr -Ubuntu unassembled undirected upvote username -Valine vectorisation vectorises versa @@ -493,10 +497,8 @@ versioning vitro vivo webserver -Wellcome whitespace wiki -Wikipedia wikis wordpress workflow @@ -504,6 +506,4 @@ workflows ws yaml yml -YPD zsh -Zymosterol From 657c834a9188f130da65a23a00e34892b281160a Mon Sep 17 00:00:00 2001 From: Michael Barton Date: Mon, 17 Aug 2015 15:42:21 -0700 Subject: [PATCH 2/7] Update solarized module Signed-off-by: Michael Barton --- solarized | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/solarized b/solarized index c350650c..e40cd413 160000 --- a/solarized +++ b/solarized @@ -1 +1 @@ -Subproject commit c350650cb74eed91895272d4b9d0fde8a335d223 +Subproject commit e40cd4130e2a82f9b03ada1ca378b7701b1a9110 From 62ce4b4e73852598b009858d62320d8deefe7269 Mon Sep 17 00:00:00 2001 From: Michael Barton Date: Sun, 20 Sep 2015 17:03:00 -0700 Subject: [PATCH 3/7] Update dictionary Signed-off-by: Michael Barton --- aspell.en.pws | 306 +++++++++++++++++++++++++------------------------- 1 file changed, 153 insertions(+), 153 deletions(-) diff --git a/aspell.en.pws b/aspell.en.pws index 25211c2f..5bd9d2d0 100644 --- a/aspell.en.pws +++ b/aspell.en.pws @@ -1,150 +1,11 @@ personal_ws-1.1 en 508 +absorbance ABySS -AI -API -ASM -ATPase ActiveRecord -Archaea -Arginine -Asparagine -Aspartate -Assemblathon -BBSRC -BMC -BioPerl -BioRuby -BioStar -Bioboxes -CLI -CMP -COGs -CRISPR -CSS -CSV -Complementation -Connotea -Cornu -Daltons -Debian -Denormalisation -DockerHub -Dockerfile -Doudoroff -EMBL -EMR -Entner -Erlang -Eubacteria -FBA -Folate -FriendFeed -GC -GFF -GMP -Gemfile -GenBank -Glycerolipid -Google -Heizer -HubMed -IEEE -Illumina -Inkscape -Inositol -Interoperability -Isoleucine -JGI's -JSON -JavaScript -KBp -KEGG -Kbp -Kmer -Kwalify -LaTeX -Loess -MAFFT -MATLAB -MBp -MCA -MOMA -Makefile -Makefiles -Mannan -Mbp -Meraculous -Metagenomics -Multivatiate -MySQL -NADH -NADPH -NCBI -NKU -NRPS -Nunn -ORF -ORFs -ORM -OSX -OTU -OTUs -Orthology -PAML -PCR -PHP -PLoS -PVD -Pentose -Phosphatidate -Phosphatidyl -Phosphatidylcholine -Phosphatidylethanolamine -Phosphatidylserine -Phospholipid -Phosphorylation -Pilus -Ploidy -Precedings -Procfile -Prokaryotes -Proteomics -Pseudomonad -Pseudomonads -Pseudomonas -PubMed -Pyruvate -RAxML -README -RSS -RSpec -Replicons -Ronn -Roraima -RubyGems -SBW -SGD -SOLiD -SQL -SVN -Saccharomyces -Shoulda -Spearman -Spearman's -Sterol -Taskfile -Threonine -Trehalose -Ubuntu -Valine -Wellcome -Wikipedia -YPD -Zymosterol -absorbance adaptated aeruginosa agglomerative +AI al aldolase amino @@ -152,25 +13,38 @@ amplicon amplicons ancova anova +API arb +Archaea archaeal arg +Arginine artefactually +ASM asn +Asparagine +Aspartate +Assemblathon assemblathons +ATPase barcode barcodes bashrc bayanus +BBSRC benchmarked benchmarking biobox +Bioboxes bioboxes bioinformatician bioinformaticians bioinformatics biomolecular biomolecules +BioPerl +BioRuby +BioStar biosynthesis biosynthetic biosynthetically @@ -181,6 +55,7 @@ blogger bloggers blogging blogs +BMC bowtie bp castellii @@ -198,46 +73,66 @@ chemoheterotrophic chemostat circos citeulike +CLI clojure clustalw +CMP codeml codon codons +COGs coli commensal +Complementation complementation +Connotea contig contigs coreutil coreutils +Cornu +CRISPR +CSS +CSV curation cyanobacterium cys +Daltons dAMP dCMP -dGMP -dN -dS -dTMP de +Debian decomplected dehydrogenase dehydrogenases dendrogram dendrograms +Denormalisation deplexed deplexing +dGMP diauxic dinucleotide discontiguous dispensability +dN dnaml +Dockerfile +DockerHub +Doudoroff downvote +dS +dTMP efflux +EMBL +EMR +Entner epistatic equilibria +Erlang essentiality et +Eubacteria eukaryotes eukaryotic evaluator @@ -248,10 +143,16 @@ extremophiles facultive fasta fastq +FBA fermentative fluorescens +Folate +FriendFeed friendfeed functionalisation +GC +Gemfile +GenBank genomer genomic genomics @@ -260,6 +161,7 @@ genotypic geochemical geochemically geomicrobiology +GFF gigabase gigabases github @@ -268,8 +170,11 @@ glu glutamic glutamine gly +Glycerolipid glycolysis glycolytic +GMP +Google gzipped hadoop haploinsufficiency @@ -277,6 +182,7 @@ haploinsufficient haploproficiency haploproficient haplotype +Heizer hemizygotes hemizygous heteroscedastic @@ -291,42 +197,66 @@ homopolymer homopolymers homopolymorphic homozygote +HubMed humic hyperthermophile hyperthermophiles -iPod +IEEE ile +Illumina img indels indices +Inkscape +Inositol +Interoperability interoperable intraspecies intron +iPod irreproducible isoenzymes +Isoleucine isomerase +JavaScript jgi +JGI's +JSON kb +KBp +Kbp +KEGG kilobase kilobases kinase kluyveri +Kmer kmer kmers kudriavzevii +Kwalify +LaTeX leu leucine +Loess loess login lys -mRNA -mRNAs +MAFFT +Makefile makefile +Makefiles makefiles +Mannan +MATLAB +MBp +Mbp +MCA mcl megabase megabases megablast +Meraculous mesophile mesophiles metabolome @@ -336,6 +266,7 @@ metadata metagenome metagenomes metagenomic +Metagenomics metagenomics microarray microbiome @@ -346,44 +277,73 @@ misassembly mmol mmols modularised +MOMA monoploid mothur +mRNA +mRNAs multi multimeric +Multivatiate mutualism +MySQL +NADH +NADPH +NCBI newbler +NKU novo +NRPS nucleotide nucleotides nucmer +Nunn oligonucleotide oligonucleotides omic online operon oppourtunisitic +ORF +ORFs +ORM ortholog orthologous orthologs +Orthology orthoquartzite +OSX +OTU +OTUs overfit overfitting +PAML paradoxus parallelisation paralog paralogs parameterised pathogenicity +PCR pdf +Pentose peptide peptone phaseolicola phe phenotypes phenotypic +Phosphatidate +Phosphatidyl +Phosphatidylcholine +Phosphatidylethanolamine +Phosphatidylserine phosphoketolase +Phospholipid +Phosphorylation photoautotrophic photoautotrophs +PHP phylip phylogenetic phylogenetically @@ -392,16 +352,22 @@ phylogenies phylogenomic phylogenomics pili +Pilus plasmid plasmids +Ploidy +PLoS plugin png polymorphisms polynucleotides powerpoint practices +Precedings priori +Procfile programmatically +Prokaryotes prokaryotic proline promer @@ -409,23 +375,30 @@ protegens proteome proteomes proteomic +Proteomics proteomics proven pseudogenes +Pseudomonad +Pseudomonads +Pseudomonas +PubMed putida +PVD pyochelin pyochelins pyoverdine pyoverdines pyrosequencing +Pyruvate quantile quantisation -rDNA -rRNA -rRNAs rakefile rakefiles +RAxML rcoffee +rDNA +README readonly readseq redox @@ -433,37 +406,54 @@ relaxase relaxases replicase replicases +Replicons reproducibility reproducibly resequencing ribosomal ribosome +Ronn +Roraima +rRNA +rRNAs +RSpec +RSS +RubyGems rubygems +Saccharomyces +SBW scaffolded scaffolder screenshot screenshots ser serine +SGD +Shoulda siderophore siderophores silico silva +SOLiD +Spearman +Spearman's speciation +SQL +Sterol stoichiometric stoichiometries stoichiometry stutzeri subtilis svd +SVN synomous synteny synthase synthases syringae -tRNA -tRNAs tandemly +Taskfile taxa terabases tetramer @@ -472,6 +462,7 @@ tetranucleotide tetranucleotides tfasty thr +Threonine topoisomerase topoisomerases tranfer @@ -479,16 +470,21 @@ transcriptome transcriptomic translocate translocating +Trehalose triose +tRNA +tRNAs trp tryptophan turbidostat typhi tyr +Ubuntu unassembled undirected upvote username +Valine vectorisation vectorises versa @@ -497,8 +493,10 @@ versioning vitro vivo webserver +Wellcome whitespace wiki +Wikipedia wikis wordpress workflow @@ -506,4 +504,6 @@ workflows ws yaml yml +YPD zsh +Zymosterol From f44bbb73c5e98f842e8a5e2244a70816231a586b Mon Sep 17 00:00:00 2001 From: Michael Barton Date: Sun, 11 Oct 2015 16:18:26 -0700 Subject: [PATCH 4/7] Update data brews --- data/brews | 1 + 1 file changed, 1 insertion(+) diff --git a/data/brews b/data/brews index 58ae1b9b..1d6baa37 100644 --- a/data/brews +++ b/data/brews @@ -1,3 +1,4 @@ +>>>>>>> Stashed changes Caskroom/cask/R Caskroom/cask/adium Caskroom/cask/cyberduck From 9cc4dc0248a86a22ecd4b55e87dba989b462155c Mon Sep 17 00:00:00 2001 From: Michael Barton Date: Sun, 11 Oct 2015 16:18:35 -0700 Subject: [PATCH 5/7] Update dictionary --- aspell.en.pws | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/aspell.en.pws b/aspell.en.pws index 5bd9d2d0..225faf86 100644 --- a/aspell.en.pws +++ b/aspell.en.pws @@ -1,4 +1,4 @@ -personal_ws-1.1 en 508 +personal_ws-1.1 en 513 absorbance ABySS ActiveRecord @@ -29,6 +29,7 @@ assemblathons ATPase barcode barcodes +barcoding bashrc bayanus BBSRC @@ -75,6 +76,7 @@ circos citeulike CLI clojure +Clum clustalw CMP codeml @@ -207,6 +209,7 @@ Illumina img indels indices +informatics Inkscape Inositol Interoperability @@ -317,6 +320,7 @@ OTU OTUs overfit overfitting +PacBio PAML paradoxus parallelisation @@ -416,6 +420,7 @@ Ronn Roraima rRNA rRNAs +RSII RSpec RSS RubyGems From ef1635aa1811ea44f3f4f263f11309041ad76b55 Mon Sep 17 00:00:00 2001 From: Michael Barton Date: Fri, 6 May 2016 09:57:55 -0700 Subject: [PATCH 6/7] Update dictionary --- aspell.en.pws | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/aspell.en.pws b/aspell.en.pws index eb775a63..9beab2cf 100644 --- a/aspell.en.pws +++ b/aspell.en.pws @@ -1,4 +1,4 @@ -personal_ws-1.1 en 519 +personal_ws-1.1 en 520 ABySS AI API @@ -277,6 +277,7 @@ glutamine gly glycolysis glycolytic +gzip gzipped hadoop haploinsufficiency From 3f16e15ef011216674efb605d4cbf28bd8afcab1 Mon Sep 17 00:00:00 2001 From: Michael Barton Date: Fri, 6 May 2016 09:58:33 -0700 Subject: [PATCH 7/7] Update list of homebrew installs --- data/brews | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/data/brews b/data/brews index 0f49c2e1..0420336a 100644 --- a/data/brews +++ b/data/brews @@ -1,4 +1,3 @@ ->>>>>>> Stashed changes Caskroom/cask/R Caskroom/cask/adium Caskroom/cask/cyberduck @@ -10,6 +9,8 @@ Caskroom/cask/inkscape Caskroom/cask/iterm2 Caskroom/cask/java Caskroom/cask/mactex +Caskroom/cask/mactex +Caskroom/cask/noisy Caskroom/cask/pastor Caskroom/cask/postico Caskroom/cask/selfcontrol