2013-11-04 1349
 On branch add_gingko_chap3
	modified:   3_chapter.tex
	modified:   3_chapter.tex.backup
	modified:   4_chapter.tex
	new file:   4_chapter.tex.backup
	modified:   acronym_terms.tex
	modified:   figures/aedesHMMsplice.tex.backup
	new file:   figures/ecr-mean-ptci-figs.tex
	new file:   figures/ecr-pairwise-ptci-figs.tex
	new file:   figures/ecrusp-graph.tex
	new file:   figures/figs/EcRUSP_graph.png
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/downAt4_gene_profiles_from_cummerbund/Aa_downAt4_cls19_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/downAt4_gene_profiles_from_cummerbund/Ag_downAt4_cls19_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/downAt4_gene_profiles_from_cummerbund/Cq_downAt4_cls19_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/ecr_and_insects_ptci1_gene_profiles_from_cummerbund/25_clusters.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/ecr_and_insects_ptci1_gene_profiles_from_cummerbund/25_clusters.pgf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/ecr_and_insects_ptci1_gene_profiles_from_cummerbund/25_clusters.png
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/upAfter4_gene_profiles_from_cummerbund/Aa_upAfter4_cls7_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/upAfter4_gene_profiles_from_cummerbund/Ag_upAfter4_cls7_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/upAfter4_gene_profiles_from_cummerbund/Cq_upAfter4_cls7_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/upAt4_gene_profiles_from_cummerbund/Aa_upAt4_cls6_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/upAt4_gene_profiles_from_cummerbund/Ag_upAt4_cls6_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_and_insects_ptci_20130903/upAt4_gene_profiles_from_cummerbund/Cq_upAt4_cls6_Ag_target_FPKMs_vb_orthos.pdf
	deleted:    figures/figs/ecr_team_ptci/mean_ptci_cum_hist.pdf
	deleted:    figures/figs/ecr_team_ptci/mean_ptci_hist.pdf
	deleted:    figures/figs/ecr_team_ptci/pairwise_ptci_cum_hist.pdf
	deleted:    figures/figs/ecr_team_ptci/pairwise_ptci_hist.pdf
	deleted:    figures/figs/ecr_team_ptci_20130903/activated_gene_profiles_from_cummerbund/Aa_activated.png
	deleted:    figures/figs/ecr_team_ptci_20130903/activated_gene_profiles_from_cummerbund/Ag_activated.png
	deleted:    figures/figs/ecr_team_ptci_20130903/activated_gene_profiles_from_cummerbund/Cq_activated.png
	deleted:    figures/figs/ecr_team_ptci_20130903/mean_ptci_cum_hist.pdf
	deleted:    figures/figs/ecr_team_ptci_20130903/mean_ptci_hist.pdf
	deleted:    figures/figs/ecr_team_ptci_20130903/pairwise_ptci_cum_hist.pdf
	deleted:    figures/figs/ecr_team_ptci_20130903/pairwise_ptci_hist.pdf
	modified:   figures/figs/ecr_team_ptci_20130918_orthodb7/mean_ptci_cum_hist.pdf
	modified:   figures/figs/ecr_team_ptci_20130918_orthodb7/mean_ptci_fdr.pdf
	modified:   figures/figs/ecr_team_ptci_20130918_orthodb7/mean_ptci_hist.pdf
	modified:   figures/figs/ecr_team_ptci_20130918_orthodb7/pairwise_ptci_cum_hist.pdf
	modified:   figures/figs/ecr_team_ptci_20130918_orthodb7/pairwise_ptci_fdr.pdf
	modified:   figures/figs/ecr_team_ptci_20130918_orthodb7/pairwise_ptci_hist.pdf
	new file:   figures/figs/ecr_team_ptci_20130918_orthodb7_20131124/mean_ptci_cum_hist.pdf
	renamed:    figures/figs/ecr_team_ptci/mean_ptci_fdr.pdf -> figures/figs/ecr_team_ptci_20130918_orthodb7_20131124/mean_ptci_fdr.pdf
	new file:   figures/figs/ecr_team_ptci_20130918_orthodb7_20131124/mean_ptci_hist.pdf
	new file:   figures/figs/ecr_team_ptci_20130918_orthodb7_20131124/pairwise_ptci_cum_hist.pdf
	renamed:    figures/figs/ecr_team_ptci_20130903/pairwise_ptci_fdr.pdf -> figures/figs/ecr_team_ptci_20130918_orthodb7_20131124/pairwise_ptci_fdr.pdf
	new file:   figures/figs/ecr_team_ptci_20130918_orthodb7_20131124/pairwise_ptci_hist.pdf
	new file:   figures/figs/gfunc_scheme/gfunc_scheme.graphml
	modified:   figures/figs/jaspar_insect_ptci_20130918_orthodb7/mean_ptci_cum_hist.pdf
	modified:   figures/figs/jaspar_insect_ptci_20130918_orthodb7/mean_ptci_fdr.pdf
	modified:   figures/figs/jaspar_insect_ptci_20130918_orthodb7/mean_ptci_hist.pdf
	modified:   figures/figs/jaspar_insect_ptci_20130918_orthodb7/pairwise_ptci_cum_hist.pdf
	modified:   figures/figs/jaspar_insect_ptci_20130918_orthodb7/pairwise_ptci_fdr.pdf
	modified:   figures/figs/jaspar_insect_ptci_20130918_orthodb7/pairwise_ptci_hist.pdf
	new file:   figures/figs/jaspar_insect_ptci_20130918_orthodb7_20131124/mean_ptci_cum_hist.pdf
	renamed:    figures/figs/ecr_team_ptci_20130903/mean_ptci_fdr.pdf -> figures/figs/jaspar_insect_ptci_20130918_orthodb7_20131124/mean_ptci_fdr.pdf
	new file:   figures/figs/jaspar_insect_ptci_20130918_orthodb7_20131124/mean_ptci_hist.pdf
	new file:   figures/figs/jaspar_insect_ptci_20130918_orthodb7_20131124/pairwise_ptci_cum_hist.pdf
	renamed:    figures/figs/ecr_team_ptci/pairwise_ptci_fdr.pdf -> figures/figs/jaspar_insect_ptci_20130918_orthodb7_20131124/pairwise_ptci_fdr.pdf
	new file:   figures/figs/jaspar_insect_ptci_20130918_orthodb7_20131124/pairwise_ptci_hist.pdf
	new file:   figures/insect-mean-ptci-figs.tex
	new file:   figures/insect-pairwise-ptci-figs.tex
	deleted:    figures/mean-ptci-figs.tex
	deleted:    figures/mean-ptci-figs.tex.backup
	deleted:    figures/pairwise-ptci-figs.tex
	modified:   fonts.tex
	modified:   glossary_terms.tex
	modified:   preliminaries.tex
	new file:   preliminaries.tex.backup
	renamed:    thesis.sublime-workspace -> thesis (vlad's conflicted copy 2013-11-24).sublime-workspace
	modified:   thesis.acn
	modified:   thesis.acr
	modified:   thesis.alg
	modified:   thesis.pdf
	modified:   thesis.sublime-workspace
	modified:   thesis.tex
	new file:   uci-thesis-latex (vlad's conflicted copy 2013-11-24).kilepr
	modified:   uci-thesis-latex.kilepr
Merge branch 'add_gingko_chap3' into my_text
 On branch my_text
	modified:   4_chapter.tex
	modified:   thesis.acn
	modified:   thesis.pdf
	new file:   uci-thesis-latex (tardis's conflicted copy 2013-11-30).kilepr
	modified:   uci-thesis-latex.kilepr
2013-12-01
commented some functional annotation tables - hid the cellular term tables - \begin{tabular}{p{.7\textwidth}r} to fix over-long rows
commiting before work on 2013-12-04
commit before starting work on 2013-12-04
2013-12-05: caution commit before running an ipynb that may change files
(ecr_U_insect_ptci_0_95_Exploring_Profiles_cls16_orthodb7)
2013-12-06: print for proofing
Dropbox botched my end of day commit lastnight.  I merged 4_chapter.tex (conflicted copy) in meld and this is what SHOULD have been commited last night!
Merge branch 'add_chap4' into my_text