Add new figures and force figures, tables and code listings
to remain in their sections using
http://tex.stackexchange.com/a/4667/6784
revise code listings
1. Replace perl with python script to remove urls and annotations from
bibtex files
2. Refactor sections into individual tex files
3. Move technical details to the models section
4. Write summary
5. Edit results and discussion section

On branch devel
Your branch is up-to-date with 'origin/devel'.

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   Makefile
	modified:   bib/books.bib
	modified:   bib/papers.bib
	modified:   bib/remove_url.pl
	new file:   bib/remove_url.py
	modified:   code/python/hypergraphcycle.py
	modified:   plos_template.tex
	modified:   tex/abstract.tex
	modified:   tex/hypergraphcycle.tex
	modified:   tex/introduction.tex
	modified:   tex/overfourapproxvol.tex

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	System.out
	beamer.pdf
	beamer.pdf.off.info
	code/biopython/
	code/polytopes/c33.poly
	code/python/C4Vol.m
	code/python/C4Vol.out
	code/python/C4kcscript.pl
	code/python/basketkcscript.pl
	code/python/clawkcscript.pl
	code/python/figs/
	code/python/flagpolekcscript.pl
	code/python/fourgraphsdim.pdf
	code/python/fourgraphsdim.svg
	code/python/fourgraphsvol.pdf
	code/python/fourgraphsvol.svg
	code/python/fourhypergraphsdim.pdf
	code/python/fourhypergraphsdim.svg
	code/python/fourhypergraphsvol.pdf
	code/python/fourhypergraphsvol.svg
	code/python/graphdata.csv
	code/python/mycube.poly
	code/python/output/C33.data
	code/python/output/C33.vertices
	code/python/output/fourgraphs.dat
	code/python/output/fourgraphs.data
	code/python/output/fourgraphs.dimension
	code/python/output/fourgraphs.summary
	code/python/output/fourgraphs.volume
	code/python/output/hypergraphhasse.dot
	code/python/output/hypergraphhasse.pdf
	code/python/output/hypergraphhasse.tex
	code/python/output/hypergraphs.data
	code/python/output/hypergraphs.dimension
	code/python/output/ncyclevolume.dat
	code/python/overfourVol.m
	code/python/overfourVol.out
	code/python/overfourkcscript.pl
	code/python/overthreekcscript.pl
	code/python/overtwo.tri
	code/python/overtwoconnect.poly
	code/python/overtwoconnect.tri
	code/python/overtwoconnectkcscript.pl
	code/python/overtwoconnectv2.tri
	code/python/overtwoconnectv2kcscript.pl
	code/python/overtwokcscript.pl
	code/python/overtwotrifacets.pl
	code/python/respaceoutput.diff
	code/python/sep_python.sublime-project
	code/python/sep_python.sublime-workspace
	code/python/testkcscript.pl
	code/python/testtest.py
	code/python/tripodkcscript.pl
	code/python/twok2kcscript.pl
	code/scheme/
	fig/build/
	fig/figure_summary.djvu
	fig/fourgraphsdim.pdf
	fig/fourgraphsdim.svg
	fig/fourgraphsvol.pdf
	fig/fourgraphsvol.svg
	fig/fourhypergraphsdim.pdf
	fig/fourhypergraphsdim.svg
	fig/fourhypergraphshasse.pdf
	fig/fourhypergraphsvol.pdf
	fig/fourhypergraphsvol.svg
	fig/hypergraphrelationships.svg
	fig/plasmid_diagram.svg
	fig/sample_expression_data.svg
	fig/threecycclust.pdf
	fig/threecycuntrained.pdf
	fig/threehypergraphshasse.pdf
	fig/threehypergraphshasse.svg
	fig/threeleveldiagram.svg
	plos_template.aux
	plos_template.bbl
	plos_template.blg
	plos_template.fdb_latexmk
	plos_template.log
	plos_template.out
	plos_template.pdf
	ref/
	sep.sublime-project
	sep.sublime-workspace
	summary.pdf
	summary.tex
	tex/abstract.aux
	tex/abstract.fdb_latexmk
	tex/abstract.log
	tex/authorsummary.tex
	tex/figures.tex
	tex/hadamardmethod.tex
	tex/marginalmapconstraints.tex
	tex/modeldescription.tex
	ximo.tex
Revise/add figures, revise text

On branch devel
Your branch is up-to-date with 'origin/devel'.

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   fig/conediagram.pdf
	modified:   fig/conediagram.svg
	new file:   fig/figure_graphs_dims_nolines.pdf
	new file:   fig/figure_graphs_dims_nolines.svg
	new file:   fig/stochdynscheme.pdf
	new file:   fig/stochdynscheme.svg
	modified:   plos_header.tex
	modified:   plos_template.tex
	new file:   tex/authorsummary.tex
	new file:   tex/figures.tex
	new file:   tex/hadamardmethod.tex
	new file:   tex/marginalmapconstraints.tex
	new file:   tex/modeldescription.tex
	modified:   tex/table_sheaf_r1.tex
	modified:   tex/table_sheaf_r2.tex
	modified:   tex/table_sheaf_r3.tex
	modified:   tex/table_sheaf_r4.tex
	new file:   texcount.pl

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	System.out
	beamer.pdf
	beamer.pdf.off.info
	code/biopython/
	code/polytopes/c33.poly
	code/python/C4Vol.m
	code/python/C4Vol.out
	code/python/C4kcscript.pl
	code/python/basketkcscript.pl
	code/python/clawkcscript.pl
	code/python/figs/
	code/python/flagpolekcscript.pl
	code/python/fourgraphsdim.pdf
	code/python/fourgraphsdim.svg
	code/python/fourgraphsvol.pdf
	code/python/fourgraphsvol.svg
	code/python/fourhypergraphsdim.pdf
	code/python/fourhypergraphsdim.svg
	code/python/fourhypergraphsvol.pdf
	code/python/fourhypergraphsvol.svg
	code/python/graphdata.csv
	code/python/mycube.poly
	code/python/output/C33.data
	code/python/output/C33.vertices
	code/python/output/fourgraphs.dat
	code/python/output/fourgraphs.data
	code/python/output/fourgraphs.dimension
	code/python/output/fourgraphs.summary
	code/python/output/fourgraphs.volume
	code/python/output/hypergraphhasse.dot
	code/python/output/hypergraphhasse.pdf
	code/python/output/hypergraphhasse.tex
	code/python/output/hypergraphs.data
	code/python/output/hypergraphs.dimension
	code/python/output/ncyclevolume.dat
	code/python/overfourVol.m
	code/python/overfourVol.out
	code/python/overfourkcscript.pl
	code/python/overthreekcscript.pl
	code/python/overtwo.tri
	code/python/overtwoconnect.poly
	code/python/overtwoconnect.tri
	code/python/overtwoconnectkcscript.pl
	code/python/overtwoconnectv2.tri
	code/python/overtwoconnectv2kcscript.pl
	code/python/overtwokcscript.pl
	code/python/overtwotrifacets.pl
	code/python/respaceoutput.diff
	code/python/sep_python.sublime-project
	code/python/sep_python.sublime-workspace
	code/python/testkcscript.pl
	code/python/testtest.py
	code/python/tripodkcscript.pl
	code/python/twok2kcscript.pl
	code/scheme/
	fig/build/
	fig/figure_summary.djvu
	fig/fourgraphsdim.pdf
	fig/fourgraphsdim.svg
	fig/fourgraphsvol.pdf
	fig/fourgraphsvol.svg
	fig/fourhypergraphsdim.pdf
	fig/fourhypergraphsdim.svg
	fig/fourhypergraphshasse.pdf
	fig/fourhypergraphsvol.pdf
	fig/fourhypergraphsvol.svg
	fig/hypergraphrelationships.svg
	fig/plasmid_diagram.svg
	fig/sample_expression_data.svg
	fig/threecycclust.pdf
	fig/threecycuntrained.pdf
	fig/threehypergraphshasse.pdf
	fig/threehypergraphshasse.svg
	fig/threeleveldiagram.svg
	plos_template.aux
	plos_template.bbl
	plos_template.blg
	plos_template.fdb_latexmk
	plos_template.log
	plos_template.out
	plos_template.pdf
	ref/
	sep.sublime-project
	sep.sublime-workspace
	summary.pdf
	summary.tex
	tex/abstract.aux
	tex/abstract.fdb_latexmk
	tex/abstract.log
	ximo.tex
1. update results
2. update fig 6
3. Add compilation pointers to the master tex file
from all those in the tex directory

On branch devel
Your branch is up-to-date with 'origin/devel'.

Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

	modified:   fig/stochdynscheme.pdf
	modified:   fig/stochdynscheme.svg
	modified:   plos_template.tex
	modified:   tex/abstract.tex
	modified:   tex/authorsummary.tex
	modified:   tex/figures.tex
	modified:   tex/graphlist4.tex
	modified:   tex/hadamardmethod.tex
	modified:   tex/hypergraphcycle.tex
	modified:   tex/hypergraphvolrat.tex
	modified:   tex/introduction.tex
	modified:   tex/listingspython.tex
	modified:   tex/marginalmapconstraints.tex
	modified:   tex/modeldescription.tex
	modified:   tex/overfourapproxvol.tex
	renamed:    plos_template.tex -> tex/results.tex
	modified:   tex/table_example.tex
	modified:   tex/table_hidvarmod.tex
	modified:   tex/table_logmat222.tex
	modified:   tex/table_pars222.tex
	modified:   tex/table_sheaf.tex
	modified:   tex/table_sheaf_r1.tex
	modified:   tex/table_sheaf_r2.tex
	modified:   tex/table_sheaf_r3.tex
	modified:   tex/table_sheaf_r4.tex

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	System.out
	beamer.pdf
	beamer.pdf.off.info
	code/biopython/
	code/polytopes/c33.poly
	code/python/C4Vol.m
	code/python/C4Vol.out
	code/python/C4kcscript.pl
	code/python/basketkcscript.pl
	code/python/clawkcscript.pl
	code/python/figs/
	code/python/flagpolekcscript.pl
	code/python/fourgraphsdim.pdf
	code/python/fourgraphsdim.svg
	code/python/fourgraphsvol.pdf
	code/python/fourgraphsvol.svg
	code/python/fourhypergraphsdim.pdf
	code/python/fourhypergraphsdim.svg
	code/python/fourhypergraphsvol.pdf
	code/python/fourhypergraphsvol.svg
	code/python/graphdata.csv
	code/python/mycube.poly
	code/python/output/C33.data
	code/python/output/C33.vertices
	code/python/output/fourgraphs.dat
	code/python/output/fourgraphs.data
	code/python/output/fourgraphs.dimension
	code/python/output/fourgraphs.summary
	code/python/output/fourgraphs.volume
	code/python/output/hypergraphhasse.dot
	code/python/output/hypergraphhasse.pdf
	code/python/output/hypergraphhasse.tex
	code/python/output/hypergraphs.data
	code/python/output/hypergraphs.dimension
	code/python/output/ncyclevolume.dat
	code/python/overfourVol.m
	code/python/overfourVol.out
	code/python/overfourkcscript.pl
	code/python/overthreekcscript.pl
	code/python/overtwo.tri
	code/python/overtwoconnect.poly
	code/python/overtwoconnect.tri
	code/python/overtwoconnectkcscript.pl
	code/python/overtwoconnectv2.tri
	code/python/overtwoconnectv2kcscript.pl
	code/python/overtwokcscript.pl
	code/python/overtwotrifacets.pl
	code/python/respaceoutput.diff
	code/python/sep_python.sublime-project
	code/python/sep_python.sublime-workspace
	code/python/testkcscript.pl
	code/python/testtest.py
	code/python/tripodkcscript.pl
	code/python/twok2kcscript.pl
	code/scheme/
	fig/build/
	fig/figure_summary.djvu
	fig/fourgraphsdim.pdf
	fig/fourgraphsdim.svg
	fig/fourgraphsvol.pdf
	fig/fourgraphsvol.svg
	fig/fourhypergraphsdim.pdf
	fig/fourhypergraphsdim.svg
	fig/fourhypergraphshasse.pdf
	fig/fourhypergraphsvol.pdf
	fig/fourhypergraphsvol.svg
	fig/hypergraphrelationships.svg
	fig/plasmid_diagram.svg
	fig/sample_expression_data.svg
	fig/threecycclust.pdf
	fig/threecycuntrained.pdf
	fig/threehypergraphshasse.pdf
	fig/threehypergraphshasse.svg
	fig/threeleveldiagram.svg
	plos_template.aux
	plos_template.bbl
	plos_template.blg
	plos_template.fdb_latexmk
	plos_template.log
	plos_template.out
	plos_template.pdf
	ref/
	sep.sublime-project
	sep.sublime-workspace
	summary.pdf
	summary.tex
	ximo.tex
refactor discussion
begin editing model description
continuation of cleaning up the model description