Added large corpus
Added RAS neighborhood sub-corpus
Oneliner.bel, for seeing RDF of single statements
Quick util script to find rules containing a protein
Added figs dir with some network PDFs
Ignore large_corpus.rdf

at > 250 mb, don't want to add to version control (plus it can be
regenerated using bel2rdf)
Make binding rules from complex statements

Very simple right now--simple adds a single binding site, 'b', for any
protein that participates in a binding rule, and then creates a bond
between these b sites for all members participating in a complex (a
"star" conformation).

A better version would be to create a named site for every binding
partner, and have the binding between proteins use that site, e.g.
A(b=1) % B(a=1).
Add rules for RAS GEFs

Looks for rules where there is a protein with an activity (the GEF) that
directly Increases the gtpBoundActivity of the object.
Get rules for GAPs (inhibitors of Ras)

Also the start of a function that looks for the activity of Ras-like
GTPases.
Determine which statements are unconverted

Wrote a function, get_all_direct_statements, that queries for all of the
statements in the corpus that have a directInc/Dec relationship, and
returns them. Also modified the other funcs to return the statements
that they have converted. The script at the end compares the two lists
to identify types of statements that have not yet been converted.

This might not be something worth keeping around (especially not in this
hacky form) but it's certainly useful to understand the conversion
process better.
Add notes on unconverted statements
Scan for kin->kin rules and suggest sites