Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Using RuleBuilder to graphically define and visualize BioNetGen-language
  patterns and reaction rules   RuleBuilder is a tool for drawing graphs that can be represented by the
BioNetGen language (BNGL), which is used to formulate mathematical, rule-based
models of biochemical systems. BNGL provides an intuitive plain-text, or
string, representation of such systems, which is based on a graphical
formalism. Reactions are defined in terms of graph-rewriting rules that specify
the necessary intrinsic properties of the reactants, a transformation, and a
rate law. Rules may also contain contextual constraints that restrict
application of the rule. In some cases, the specification of contextual
constraints can be verbose, making a rule difficult to read. RuleBuilder is
designed to ease the task of reading and writing individual reaction rules, as
well as individual BNGL patterns similar to those found in rules. The software
assists in the reading of existing models by converting BNGL strings of
interest into a graph-based representation composed of nodes and edges.
RuleBuilder also enables the user to construct de novo a visual representation
of BNGL strings using drawing tools available in its interface. As objects are
added to the drawing canvas, the corresponding BNGL string is generated on the
fly, and objects are similarly drawn on the fly as BNGL strings are entered
into the application. RuleBuilder thus facilitates construction and
interpretation of rule-based models.

32
The categories of this paper are: atom-ph
5
The categories of this paper are: gr-qc
22
The categories of this paper are: chao-dyn
33
The categories of this paper are: plasm-ph
3
The categories of this paper are: physics
31
The categories of this paper are: ao-sci
16
The categories of this paper are: stat
20
The categories of this paper are: acc-phys
34
The categories of this paper are: chem-ph
7
The categories of this paper are: hep-th
24
The categories of this paper are: dg-ga
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The categories of this paper are: supr-con
27
The categories of this paper are: comp-gas
4
The categories of this paper are: cond-mat
25
The categories of this paper are: patt-sol
17
The categories of this paper are: q-fin