From 4e0d2db04b2b3e56d5bfe58601ac0831c62b8396 Mon Sep 17 00:00:00 2001 From: Kyle Niemeyer Date: Wed, 4 Apr 2018 07:46:16 -0700 Subject: [PATCH] minor edits to paper --- joss-paper/paper.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/joss-paper/paper.md b/joss-paper/paper.md index 2b9e62e1..24076710 100644 --- a/joss-paper/paper.md +++ b/joss-paper/paper.md @@ -8,7 +8,7 @@ authors: orcid: 0000-0003-0596-0222 affiliation: 1 affiliations: - - name: KTH Royal Institute of Technology + - name: KTH Royal Institute of Technology, Stockholm, Sweden index: 1 date: 26 January 2018 bibliography: paper.bib @@ -26,7 +26,7 @@ literature. Its intended audience is primarily researchers and engineers who need to perform modelling work. But since the intermediate representations -of e.g., ODE systems and systems of non-linear equations are available +of, e.g., ODE systems and systems of non-linear equations are available symbolically, ChemPy may also be used in an educational setting. Substances are represented by a class that holds their names and, optionally, @@ -37,7 +37,7 @@ parser. Reactions are represented through their stoichiometry and thermodynamic/kinetic parameters. If the stoichiometry of a reaction is unknown, ChemPy can balance it based on the composition of the substances. The classes for representing systems of reactions provide -methods to analyze e.g., if there are disjoint sets of reactions, or if all +methods to analyze, e.g., if there are disjoint sets of reactions, or if all are connected in the same network. The classes also offer a series of checks performed at initialization, ensuring balanced reactions with sane coefficients and consistent units. @@ -55,7 +55,7 @@ The under-determined formulation can also be expressed in a canoncial form with coefficients minimzed using PuLP [@mitchell2011pulp;@lougee2003common]. In fact, most equations and parametrizations in ChemPy support---in addition to NumPy arrays [@vanderWalt2011]---also symbolic input, as well as arrays -with explicit units. The latter allows ChemPy to check that e.g., the correct +with explicit units. The latter allows ChemPy to check that, e.g., the correct dimensionality with respect to reaction order is used for rate constants. # Features