Update paper

.github/workflows/draft-pdf.yml

@@ -0,0 +1,24 @@
+name: Draft PDF
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

paper/paper.md

@@ -1,3 +1,30 @@
+---
+title: 'ratesb_python: A Python Package for Analyzing Rate Laws in Biological Models'
+tags:
+  - Python
+  - SBML
+  - Systems Biology
+  - Kinetics
+  - Rate Laws
+authors:
+  - name: Longxuan Fan
+    orcid: 0009-0006-6523-8302
+    affiliation: 1
+  - name: Joseph L. Hellerstein
+    affiliation: 2
+  - name: Herbert M. Sauro
+    affiliation: 3
+affiliations:
+  - name: Viterbi School of Engineering, University of Southern California
+    index: 1
+  - name: eScience Institute, University of Washington
+    index: 2
+  - name: Department of Bioengineering, University of Washington
+    index: 3
+date: 14 October 2024
+bibliography: paper.bib
+---
+
 # Summary
 
 `ratesb_python` is a Python package that analyzes mechanistic models of biological systems that consist of networks of chemical reactions like $2 H_2 + O_2 \rightarrow 2 H_2O$ [with rate laws such as $k [h_2]^2 [O_2]$ that describe the rate at which the reaction proceeds]. The package focuses on rate laws of reactions, algebraic expressiona that specify the rate at which reactants (e.g., $H_2, O_2$) are converted into products (e.g., $O_2$). ``ratesb_python`` analyzes rate laws to detect errors and warnings that affect the robustness and accuracy of models that use the SBML (Systems Biology Markup Language) community standard for model model descriptions [@Hucka2003].
@@ -52,4 +79,8 @@ Error and warning messages generated during the analysis are systematically mana
 
 # Future Work
 
-Future developments for `ratesb_python` include enriching the library of checks and optimizing the performance of classification algorithms. The goal is to expand the tool's capabilities, making it a more comprehensive resource for developers and researchers alike, and to introduce customization options for error and warning management, further enhancing its utility in systems biology.
+Future developments for `ratesb_python` include enriching the library of checks and optimizing the performance of classification algorithms. The goal is to expand the tool's capabilities, making it a more comprehensive resource for developers and researchers alike, and to introduce customization options for error and warning management, further enhancing its utility in systems biology.
+
+---
+bibliography: paper.bib
+---

paper/paper.yaml

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+title: 'ratesb_python: A Python Package for Analyzing Rate Laws in Biological Models'
+tags:
+  - Python
+  - SBML
+  - Systems Biology
+  - Kinetics
+  - Rate Laws
+authors:
+  - name: "Longxuan Fan"
+    orcid: "0009-0006-6523-8302"
+    affiliation: 1
+  - name: "Joseph L. Hellerstein"
+    affiliation: 2
+  - name: "Herbert M. Sauro"
+    affiliation: 3
+affiliations:
+  - name: "Viterbi School of Engineering, University of Southern California"
+    index: 1
+  - name: "eScience Institute, University of Washington"
+    index: 2
+  - name: "Department of Bioengineering, University of Washington"
+    index: 3
+date: 2024-10-14
+bibliography: paper.bib
+repository: "https://github.com/sys-bio/ratesb_python"