diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml new file mode 100644 index 0000000..f8e0362 --- /dev/null +++ b/.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 \ No newline at end of file diff --git a/paper/paper.md b/paper/paper.md index e20e1fd..24f5710 100644 --- a/paper/paper.md +++ b/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. \ No newline at end of file +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 +--- diff --git a/paper/paper.pdf b/paper/paper.pdf new file mode 100644 index 0000000..ca2d1a5 Binary files /dev/null and b/paper/paper.pdf differ diff --git a/paper/paper.yaml b/paper/paper.yaml new file mode 100644 index 0000000..d716d03 --- /dev/null +++ b/paper/paper.yaml @@ -0,0 +1,25 @@ +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"