Figure 1
Flowchart of overall study design to identify biodata resources from the scientific literature. The fine-tuning procedure is not shown. Reproduced unmodified from (Imker et al. 2023) under Creative Commons Attribution License.
Figure 2
Graphical overview of the objectives of the study and the tools and methods used to address them regarding reproducibility, code quality, and data standards. The execution of these objectives was assessed by external review and validation.
Table 1
Glossary of Software.
| NAME | DESCRIPTION | REFERENCE |
|---|---|---|
| conda | Package and environment management system | (Conda 2017) |
| flake8 | Python linter (static code checking) | (Ziade and Cordasco 2011) |
| Make | Build automation tool, used here for creating shell command aliases | (GNU Make 1988) |
| Mermaid | Diagram generator for Markdown | (Sveidqvist 2014) |
| mypy | Static type checker for Python | (Lehtosalo 2012) |
| pip | Package manager for Python | (pypi n.d.) |
| pylint | Python linter (static code checking) | (Thénault 2001) |
| pytest | Python testing framework | (Krekel 2004) |
| pytest-flake8 | Pytest plugin to run flake8 | (Lockhert 2015) |
| pytest-mypy | Pytest plugin to run mypy | (Bader 2016) |
| pytest-pylint | Pytest plugin to run pylint | (Gee 2015) |
| renv | Dependency manager for R | (Ushey 2022) |
| snakefmt | Code formatter for Snakemake | (Hall and Letcher 2020) |
| Snakemake | General-purpose workflow manager | (Köster and Rahmann 2012) |
| styler | Code formatter for R | (Müller et al 2021) |
| yapf | Code formatter for Python | (Google Inc.) |