<b>Metabolomics data for GEM-iPfu 2,3-BDO strain (O'Quinn et al., 2026 & Vailionis et al., 2026)</b>

<p dir="ltr">This figshare item mirrors the processed metabolomics data files associated with the GEM-iPfu genome-scale metabolic model repository, supporting the manuscripts O'Quinn <i>et al. </i>(2026) and Vailionis <i>et al. </i>(2026). It is provided as a convenience download and manual backup for the corresponding files tracked with Git LFS in the primary GitHub/Zenodo release.</p><p dir="ltr"><b>Contents:</b> Targeted and untargeted LC-MS metabolomics data for <i>Pyrococcus furiosus</i> strains Pfu-COM1 and Pfu-BDO, including long-format measurement tables, expression matrices, sample and feature metadata, and limma differential abundance results.</p><p dir="ltr"><b>Files:</b></p><ul><li><code>data/metabolomics/2026-04-01_targeted_df_long.tsv</code> — targeted metabolomics measurements (long format)</li><li><code>data/metabolomics/</code><code>2026-04-01_targeted_expr_matrix.tsv</code> — targeted metabolomics expression matrix</li><li><code>data/metabolomics/</code><code>2026-04-01_targeted_feature_metadata.tsv</code> — targeted feature annotations</li><li><code>data/metabolomics/</code><code>2026-04-01_targeted_sample_metadata.tsv</code> — targeted sample metadata</li><li><code>data/metabolomics/</code><code>2026-04-01_untargeted_df_long.tsv</code> — untargeted metabolomics measurements (long format)</li><li><code>data/metabolomics/</code><code>2026-04-01_untargeted_expr_matrix.tsv</code> — untargeted metabolomics expression matrix</li><li><code>data/metabolomics/</code><code>2026-04-01_untargeted_feature_metadata.tsv</code> — untargeted feature annotations</li><li><code>data/metabolomics/</code><code>2026-04-01_untargeted_sample_metadata.tsv</code> — untargeted sample metadata</li><li><code>data/metabolomics/</code><code>2026-04-05_Pfu_targeted_limma_results.csv</code> — limma differential abundance results (targeted)</li><li><code>data/metabolomics/</code><code>2026-04-05_Pfu_untargeted_limma_results.csv</code> — limma differential abundance results (untargeted)</li><li><code>output/samples_dict.pkl</code>— python pickle file containing a dictionary of dataframes with random flux samples used for manuscript figures</li></ul><p dir="ltr"><b>Primary release:</b> The full model, analysis scripts, and version history are available at:</p><ul><li>GitHub: <a href="github.com/zhanglab/GEM-iPfu" target="_blank">github.com/zhanglab/GEM-iPfu</a></li><li>Zenodo (v1.2.1): <a href="doi.org/10.5281/zenodo.7915812" target="_blank" rel="noreferrer">doi.org/10.5281/zenodo.791581</a></li></ul><p dir="ltr">These same files are tracked with Git LFS in the primary repository under <code>manuscript/OQuinn_Vailionis_2026/</code>.

See the repository README for instructions on retrieving them via <code>git lfs pull</code>.</p>