https://dataleaf-642346.gitlab.io/tags/research-practice/Recent content in Research Practice on DataLeafHugoen-USFri, 14 Nov 2025 00:00:00 +0000https://dataleaf-642346.gitlab.io/posts/rerunning-an-old-analysis/Fri, 14 Nov 2025 00:00:00 +0000https://dataleaf-642346.gitlab.io/posts/rerunning-an-old-analysis/<p>A reviewer asked for one more column in a table produced two years ago. Adding a column means rerunning the analysis, and rerunning it means first showing that the old numbers come back. This entry records what that took.</p> <div class="dataleaf-heading"><h2 id="checklist">Checklist</h2> <a class="dataleaf-heading-anchor" href="#checklist" aria-label="Permalink to Checklist" data-heading-anchor data-heading-copy="Copy link to Checklist" data-heading-copied="Copied link to Checklist.">#</a> </div> <ul> <li><input checked="" disabled="" type="checkbox"> Check out the tagged commit that produced the submitted table</li> <li><input checked="" disabled="" type="checkbox"> Recreate the environment from the lock file</li> <li><input checked="" disabled="" type="checkbox"> Verify the input data against the recorded checksums</li> <li><input checked="" disabled="" type="checkbox"> Rerun the pipeline end to end and compare every cell</li> <li><input disabled="" type="checkbox"> Record the seed of every random step</li> <li><input disabled="" type="checkbox"> Add the new column and log the rerun</li> </ul> <p>The first four steps took an afternoon:</p>https://dataleaf-642346.gitlab.io/posts/what-a-research-notebook-is-for/Fri, 21 Apr 2023 00:00:00 +0000https://dataleaf-642346.gitlab.io/posts/what-a-research-notebook-is-for/<p>Laboratory scientists learn early that an experiment not written down did not happen. The bound notebook, with numbered pages and dated entries in ink, is one of the oldest instruments of experimental science, and it survives because it does something no other record does: it captures what the experimenter knew and intended at the moment of acting.</p> <p>Computational work has inherited the experiments but not, in most places, the notebook. A modern analysis leaves behind a repository full of code, a directory full of outputs, and perhaps a commit history. It is easy to believe that this is a complete record. It is a record of what was done. It is almost never a record of why.</p>