Latest writing
Product updates, learnings, and stories from the Runcell team.
Dam/Dcm Methylation Tutorial: Which Restriction Sites Are Blocked in pUC19, pBR322, pACYC184 and Lambda
A site-by-site table of which restriction sites Dam and Dcm methylation block in four standard DNAs, for the 114 enzymes in Runcell's restriction site finder, using REBASE sensitivity data. Covers the enzymes that are on the 'blocked' list but still cut your vector, how often a cloning junction creates a new blocked site, and a script to check your own plasmid.Read More →
ipynb vs py: What Breaks When a Notebook Becomes a Script (Tested Matrix)
Twelve notebook constructs, converted with nbconvert and jupytext, each run under python and ipython: which ones crash, which ones exit 0 having silently done nothing, the plain-Python replacement for each, and what a re-run does to your git diff in .ipynb vs .py.Read More →
PyInstaller vs Nuitka vs cx_Freeze: A Measured Packaging Benchmark (Build Time, Size, Launch Time)
Three probe scripts (stdlib, pandas, matplotlib) built five ways — PyInstaller onedir and onefile, Nuitka standalone and onefile, cx_Freeze — then launched six times each, on macOS. Onefile builds cost 3–36 seconds on every launch, PyInstaller's matplotlib builds rebuild the font cache each run, and Nuitka's folder builds take 5–10× longer than PyInstaller's without a smaller folder for the pandas and matplotlib scripts.Read More →
BCA vs Bradford: How Far Off Each Assay Reads 13 Proteins Against a BSA Standard
A protein-by-protein bias table for BCA, Micro BCA, Modified Lowry, Bradford and Bradford Plus, built from the vendor's own response ratios, plus an A280 column computed from UniProt. Shows where the assays disagree by up to 3.4×, what switching to a BGG standard fixes for antibodies, and why the Bradford numbers are a best case.Read More →
Primer Dimer Check Tutorial: Testing ΔG Rules on the CDC qPCR Primers
We ran the CDC SARS-CoV-2 N1, N2, N3 and RNase P primers and probes through two dimer models and Primer3. A consecutive-pair checker at common ΔG limits misses the N3 set that CDC withdrew. Ranked by Primer3's 3′-end stability, the N3 pair comes first and two of three reported N2 interactions land in the top four. With the numbers, the code, and how to read a dimer flag.Read More →
A280 Protein Concentration Tutorial: ε280 for 11 Proteins, and Why A280 ≠ mg/mL
Computed ε280, molecular weight and Abs 0.1% for 11 common lab proteins from UniProt mature chains. Shows how far the '1 A280 = 1 mg/mL' shortcut is off (0.17× to 2.65×), what pasting the precursor sequence costs, and why nucleic-acid contamination skews proteins with a low Abs 0.1% the most.Read More →
Jupyter to PDF: A Measured Fidelity Benchmark of nbconvert's Three Export Paths
Nine probe notebooks, three export paths, twenty-seven conversion attempts, and a count of what actually survives into each PDF. The LaTeX route keeps every column of a wide DataFrame and drops four of eight Unicode strings; the browser routes do the reverse, and clip a long source line as well.Read More →
ModuleNotFoundError in Jupyter: A Reproduced Kernel Failure Matrix
The package imports in your terminal and fails in the notebook. Four virtual environments, nine notebook runs, and the one line of jupyter_client source that decides which Python your kernel actually runs — with the audit script that answers it for your machine.Read More →
DNA Molecular Weight in Python: A Runnable ng/µL → nM Workflow
Why ng/µL → nM calculators disagree by 7%, measured on real NCBI sequences with Biopython. Covers free acid vs sodium salt, the 650/660/330 rules of thumb, 5' phosphates, and a full pUC19 digest-to-ligation workflow.Read More →
nbconvert PDF Export Errors: A Complete Troubleshooting Reference
The common nbconvert PDF export errors, each with real terminal output, the actual cause, and a fix. Covers PandocMissing, xelatex not found, missing .sty files, webpdf/Playwright, and kernel errors.Read More →
OpenClaw: Self-Hosted AI Assistant You Can Message From Anywhere
Learn how to deploy OpenClaw, a self-hosted AI Gateway that connects to WhatsApp, Telegram, and Discord. Step-by-step setup with deployment options included.Read More →
RDKit Python Tutorial for Chemists (With Examples)
Step-by-step RDKit tutorial for chemists. Install RDKit, draw molecules, calculate properties, and run similarity searches in Python — no coding experience required.Read More →
DESeq2 in Python: Step-by-Step PyDESeq2 Tutorial
Run DESeq2 differential expression analysis entirely in Python with PyDESeq2. Covers count matrices, normalization, statistical testing, LFC shrinkage, and visualization.Read More →
How to Remove Data Validation in Excel (Step-by-Step)
Remove data validation in Excel in 4 clicks: select cells, go to Data > Data Validation > Clear All > OK. Works for drop-down lists, rules, and entire sheets.Read More →
Differential Expression Analysis: Guide with R & Python Code
Complete guide to differential expression analysis for RNA-seq. Includes ready-to-run code for DESeq2, edgeR, limma-voom, and Scanpy with bulk and single-cell workflows.Read More →
Jupyter nbconvert: Convert Notebooks to HTML, PDF & Python
Learn how to use Jupyter nbconvert to export .ipynb notebooks to HTML, PDF, Python scripts, Markdown, and slides. Includes commands and examples for every output format.Read More →
How to Delete a Column in Pandas (5 Methods With Examples)
Delete columns in a pandas DataFrame with drop(), del, pop(), column selection and loc/iloc. Every example was run on pandas 3.0.6 with its real output shown, plus how to avoid the KeyError and a memory test: inplace=True saves nothing, but del and pop() avoid a 64 MB copy that drop() makes.Read More →
What Is .ipynb_checkpoints? Deleting It, and the Git Commands That Actually Untrack It
What Jupyter's .ipynb_checkpoints folders are, whether it is safe to delete them, and why adding them to .gitignore does not untrack the ones you already committed - with a throwaway repository showing exactly what each untracking command does to your index.Read More →
How to Install Jupyter Notebook on macOS
Install Jupyter Notebook on Mac with a venv, Conda, Homebrew, or JupyterLab Desktop — including the real "externally-managed-environment" error a global pip install hits on Homebrew Python, and the versions a clean venv install gets today.Read More →