Our Work

Published in JSBX: Kanta Kumaki, Katsuhiro Kawaai, Shinobu Noji, Yukiko Kuroda, Koichi Matsuo, Bipixel rotation method: An algorithm for chirality analysis of biological mesh network, Journal of Struc…

Published in JSBX: Kanta Kumaki, Katsuhiro Kawaai, Shinobu Noji, Yukiko Kuroda, Koichi Matsuo, Bipixel rotation method: An algorithm for chirality analysis of biological mesh network, Journal of Structural Biology: X, Volume 14, 2026, 100154, https://doi.org/10.1016/j.yjsbx.2026.100154

A reproducible Python workflow for extracting internal stresses, determining fatigue life and fatigue-stage fractions, and calculating cyclic plastic dissipation energy from strain-controlled low-cycl…

A reproducible Python workflow for extracting internal stresses, determining fatigue life and fatigue-stage fractions, and calculating cyclic plastic dissipation energy from strain-controlled low-cycle-fatigue tests of OFHC copper.

Code for TB-TIGIT-NK manuscript: scRNA-seq, bulk RNA-seq, metabolomics, and super-enhancer analysis of TIGIT+ NK cell metabolic exhaustion in tuberculosis

Read Olympus/Evident OIR and POIR files Oirfile is a Python library to read images and metadata from OIR (Olympus Image Format Raw) files and POIR archives (ZIP collections of OIR files) produced by O…

Read Olympus/Evident OIR and POIR files Oirfile is a Python library to read images and metadata from OIR (Olympus Image Format Raw) files and POIR archives (ZIP collections of OIR files) produced by Olympus/Evident FluoView fluorescence microscopy software. Changes Fix spatial and time coordinates. Add OirFile.timestamps, scanner, and is_linescan properties.

P1 instrument + multi-domain residual pack Frozen chaos-band detector ((w=13), (\theta=0.41), lead [4,6]): | Face | Result | |------|--------| | Synthetic plant G1–G4 | INSTRUMENT_PASS (20/20 hits) | …

P1 instrument + multi-domain residual pack Frozen chaos-band detector ((w=13), (\theta=0.41), lead [4,6]): | Face | Result | |------|--------| | Synthetic plant G1–G4 | INSTRUMENT_PASS (20/20 hits) | | C1 ambient noise | C1_STRESS_FAIL (FP rate 1.0) | | Aedes Vitória | 0/5 yearly peaks | | ILI HHS→FluSurv | peak 0/10 · p75 1/10 | | EEG CHB-MIT | pilots archived; track paused | Honest synthesis: docs/P1_FAIL_TRIPTYCH.md Short-note outline: papers/p1-instrument-note/ Reproduce: python notebooks/16_p1_synthetic_canonical.py run · c1 · pytest tests/test_p1_synthetic.py Not claimed Multi-domain EWS skill Dengue / flu / seizure forecasting C1 guard (design only) Notes CHB-MIT raw EDFs are not redistributed Zenodo version DOI pending (API file-upload 400 at publish time); concept DOI remains 10.5281/zenodo.21516059 Commit: 76c1641

R scripts used to identify MYOD1-related loop-chained enhancer modules, characterize enhancer nexus connectivity, link enhancer modules to gene promoters, and calculate ABC-like regulatory scores in W…

R scripts used to identify MYOD1-related loop-chained enhancer modules, characterize enhancer nexus connectivity, link enhancer modules to gene promoters, and calculate ABC-like regulatory scores in WT and SMCHD1-KO cells.

Final release including the complete geospatial fuzzy logic model workflow, environment fixes, and updated documentation. Earth Data Analytics - CU Boulder Capstone | Nym Griggs

Python script to compute cholesterol-sensor sensitivity from chronoamperometry calibration traces by averaging the current over a fixed window at each plateau and regressing the averaged currents agai…

Python script to compute cholesterol-sensor sensitivity from chronoamperometry calibration traces by averaging the current over a fixed window at each plateau and regressing the averaged currents against the known cholesterol concentrations.

Differentiable structured direct solves, preconditioned and recycled Krylov methods, physics-agnostic preconditioners, mixed-precision iterative refinement, and structure-preserving discrete adjoints,…

Differentiable structured direct solves, preconditioned and recycled Krylov methods, physics-agnostic preconditioners, mixed-precision iterative refinement, and structure-preserving discrete adjoints, all jit/vmap/grad-transparent on CPU and GPU. Releases archive the library together with its benchmark drivers and committed measurement records for independent reproduction.

laserbeamsize is a Python library for analyzing laser beam quality according to the ISO 11146 standard. It provides tools for calculating beam center, diameter, divergence, and M² parameter from beam …

laserbeamsize is a Python library for analyzing laser beam quality according to the ISO 11146 standard. It provides tools for calculating beam center, diameter, divergence, and M² parameter from beam profile images. The package implements variance-based beam size calculations, background noise handling, and beam propagation analysis for TEM00 and higher-order modes. It is intended for education, research, and engineering applications in laser metrology and beam characterization.