The Bonham research lab both makes and uses a variety of software tools (Dr. Bonham’s Github page).

Tools We’ve Made

  • SWV AnyPeakFinder — software for analysis of peak height in square-wave voltammetry data from potentiostats.
  • Pyllelic — software for the analysis of allelic methylation patterns in human bisulfite DNA sequencing.
  • Fealden — a tool for the automated creation of Transcription Factor Beacons, novel biosensor probes for transcription factor activity and quantity. (down for retooling; older version of this concept was called SwitchGen)
  • A variety of helpful scripts

Github Repositories

pHcalcSystematic pH calculation package for Python
rust_qumaAn implementation of the quma module from Pyllelic in Rust
quickapiA generic quick API for single purpose python APIs
biochemistry-protocolsBiochemistry and other science protocols to facilitate collaborative methods development.
mamba-how-toUsing Mamba-forge for Python environment management
dash-templateCookiecutter template for a Plotly Dash webapp with modern structure and tooling.
bio-falsehoodsWeb app to dispel common biology falsehoods
pyllelic-webWeb frontend for pyllelic bisulfite DNA analysis.
bonhamcode.comSource code for
pyLIDARpython scripts to interact with the LD06 LIDAR
scholar-updateScripts for processing google scholar citation data.
pyfitnesspalA quick streamlit app to chart weight loss via MyFitnessPal.
msu-chairpayQuick streamlit dashboard to calculate alternative chair pay.
SACMESSoftware for the Analysis and Continuous Monitoring of Electrochemical Systems.
msu-che-enrollmentAn enrollment dashboard for MSU Denver Chemistry & Biochemistry
pyllelicpyllelic: a tool for detection of allele-specific methylation variation in bisulfite DNA sequencing.
msu-covid-trackerA web app of daily covid cases at MSU Denver.
pychemistryA collection of python scripts for chemistry and biochemistry
academia-admin-automationMiscellaneous scripts to automate administrative tasks in academia
fealdenTool for generating optimized nucleic acid biosensor sequences
SWVAnyPeakFinderGUI application for resolving peak heights in square-wave voltammetry datafiles.