Software
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
| Repository | Description |
|---|---|
| DataVizBible | Friends don't let friends make certain types of data visualization - What are they and why are they bad. |
| pHcalc | Systematic pH calculation package for Python |
| rust_quma | An implementation of the quma module from Pyllelic in Rust |
| quickapi | A generic quick API for single purpose python APIs |
| biochemistry-protocols | Biochemistry and other science protocols to facilitate collaborative methods development. |
| IPEDS_streamlit | |
| langmuir_streamlit | |
| mamba-how-to | Using Mamba-forge for Python environment management |
| dash-template | Cookiecutter template for a Plotly Dash webapp with modern structure and tooling. |
| bio-falsehoods | Web app to dispel common biology falsehoods |
| pyllelic-web | Web frontend for pyllelic bisulfite DNA analysis. |
| bonhamcode.com | Source code for BonhamCode.com |
| pyLIDAR | python scripts to interact with the LD06 LIDAR |
| scholar-update | Scripts for processing google scholar citation data. |
| pyfitnesspal | A quick streamlit app to chart weight loss via MyFitnessPal. |
| msu-chairpay | Quick streamlit dashboard to calculate alternative chair pay. |
| SACMES | Software for the Analysis and Continuous Monitoring of Electrochemical Systems. |
| msu-che-enrollment | An enrollment dashboard for MSU Denver Chemistry & Biochemistry |
| pyllelic | pyllelic: a tool for detection of allele-specific methylation variation in bisulfite DNA sequencing. |
| msu-covid-tracker | A web app of daily covid cases at MSU Denver. |
| pychemistry | A collection of python scripts for chemistry and biochemistry |
| academia-admin-automation | Miscellaneous scripts to automate administrative tasks in academia |
| fealden | Tool for generating optimized nucleic acid biosensor sequences |
| SWVAnyPeakFinder | GUI application for resolving peak heights in square-wave voltammetry datafiles. |