Campbell Muscle Lab GitHub

Open-source systems developed by the Campbell Muscle Lab at the University of Kentucky.

Code

Muscle modeling

• MATMyoSim
  • Huxley-type modeling of half-sarcomeres
• FiberSim
  • spatially-explicit modeling of half-sarcomeres

Cardiovascular modeling

• PyMyoVent
  • a ventricle driven by a single MyoSim half-sarcomere that pumps blood around a circulation
• FiberVent
  • a ventricle driven by a single FiberSim half-sarcomere that pumps blood around a circulation and grows based on hemodynamics and ATP-usage

Muscle mechanics - data acquisition and analysis

• SLControl
  • the code underlying the data acquisition system we’ve been using since 2000!
• SLControl utilities
• SLControl analysis
  • code written in MATLAB to automate analysis of large sets of SLControl files
• SLControl MAT analysis
  • new, simpler? code written in MATLAB to automate analysis of large sets of SLControl files
• SLMeasure
  • A MATLAB app to help measure sarcomere length using brightfield images or camera feeds of multicellular preparations.

Image processing

• Python_MyoVision
  • a Python-based version of MyoVision

Gel and blot analysis

• GelBandFitter
  • a computer program that uses non-linear regression techniques to fit mathematical functions to densitometry profiles of protein gels.
  • developed by Mihail Mitov, Marion Greaser (UW-Madison) and Ken Campbell
• GelBox
  • an updated workflow for analysis of gel electrophoresis and immunoblotting

General utilities - curve-fitting, plotting, etc

• MATLAB_Utilities
  • resources we use in many of our projects
• Python_Utilities
  • Not as big but better documented than the MATLAB version above

Statistics

• MATLAB_SAS
  • code for running linear mixed models in SAS from MATLAB

Tool-kits

• MATLAB_UKTCVR
  • a suite of tools for statistics, curve-fitting, and creating publication-quality figures

Teaching

• PGY630_QM
  • website for PGY630: Quantitative Methods in Biomedical Sciences

Protocols

• Protocols
  • website for Campbell Muscle Lab protocols

Howtos

Tutorials, tips and tricks, and general guidance

• GitHub
• JSON
• Linear mixed models
• Making figures
• MATLAB
• Python