Data

All data of this study can be found on the Github repository. Data consists of:

• Synthetically generated data to mimic quick-release, step-ramp, and isometric experiments on isolated animal muscle. All scripts to generate this data can be found here.
  
• In situ experimentally measured data on rat gastrocnemius medialis muscle. Details can be found on the project website of the study in which the data was collected.

Top-level hierarchy

Level 1 – Rat

• GMsX/ → Simulated data
  • ‘Experimental’ data here are simulated datasets created with a Hill-type MTC model using parameters from literature.
    
  • Each folder represents a parameter set (X = 1, 2, 3, ...).
• GMeX/ → In situ rats
  • Experimental data here come from actual in situ experiments on rat gastrocnemius medialis muscle.
    
  • Each folder corresponds to an individual rat (X = 1, 2, 3, ...).

Level 2 – Kind of Data

Within each rat folder, data are grouped by type:

• dataExp/
  Folder containing experimental data.

  • For GMsX/, this is simulated data.
    
  • For GMeX/, this is actual experimental data.

• dataMC/ (simulated data only)
  Folder containing Monte Carlo–perturbed datasets.

  • Contains 01, 02, …, 50, representing 50 independent perturbed datasets.

• parameters/
  Model parameters for the rat or parameter set.

• simsExp/
  Simulations result performed using data of dataExp as input.

• simsMC/ (simulated data only)
  Simulations results performed using data of dataMC as input.

  • Structure mirrors expMC/.

Level 3 – Experiment

Within dataExp/, dataMC/, simsExp/, and simsMC/, data are organized by experiment type:

• QR/ – Quick-release
  
• SR/ – Step-ramp
  
• ISOM/ – Isometric
  
• SSC/ – Stretch–shortening cycles (in situ only), where files with SSC_PA have a 4 mm MTC length excursions and files with SSC_PB have an 8 mm MTC length excursion

Level 4 - Dataset

Note, the pertubed data for the Monte Carlo simulations introduce and extra level.

• 01/ – Set number 01
• 02/ – Set number 02
• 03/ – Set number 03
• …
• 50/ – Set number 50

Folder Structure

data/
├─ GMs1/                      # 'rat 1' (i.e., parameter set 1)
│   ├─ dataExp/               # 'Experimental data' (here: data generated by simulations)
│   │   ├─ QR/                # Quick-release data
│   │   ├─ SR/                # Step-ramp data
│   │   └─ ISOM/              # Isometric data
│   │
│   ├─ dataMC/                 # Monte Carlo perturbed experimental datasets
│   │   ├─ QR/                # Quick-release data
│   │   │   ├─ 01/            # Dataset 01
│   │   │   ├─ 02/
│   │   │   ├─ 03/
│   │   │   ├─ ../
│   │   │   └─ 50/
│   │   ├─ SR/
│   │   │   ├─ 01/            
│   │   │   ├─ 02/
│   │   │   ├─ 03/
│   │   │   ├─ ../
│   │   │   └─ 50/
│   │   └─  SR/
│   │       ├─ 01/            
│   │       ├─ 02/
│   │       ├─ 03/
│   │       ├─ ../
│   │       └─ 50/
│   │
│   ├─ parameters/            # Folder containing pickles with parameter values
│   │   ├─ GMs1_OR.pkl        # 'Actual' parameter values
│   │   ├─ GMs1_TM.pkl        # Estimated parameters (w/ Traditional Method)
│   │   ├─ GMs1_IM.pkl        # Estimated parameters (w/ Improved Method)
│   │   ├─ GMs1_TM_QR.pkl     # Estimated parameters (Traditional Method, Quick-release data to estimate excitation dynamics)
│   │   ├─ GMs1_TM_SR.pkl     # Estimated parameters (Traditional Method, Step-ramp data to estimate excitation dynamics)
│   │   │
│   │   ├─ interdep/          # Folder containing files of the interdependency analysis
│   │   │   ├─ GMs1_a_095.pkl # Estimated parameters (a = 95% of baseline)
│   │   │   ├─ GMs1_a_105.pkl # Estimated parameters (a = 105% of baseline)
│   │   │   └─ ... etc
│   │   │
│   │   └─ mc/                # Folder containing files of the Monte Carlo simulations
│   │       ├─ GMs1_MC01.pkl  # Estimated parameters of Monte Carlo simulation no. 1
│   │       ├─ GMs1_MC02.pkl  # Estimated parameters of Monte Carlo simulation no. 2
│   │       └─ ... etc
│   │ 
│   ├─ simsExp/               # Simulations based on experimental data (i.e., lmtc(t) and stim(t) as inputs)
│   │   ├─ QR/
│   │   ├─ SR/
│   │   └─ ISOM/
│   │
│   └─ simsMC/                # Simulations based on monte carlo datasets
│       ├─ QR/
│       │   ├─ 01/
│       │   ├─ 02/
│       │   ├─ ../
│       │   └─ 50/
│       ├─ SR/
│       │   ├─ 01/
│       │   ├─ 02/
│       │   ├─ ../
│       │   └─ 50/
│       └─ ISOM/
│           ├─ 01/
│           ├─ 02/
│           ├─ ../
│           └─ 50/
│
├─ GMs2/
│   ├─ dataExp/
│   ├─ dataMC/
│   ├─ parameters/
│   ├─ simsData/
│   └─ simsExpMC/
│
├─ GMs3/
│   ├─ dataExp/
│   ├─ dataMC/
│   ├─ parameters/
│   ├─ simsData/
│   └─ simsExpMC/
│
├─ GMe1/                      # Datafolder or rat 1 of the in situ experiment                    
│   ├─ dataExp/               # Experimentally measured data
│   │   ├─ QR/                # Quick-release data
│   │   ├─ SR/                # Step-ramp data
│   │   ├─ ISOM/              # Isometric data
│   │   └─ SSC_PA/            # Stretch-shortening cycles data
│   │
│   ├─ parameters/
│   │
│   └─ simsExp/               # Simulations based on experimental data (i.e., lmtc(t) and stim(t) as inputs)
│       ├─ QR/
│       ├─ SR/
│       └─ ISOM/
|
├─ GMe2/
│   ├─ dataExp/
│   ├─ parameters/
│   └─ simsExp/
|
└─ GMe3/
    ├─ dataExp/
    ├─ parameters/
    └─ simsExp/