| description = [ |
| { |
| "description": "Analyze cell migration metrics from time-lapse microscopy images.", |
| "name": "analyze_cell_migration_metrics", |
| "optional_parameters": [ |
| { |
| "default": 1.0, |
| "description": "Conversion factor from pixels to micrometers", |
| "name": "pixel_size_um", |
| "type": "float", |
| }, |
| { |
| "default": 1.0, |
| "description": "Time interval between consecutive frames in minutes", |
| "name": "time_interval_min", |
| "type": "float", |
| }, |
| { |
| "default": 10, |
| "description": "Minimum number of frames a cell must be tracked to be included in analysis", |
| "name": "min_track_length", |
| "type": "int", |
| }, |
| { |
| "default": "./", |
| "description": "Directory to save output files", |
| "name": "output_dir", |
| "type": "str", |
| }, |
| ], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Path to the directory containing time-lapse images or path to a multi-frame TIFF file", |
| "name": "image_sequence_path", |
| "type": "str", |
| } |
| ], |
| }, |
| { |
| "description": "Simulates CRISPR-Cas9 genome editing process including guide " |
| "RNA design, delivery, and analysis.", |
| "name": "perform_crispr_cas9_genome_editing", |
| "optional_parameters": [], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "List of guide RNA sequences (20 " |
| "nucleotides each) targeting the " |
| "genomic region of interest", |
| "name": "guide_rna_sequences", |
| "type": "List[str]", |
| }, |
| { |
| "default": None, |
| "description": "Target genomic sequence to be " |
| "edited (should be longer than guide " |
| "RNA and contain the target sites)", |
| "name": "target_genomic_loci", |
| "type": "str", |
| }, |
| { |
| "default": None, |
| "description": "Type of cell or tissue being edited (affects delivery efficiency and editing outcomes)", |
| "name": "cell_tissue_type", |
| "type": "str", |
| }, |
| ], |
| }, |
| { |
| "description": "Analyze calcium imaging data to quantify neuronal activity " |
| "metrics including cell counts, event rates, decay times, and " |
| "signal-to-noise ratios.", |
| "name": "analyze_calcium_imaging_data", |
| "optional_parameters": [ |
| { |
| "default": "./", |
| "description": "Directory to save output files", |
| "name": "output_dir", |
| "type": "str", |
| } |
| ], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Path to the time-series stack of fluorescence microscopy images (TIFF format)", |
| "name": "image_stack_path", |
| "type": "str", |
| } |
| ], |
| }, |
| { |
| "description": "Analyzes in vitro drug release kinetics from biomaterial formulations.", |
| "name": "analyze_in_vitro_drug_release_kinetics", |
| "optional_parameters": [ |
| { |
| "default": "Drug", |
| "description": "Name of the drug being analyzed", |
| "name": "drug_name", |
| "type": "str", |
| }, |
| { |
| "default": None, |
| "description": "Total amount of drug initially " |
| "loaded in the formulation. If None, " |
| "the maximum concentration is used " |
| "as 100%", |
| "name": "total_drug_loaded", |
| "type": "float", |
| }, |
| { |
| "default": "./", |
| "description": "Directory to save output files", |
| "name": "output_dir", |
| "type": "str", |
| }, |
| ], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Time points at which drug concentrations were measured (in hours)", |
| "name": "time_points", |
| "type": "List[float] or numpy.ndarray", |
| }, |
| { |
| "default": None, |
| "description": "Measured drug concentration at each time point", |
| "name": "concentration_data", |
| "type": "List[float] or numpy.ndarray", |
| }, |
| ], |
| }, |
| { |
| "description": "Quantifies morphological properties of myofibers in microscopy images of tissue sections.", |
| "name": "analyze_myofiber_morphology", |
| "optional_parameters": [ |
| { |
| "default": 2, |
| "description": "Channel index containing nuclei staining (DAPI, Hoechst, etc.)", |
| "name": "nuclei_channel", |
| "type": "int", |
| }, |
| { |
| "default": 1, |
| "description": "Channel index containing myofiber staining (α-Actinin, etc.)", |
| "name": "myofiber_channel", |
| "type": "int", |
| }, |
| { |
| "default": "otsu", |
| "description": "Method for thresholding ('otsu', 'adaptive', or 'manual')", |
| "name": "threshold_method", |
| "type": "str", |
| }, |
| { |
| "default": "./", |
| "description": "Directory to save output files", |
| "name": "output_dir", |
| "type": "str", |
| }, |
| ], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Path to the microscopy image file " |
| "(typically a multichannel image " |
| "with nuclei and myofiber staining)", |
| "name": "image_path", |
| "type": "str", |
| } |
| ], |
| }, |
| { |
| "description": "Model neural activity trajectories and decode behavioral variables.", |
| "name": "decode_behavior_from_neural_trajectories", |
| "optional_parameters": [ |
| { |
| "default": 10, |
| "description": "Number of principal components to use for dimensionality reduction", |
| "name": "n_components", |
| "type": "int", |
| }, |
| { |
| "default": "./", |
| "description": "Directory to save output files", |
| "name": "output_dir", |
| "type": "str", |
| }, |
| ], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Neural spiking activity data, shape (n_timepoints, n_neurons)", |
| "name": "neural_data", |
| "type": "numpy.ndarray", |
| }, |
| { |
| "default": None, |
| "description": "Behavioral data, shape (n_timepoints, n_behavioral_variables)", |
| "name": "behavioral_data", |
| "type": "numpy.ndarray", |
| }, |
| ], |
| }, |
| { |
| "description": "Simulate a whole-cell model represented as a system of ordinary differential equations (ODEs).", |
| "name": "simulate_whole_cell_ode_model", |
| "optional_parameters": [ |
| { |
| "default": None, |
| "description": "Function defining the system of " |
| "ODEs. Should take arguments (t, y, " |
| "*args) where t is time, y is the " |
| "state vector, and args contains " |
| "additional parameters. If None, a " |
| "simple example whole-cell model " |
| "will be used.", |
| "name": "ode_function", |
| "type": "callable", |
| }, |
| { |
| "default": "(0, 100)", |
| "description": "Tuple of (start_time, end_time) for the simulation.", |
| "name": "time_span", |
| "type": "tuple", |
| }, |
| { |
| "default": 1000, |
| "description": "Number of time points to evaluate.", |
| "name": "time_points", |
| "type": "int", |
| }, |
| { |
| "default": "'LSODA'", |
| "description": "Numerical integration method to use (e.g., 'RK45', 'LSODA', 'BDF').", |
| "name": "method", |
| "type": "str", |
| }, |
| ], |
| "required_parameters": [ |
| { |
| "default": None, |
| "description": "Initial values for each state " |
| "variable in the model. If dict, " |
| "keys are variable names and values " |
| "are initial concentrations/values. " |
| "If array-like, order must match the " |
| "order expected by the ODE function.", |
| "name": "initial_conditions", |
| "type": "dict or array-like", |
| }, |
| { |
| "default": None, |
| "description": "Model parameters required by the " |
| "ODE function. Keys are parameter " |
| "names and values are parameter " |
| "values.", |
| "name": "parameters", |
| "type": "dict", |
| }, |
| ], |
| }, |
| ] |
|
|
