Kinetics

Apps

iocbio.kinetics.app.gui.handle_schema_changes(database, version)[source]

Handles changes in schema induced by updates. Returns true if successful

iocbio.kinetics.app.banova.analyze_dict(data, keys=None, sample_id=None, value=None, nullmodel=None, plot=None)[source]

Analyze by BANOVA dataset in the form of dictionary with list of vectors

iocbio.kinetics.app.banova.analyze_r(robj)[source]

Analyze BANOVA results as obtained in R

As an input, use result from anovaBF

iocbio.kinetics.app.banova.analyze_rows(rdict, keys=None, sample_id=None, value=None, nullmodel=None, plot=None)[source]

Analyze by BANOVA dataset in the form of iterative of dictionaries, like returned by DictReader, and records SQL query

iocbio.kinetics.app.banova.analyze_sql(sql, user=None, db='sysbio-db.kybi/experiments_v2', keys=None, sample_id=None, value=None, nullmodel=None, plot=None)[source]

Load data using IOCBIO Kinetics fetch

iocbio.kinetics.app.banova.star(v)[source]

Statistical evidence categories for Bayes Factor

codes

Calc

class iocbio.kinetics.calc.mm.AnalyzerMM(x, y)[source]

Michaelis-Menten kinetics fitter

class iocbio.kinetics.calc.mean_med_std.AnalyzerMeanMedStd(x, y)[source]

Analyzer finding mean, median, and std

class iocbio.kinetics.calc.linreg.AnalyzerLinRegress(x, y)[source]

Linear regression analyzer

class iocbio.kinetics.calc.generic.Stats(human, unit, value)
human

Alias for field number 0

unit

Alias for field number 1

value

Alias for field number 2

class iocbio.kinetics.calc.generic.XYData(x, y)
x

Alias for field number 0

y

Alias for field number 1

class iocbio.kinetics.calc.explin_fit.AnalyzerExpLinFit(x, y)[source]

Analyser for exponential + linear fitting

class iocbio.kinetics.calc.current.AnalyzerCurrent(x, y, baseline_subtraction=True)[source]

Current analyzer

class iocbio.kinetics.calc.composer.AnalyzerCompose[source]

Generic analyzer consisting of sub-analyzers

class iocbio.kinetics.calc.bump.AnalyzerBump(x, y)[source]

Bump analyzer

Handler

class iocbio.kinetics.handler.experiment_generic.ExperimentGeneric(db)[source]

Collection of methods used by all experiments

class iocbio.kinetics.handler.roi.ROIHandler(database, data, Analyzer)[source]

class that holds ROIs

Gui

io

class iocbio.kinetics.io.data.Data(experiment_id, comment=None, data={}, xname=None, xunit=None, xlim=None, config={}, type=None, type_generic=None, name=None, time=None, data_id=None, add_range=0.05)[source]

Class for representing recorded data

class iocbio.kinetics.io.db.DatabaseInterface(dbtype='sqlite3')[source]

Database interface and helper functions

grant(user)[source]

Grant access permissions for user

grant_groups()[source]

Set default permissions for all tables

revoke(user)[source]

Revoke access permissions for user

schema()[source]

Check the present schema version, create if missing and return the version of current schema

class iocbio.kinetics.io.modules.Modules[source]

Interface to modules

Modules

Sysbio

Confocal-catransient
Electrophysiology
Mechanics
class iocbio.kinetics.modules.sysbio.mechanics.experiment_mechanics.ExperimentMechanics(database, data)[source]

General description of experiment performed on SBMicroscope Mechanics

class iocbio.kinetics.modules.sysbio.mechanics.mech_ufreqcasl.AnalyzerMechFreqCa(database, data, database_table, signal, peak)[source]

Calcium fluorescence analyzer, included in the main analyzer

class iocbio.kinetics.modules.sysbio.mechanics.mech_ufreqcasl.AnalyzerMechFreqCaSL(database, data)[source]

Main analyzers

class iocbio.kinetics.modules.sysbio.mechanics.mech_ufreqcasl.AnalyzerMechFreqmech(database, data, database_table, signal, peak)[source]

Sarcomere length, fiber deformation analyzer, included in the main analyzer

class iocbio.kinetics.modules.sysbio.mechanics.mech_ufreqcasl_lowhigh.AnalyzerMechUFreqCaSL_High(database, data)[source]

High calcium

class iocbio.kinetics.modules.sysbio.mechanics.mech_ufreqcasl_lowhigh.AnalyzerMechUFreqCaSL_Low(database, data)[source]

Low calcium

iocbio.kinetics.modules.sysbio.mechanics.mech_ufreqcasl_lowhigh.analyzer(database, data)[source]

ModuleAPI

Misc
Respiration
class iocbio.kinetics.modules.sysbio.respiration.experiment_strathkelvin.ExperimentStrathkelvin(database, data, gen_config_table)[source]

General description of experiment performed on Strathkelvin

class iocbio.kinetics.modules.sysbio.respiration.reader.Time[source]

Base class to time quantity with units.

See also

iocbio.timeunit

class iocbio.kinetics.modules.sysbio.respiration.reader.Seconds[source]

Time in seconds.

See also

iocbio.timeunit

class iocbio.kinetics.modules.sysbio.respiration.reader.Minutes[source]

Time in minutes.

See also

iocbio.timeunit

class iocbio.kinetics.modules.sysbio.respiration.reader.Hours[source]

Time in hours.

See also

iocbio.timeunit

Spectro
class iocbio.kinetics.modules.sysbio.spectro.experiment_spectro.ExperimentSpectro(database, data)[source]

General description of experiment performed on Spectrophotomer Thermo Evolution 600

Indices and tables