BRAID Analysis WebApp

BRAID Analysis Web Service

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Effect Transform: Determines how effect data is represented. If "Logarithmic", data is interpreted as a base-10 logarithm of the measured effect. If "Linear" (the default), data is intepreted as a linear function of the original measured effect.
Default Initial Value: Default initial effect value used in BRAID model selection, representing expected effect when no drug is present. For example, if effect values have been normalized to range from 0% to 100%, an appropriate value would be 0. If left blank, it will be estimated from overall experimental values.
Default Maximal Value: Default maximal effect value used in BRAID model selection, representing expected maximum effect at high concentrations. For example, if effect values have been normalized to range from 0% to 100%, an appropriate value would be 100. If left blank, it will be estimated from overall experimental values.
Comparison Values: Additional values representing synergy or antagonism that will be fit for each drug combination.
URSA α parameter The best fit value of the interaction parameter α in the URSA response surface model (Greco, Park, and Rustum, 1990), estmated using unweighted non-linear optimization.
Combination Index (nonlinear fit) Estimate of the combination index, calculated using non-linear optimization to fit dose response behavior. Requires at least 5 distinct concentrations of each drug in isolation, as well as 5 distinct concentrations of one constant ratio combination.
Combination Index (median effect) Estimate of the combination index, calculated using the median effect method to fit dose response behavior. Requires at least 5 distinct concentrations of each drug in isolation, as well as 5 distinct concentrations of one constant ratio combination.
Bliss Volume Average normalized deviation between measured combined response and response predicted by Bliss independence. Requires at least 5 distinct concentrations of each drug in isolation.
Irregular Dose Spacing Reflects whether dose pairs tested in combinations lie on a regularly spaced grid. If concentrations were laid out on a traditional checkerboard or in a single constant-ratio combinaton, select "False" (representing regular concentration spacing). If "Auto" (the default), spacing class will be determined automatically for each combination tested. Note that this value does not impact analysis results, only visualization.

Instructions

The only required input for a BRAID analysis submission is the main data file containing the concentrations and measurements to be fit. This CSV (comma separated value) file must contain the following five columns, labelled in the first row: "Sample1", "Sample2", "Conc1", "Conc2", and "Act". "Sample1" should contains the name or some other string identifying the first drug tested in a given measurement; likewise, "Sample2" specifies the second drug tested. "Conc1" contains the concentration of the first drug tested, and "Conc2" contains the concentration of the second drug tested; all concentrations are assumed to be in molar. If either concentration value for a given measurement is 0, the measurement is assumed to be a single-agent dose response measurement for the other compound; if both concentrations are 0, the measurement is assumed to be a negative control measurement. "Act" contains the measured effect, or activity, for a given measurement, which the BRAID model will be fit to. The file may also contain an optional column titled "Experiment" which specifies blocks of data that should be fit and analyzed separately. A more in-depth explanation of the BRAID input file can be found here.

You may also include an optional CSV file containing additional information about the compounds or samples tested. This CSV file must contain a column titled "Sample", which contains the sample identifiers used in the main data file. If you wish to use a different set of compound synonyms in the finished BRAID analysis report you can include a column titled "Synonym" containing the synonym to be used in the report for each sample. By default, samples are identified in charts and tables using an abbreviation of the sample name or synonym consisting of the first three letters. If you would like to specify custom abbreviations for your samples, include a column titled "Abb" in this file. Finally, the BRAID analysis calculates the index of achievable efficacy (IAE) for each combination assuming a concentration limit of 1 micromolar for each sample; if you wish to specify a concentration limit for each compound, include a column titled "Limit" in this file containing each compound's concentration limit in molar.