St. Jude
BRAID Analysis Web Service
Data File*:
REQUIRED. A CSV (comma separated value) file containing the experimental combination data to be fit. See instructions below for a detailed description of contents.
An optional e-mail address used to notify you when your submission has finished being processed.
Compound data:
An optional CSV file containing additional information about the samples or compounds tested. See instructions below for a detailed description of contents.
Job Name:
An optional but recommended string (may contain spaces) identifying the job to be submitted. This name will be used in the naming of files output by the analysis, and can be used to locate the ID of the job if the URL to the job status page is lost.
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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.

If you provide a valid e-mail address, an e-mail will be sent to you notifying you when the processing of your submission has completed. This e-mail will contain a hyperlink to the page where you can view the results of your submission. Regardless of whether you include an e-mail address, after submittig your job you will be redirected to the URL where you can monitor the status of your submission and view results when it is finished. However, if you do not submit an email address, we will be unable to notify when the job is complete, and you will be responsible for recording the URL for viewing the status and results of your submission.

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.

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