The simplest data input

Want a really simple method to input EC50 data, without programming or hassle?

The "eccpy|xlsx|generic|vertical" is our name for the simplest input format. You open an excel template, paste in your data values, and then automatically calculate, combine and compare EC50 values with eccpy.

Method

• read/follow the "eccpy installation" and "getting-started" pages in this wiki
• Get the excel input data template
  • find the eccpy folder (where you installed or unpacked eccpy)
  • copy and rename eccpy\templates\eccpy-xlsx-generic-vertical_template.xlsx
• replace the data with your own in the first two tabs
  
  
  • the dose data is the concentration of whatever you are varying (e.g. Ampicillin in an LD50 assay)
  • the response data are the values that you have measured (e.g. cell concentration in an LD50 assay)
• write your sample names at the top
  • these sample names are used to name output files. Don't write anything here you wouldn't put in a filename.
  • avoid symbols (&%$§), non-ASCII characters (äöüæß), and also the period (.).
  • eccpy can normalise data from samples against a control (which can have any name), as defined in the "samplenames" tab of the settings file. However if you don't have a control, it's not necessary.
  • if you have replicates that you want combined, give them EXACTLY the same name in each input file, and in the input files for different days or replicates.
    • "sample_1", "sample_1"
  • if you have replicates that you want to examine separately, give them unique names
    • "sample_1_replicate_1", "sample_1_replicate_2"
  • sample names should be EXACTLY THE SAME on the dose and response tabs
  • there's no limit on the number of samples. However the figures produced by eccpy are optimised for ~3-30 samples. Eccpy is usually used to test smaller numbers of samples, and compare their results over a number of days or replicates.
• paste your data vertically underneath the sample name
  • data in the dose and response tabs should match (e.g. position "A2" on the dose tab will be matched to "A2" on the response tab)
  • there's no limit on the number of datapoints. As long as the dose and response tabs for that sample have exactly the same number of datapoints. Gaps within the pasted data are not recommended. A different number of datapoints for different samples should be tolerated.
• don't alter the third "template identifier" tab. This should have a single value, "eccpy|xlsx|generic|vertical", which informs eccpy regarding the data format.
• save and close the input data file
• open your excel eccpy settings file (see Create a settings file in the Wiki if you haven't done this already)
• paste in the folder location and filename for your data input file
• since you don't have separate files for dose and response data, paste the filename in the "response data file" column, and write None in the "dose data file" column as shown in the example below.

• open up the python jupyter/ipython console in your web-browser
• run the curve-fitting program on your data

import eccpy
settings = r"D:\data\ECCpy_settings.xlsx"
eccpy.run_curvefit(settings)

• TIP: start with only YOUR BEST DATA, which gives you perfect sigmoidal curves
• follow the tips in Adjust user settings until eccpy filtering and curve-fitting works correctly. If you have trouble understanding the user settings, play around with them using the generated data as shown in the ECCpy usage snapshot, before applying them to your own data.
• when the analysis is working for a single input file, test the gathering and combination of multiple experiments (different days or replicates) in eccpy with the "run_gatherer" command

import eccpy
settings = r"D:\data\ECCpy_settings.xlsx"
eccpy.run_gatherer(settings)

• if you have any trouble: don't hesitate to contact us, send us your example data to test, or add an issue on GitHub.