Package: eccpy
ECCpy, a program for EC50 calculation in python.The EC50, or the “half maximal effective concentration”, is a key measure of the effectiveness of a compound to affect a biological system.
It is commonly used in pharmacology, biology and biochemistry. The EC50 is calculated by fitting the dose-response data to a sigmoidal curve,
typically using the Hill equation. Variants include the half maximal “lethal dose” (LD50), and “inhibitor concentration” (IC50).FeaturesRobust data analysisfully automatedfitting of sigmoidal curves to dose-response datacalculation of EC50, LD50 or IC50 values.high-throughput analysiscomparison of EC50 values from different experimentscalculation of EC25 or EC75 valuesaccepts REAL biological datapre-filtering excludes nonsense datajudgefit module identifies low-quality EC50 valuesDesigned for humanseasy-to-use excel files:excel settings fileexcel input file with dose and response dataexcel output file with EC50 valuessimple graphical output:
- sigmoidal curves with EC50 shown on graph
- daily summary barcharts and curvesCustomisablesimple python syntaxopen-source softwarebuilt on powerful numpy, scipy, and pandas packagesDevelopment statusECCpy has been used extensively for the analysis of LD50 assays by bachelor, master and PhD students within the lab of Dieter Langosch
at the Technical University of Munich in Germany. However this software is released “as is”, and may contain bugs
related to particular data types, python versions or operating systems.Installationpip install eccpyECCpy is written for python 3. We recommend theAnaconda python distribution,
which contains all the required python packages (numpy, scipy, pandas and matplotlib). If you encounter dependency issues, we suggest
creating a python virtual environment withcondaorvirtualenv, and installing the exact package versions
specified in therequirements.txtUsageAs described in thewiki, ECCpy requires only the following three steps:1) Prepare your data.use the excel or microplate templates in the eccpy/templates folderfor the generic excel format, simply open the template and paste in your dose and response data.2) Update an excel settings filecopy the ECCpy_settings_template.xlsx from eccpy/templatesopen the excel file, input the name and location of your datafiles, and the desired location for your output fileswrite “TRUE” next to the files you want to examine3) Run ECCpyrun the ipython/jupyter notebook, which opens a python interpreter in your web browserpaste in the following four lines. Replace the location of your settings file.hit Ctrl-Enter to runbased on your output, adjust the quality thresholds in the settings file to suit your dataExample:import eccpy
settings = r"D:\data\ECCpy_settings.xlsx"
eccpy.run_curvefit(settings)
eccpy.run_gatherer(settings)Testbefore processing your own data, run eccpy on the provided example files provided, following the instructions in theECCpy wiki.example data is available ineccpy/examples/example_dataexample settings are available ineccpy/examples/example_settingsTIP: when downloading ECCpy from github, runpytestin the ECCpy repository directory to automatically start functional testsECCpy outputrun_curvefit programindividual dose-response curvesautomatic judging of data qualitydaily summary curves, barchart and more!run_gatherer programcombines data from multiple experimentsexcludes EC50 values that are not of sufficient quality, according to user-defined thresholdsbar charts with mean and SEM over all selected experimentsscatter plots showing individual datapoints for each day/experiment, and more!compare_rawdata programcollects raw data and dose-response curves from multiple experimentscompares datapoints and fitted curves between the selected samplesContributeIf you encounter a bug or ECCpy doesn’t work for any reason, please send an email to Mark Teese (contact details below) or initiate an issue in Github.Non-programmers can contribute by:testing ECCpy with your particular datasetssuggesting featuresimproving the readme and documentationPull requests are also very welcome.LicenseECCpy is free software distributed under the permissive MIT license.ReleasesRelease-notes are found in/docs/releases.rstCitationIf you use ECCpy in your research, please use the following citation.Schanzenbach C, Schmidt FC, Breckner P, Teese MG, & Langosch D (2017) Identifying ionic interactions within a membrane using BLaTM, a genetic tool to measure homo-and heterotypic transmembrane helix-helix interactions. Scientific Reports 7(7):43476.https://www.ncbi.nlm.nih.gov/pubmed/28266525ContactECCpy is currently maintained by Mark Teese ofTNG Technology Consulting GmbH, formerly of theLangosch labof the Technical University of Munich.For contact details, see the image below.