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{"title"=>"Cheburator software for automatically calculating drug inhibitory concentrations from in vitroscreening assays", "type"=>"journal", "authors"=>[{"first_name"=>"Dmitry", "last_name"=>"Nevozhay", "scopus_author_id"=>"8561272000"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84906998215", "pui"=>"600017515", "doi"=>"10.1371/journal.pone.0106186", "sgr"=>"84906998215", "pmid"=>"25184280"}, "id"=>"746338be-81d8-36a6-925e-84341277c805", "abstract"=>"In the process of new cancer drug development, as the first step of their assessment, their activities are usually studied in vitro against a panel of cancer cell lines. The results of these in vitro drug screening assays are commonly expressed as inhibitory concentration 50% (IC50): the concentration of the tested agent that inhibits the proliferation of the cancer cell population to 50% of the theoretically possible effect (absolute IC50) or maximum effect practically achieved by the drug (relative IC50). The currently available software for calculating IC50 values requires manual data entry, is time consuming, and is prone to calculation errors. Thus, we have developed open source, free, easy-to-use software for performing standardized data evaluations and automatically calculating the IC50. This software eliminates the laborious and error-prone manual entry of data, substantially reduces the amount of time spent for data analysis. It has been extensively used in our department as the main tool for in vitro data processing during the past several years and can be useful for other research groups working in the area of anticancer drug discovery, either alone or combined with other software packages. The current version of our program, Cheburator, together with sample data, source code, and documentation, is freely available at the following URL: http://www.cheburator.nevozhay.com (it is free for academic use, but a license is required for commercial use).", "link"=>"http://www.mendeley.com/research/cheburator-software-automatically-calculating-drug-inhibitory-concentrations-vitroscreening-assays", "reader_count"=>20, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>4, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>4, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>6, "Medicine and Dentistry"=>1, "Chemistry"=>3, "Computer Science"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"India"=>1}, "group_count"=>0}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1660641"], "description"=>"<p>The line containing the data from the first row of the plate is selected in the picture. Other rows have to follow immediately after the first row. All rows before and after the plate data will be discarded. Each row is then divided into separate values using the delimiter specified in the combo box below (semicolon is the default, but other delimiters are also supported). Since each row could contain more values than the number of wells, the user also has to specify in the edit box below which value in the row will be treated as the optical density value for the first well. Data for the subsequent wells have to follow immediately after, separated by delimiters. Note that the user can use a period or comma as the decimal separator for data files. Cheburator will automatically convert all decimal separators into periods, which are the default.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160416, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g003", "stats"=>{"downloads"=>1, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_built_in_converter_for_csv_files_/1160416", "title"=>"The built-in converter for.csv files.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660650"], "description"=>"<p>This window allows the user to change or discard particular values from the analysis. Any changes will be noted in the final report.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160425, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Edit_data_window_/1160425", "title"=>"Edit data window.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660649"], "description"=>"<p>The absorbance values in wells are highlighted with the intensities proportional to the ratio between their respective values and control values.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160424, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g004", "stats"=>{"downloads"=>3, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Main_window_of_the_program_showing_the_test_parameters_and_plate_data_table_/1160424", "title"=>"Main window of the program, showing the test parameters and plate data table.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660661"], "description"=>"<p>This sheet contains the original file’s name, date and time, the name and date of the test, the calculated IC₅₀ values, its type, 95% confidence intervals, and goodness of fit (for regression analysis), the percentages of growth inhibition for every concentration and compound, the dose-response curves, the mean optical densities and their standard deviations, the test control values, and the type of the method used for calculation. A table with raw plate data is printed at the bottom part of the report.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160431, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g009", "stats"=>{"downloads"=>4, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_test_report_printed_by_Cheburator_/1160431", "title"=>"Example of test report printed by Cheburator.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660662"], "description"=>"<p>This tab allows user to customize different analysis and report parameters of the software.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160432, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g010", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Options_tab_/1160432", "title"=>"The Options tab.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660659"], "description"=>"<p>It is showing the dose-response curves, individual values of percentages of inhibition for each data point, method of calculation used, IC₅₀ values, its type, 95% confidence intervals, and goodness of fit (for regression analysis).</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160430, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g008", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Graphs_tab_after_the_analysis_/1160430", "title"=>"The Graphs tab after the analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660652"], "description"=>"<p>It is showing the dose range applied, mean and standard deviations of absorbance values for every triplicate, calculated respective percentages of inhibition of cell proliferation, estimated IC₅₀ values, its type, method of calculation, and 95% confidence intervals (for regression analysis).</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160427, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g007", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Results_tab_after_the_analysis_/1160427", "title"=>"The Results tab after the analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660651"], "description"=>"<p>Changed values appear in red, and discarded values are crossed out after data modification.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160426, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Marking_of_the_discarded_and_changed_values_/1160426", "title"=>"Marking of the discarded and changed values.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660628"], "description"=>"<p>(<b>A</b>) Two types of IC₅₀ which can be estimated by the software. Absolute IC₅₀ is defined as the concentration of tested compound which results in 50% inhibition of cell growth as defined by assay controls (pink lines). Relative IC₅₀ is defined as the concentration of tested compound which results in half of the maximum inhibition of cell growth attainable for that particular compound (orange lines). I_max is defined as upper plateau of the dose-response curve (solid orange line). (<b>B</b>) Example of a dose-response curve drawn on the basis of 4 values (black circles). The simple two-point method uses 2 data points bracketing 50% inhibition of proliferation (green lines) to estimate the IC₅₀. In the second method, a linear model is built with the intercept and the slope, which are calculated by linear regression analysis using data points which are >0% and <100% (red lines). These parameters are later used to estimate IC₅₀. In the third method, the software uses all data points to build nonlinear regression model and estimate IC₅₀ (blue lines). Absolute IC₅₀ values are shown on this plot, but software can also estimate relative IC₅₀ in linear and nonlinear regression analysis.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160407, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g002", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graphical_explanation_of_data_analysis_algorithms_used_in_Cheburator_/1160407", "title"=>"Graphical explanation of data analysis algorithms used in Cheburator.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}
• {"files"=>["https://ndownloader.figshare.com/files/1660627"], "description"=>"<p>The sample plate with 1 control row (H), 1 row for the reference drug (A), and 4 rows for 4 novel studied compounds (B, C, D, and E, respectively) tested in 4 concentrations. Please note that not all rows have to be used on the plate, and different ranges of concentrations for different compounds can be applied in the test. Concentrations are highlighted in red. Control of untreated cells (CC) and control of media (CM) are in blue and green, respectively.</p>", "links"=>[], "tags"=>["data entry", "url", "data evaluations", "software packages", "IC 50.", "IC 50 values", "Source code", "data analysis", "research groups", "drug screening assays", "Sample Data", "Vitro Screening Assays", "Data processing", "calculation errors", "cancer cell lines", "cancer drug development", "cancer cell population", "Cheburator Software", "anticancer drug discovery", "Drug Inhibitory Concentrations"], "article_id"=>1160406, "categories"=>["Biological Sciences"], "users"=>["Dmitry Nevozhay"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106186.g001", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_test_plate_designed_to_be_processed_in_Cheburator_/1160406", "title"=>"Example test plate designed to be processed in Cheburator.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-03 03:54:35"}

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Relative Metric

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F1000Prime