*** Starter Wiki Page *** This page is under development. Comments are welcome, but please load any comments in the comments section at the bottom of the page. Please include your wiki MONIKER and date in your comment with the same courtesy that I will give you. Aside from your courtesy, your wiki MONIKER and date as a signature and minimal good faith of any internet post are the rules of this TCL-WIKI. Its very hard to reply reasonably without some background of the correspondent on his WIKI bio page. Thanks, [gold] 12Jan2019 ---- Title: Biological Mutation Rate and TCL demo example calculator, numerical analysis <> ***Preface*** [gold]12Jan2019. Here are some calculations using TCL expressions on biological mutation rate. ---- ***Introduction*** The first testcase was published by Dr Sene Carroll, HHMI. The mutation rate is 1 in 25E6. The offspring equals 5000 females times 5 offspring per year or 25000 offspring per year. The mutation should occur 25E6/25000 or every 1000 years. The geologic interval was 1.7E6 years. Mutation would occur 1.7E6/1000 or 1700 times over the geologic interval. ---- *** Calculator Usage*** As as alternate way of using the calculator *** Expressions into TCL. *** ---- ***Testcases are important in development of TCL programs. *** ---- ***Conclusions*** By inspection ---- *** Table 1: Tables*** ---- *** Table 2: Tables *** ---- ---- ***Testcases Section*** ---- **** Testcase 1 **** %|table 1 |printed in| tcl format|% &| quantity| value| comment, if any|& &| 1 :|testcase_number | |& &| 25000000.0 :|mutation rate years (1/N): | |& &| 5000.0 :|number of females: | |& &| 5.0 :|offspring per female: | |& &| 1700000.0 :|geologic interval years: | |& &| 1000.0 :|mutation years: | |& &| 1000.0 :|mutation years: | |& &| 1000.0 :|mutation years: | |& &| 1700.0 :|mutations per geologic interval: | |& ---- **** Testcase 2 **** ---- %|table 2 |printed in| tcl format|% &| quantity| value| comment, if any|& &| 2 :|testcase_number | |& &| 20000000.0 :|mutation rate years (1/N): | |& &| 7000.0 :|number of females: | |& &| 5.0 :|offspring per female: | |& &| 600000.0 :|geologic interval years: | |& &| 1000.0 :|mutation years: | |& &| 571.428 :|mutation years: | |& &| 571.428 :|mutation years: | |& &| 1050.0 :|mutations per geologic interval: | |& ---- **** Testcase 3 **** ---- %|table 3 |printed in| tcl format|% &| quantity| value| comment, if any|& &| 3 :|testcase_number | |& &| 10000000.0 :|mutation rate years (1/N): | |& &| 9000.0 :|number of females: | |& &| 5.0 :|offspring per female: | |& &| 800000.0 :|geologic interval years: | |& &| 1000.0 :|mutation years: | |& &| 222.222 :|mutation years: | |& &| 222.222 :|mutation years: | |& &| 3600.0 :|mutations per geologic interval: | |& ---- ---- ***Screenshots Section*** **** figure 1. Calculator Screenshot **** [Biological Mutation Rate and TCL calculator screenshot] **** figure 2. Console Screenshot **** [Biological Mutation Rate and TCL demo example calculator printout] ---- ***References:*** * google search engine < Rock pocket mice > * Wikipedia search engine < hardy-weinberg > * Wikipedia search engine < Sene Carroll > * startpage search engine * TCL-WIKI search engine < biology > * On S.N. Bernstein’s derivation of Mendel’s Law * and ‘rediscovery’ of the Hardy-Weinberg distribution * Alan Stark and Eugene Seneta, University of Sydney * Rock Pocket Mice, University of Utah * Hardy-Weinberg Equilibrium Model, by Dennis O'Neil * Albinism: a sample hardy-weinberg problem, * by Dennis O'Neil * Allele and phenotype frequencies * in rock pocket mouse populations,hhmi * Mendelian Proportions in a Mixed Population, Hardy, * Trinity College, 1908 * Wikipedia, Hardy-Weinberg principle * Wikipedia, Wahlund effect * Wikipedia, Multinomial distribution * Hardy-Weinberg Principle of Equilibrium * UC Davis Library, the California State University ---- ***Pseudocode & Equations Section*** ====== more than one formula for 1) calculator shell ====== ---- **Appendix Code** *** Trial Code *** ====== # TCL source code follows # pretty print from autoindent and ased editor # Biological Mutation Rate calculator V2 # written on Windows XP on TCL # working under TCL version 8.6 # gold on TCL Club, 12Dec2018 package require Tk package require math::numtheory namespace path {::tcl::mathop ::tcl::mathfunc math::numtheory } set tcl_precision 17 frame .frame -relief flat -bg aquamarine4 pack .frame -side top -fill y -anchor center set names {{} {mutation rate years (1/N) :} } lappend names {number of females:} lappend names {offspring per female: } lappend names {geologic interval years : } lappend names {mutation years:} lappend names {mutation years: } lappend names {mutation years: } lappend names {mutations per geologic interval: } foreach i {1 2 3 4 5 6 7 8} { label .frame.label$i -text [lindex $names $i] -anchor e entry .frame.entry$i -width 35 -textvariable side$i grid .frame.label$i .frame.entry$i -sticky ew -pady 2 -padx 1 } proc about {} { set msg "Calculator for Biological Mutation Rate from TCL # gold on TCL Club, 12Dec2018 " tk_messageBox -title "About" -message $msg } proc self_help {} { set msg " Biological Mutation Rate V2 from TCL , # self help listing # problem, Biological Mutation Rate V2 # Recommended procedure is push # testcase and fill frame, # change first three entries etc, push solve, # and then push report. Report allows copy and paste # from console to conventional texteditor. # For testcases, th # testcase number is internal to the calculator and # will not be printed until the report button is pushed # for the current result numbers. # >>> copyright notice <<< # This posting, screenshots, and TCL source code is # copyrighted under the TCL/TK license terms. # Editorial rights and disclaimers # retained under the TCL/TK license terms # and will be defended as necessary in court. Conventional text editor formulas or grabbed from internet screens can be pasted into green console. # gold on TCL Club, 12Dec2018 " tk_messageBox -title "Self_Help" -message $msg } proc calculate { } { global answer2 global side1 side2 side3 side4 side5 global side6 side7 side8 global testcase_number incr testcase_number set side1 [* $side1 1. ] set side2 [* $side2 1. ] set side3 [* $side3 1. ] set side4 [* $side4 1. ] set side5 [* $side5 1. ] set side6 [* $side6 1. ] set side7 [* $side7 1. ] set side8 [* $side8 1. ] set generation_interval_years $side1 set females $side2 set offspring $side3 set geologic_interval $side4 set offspring_over_interval [* $females $offspring ] set mutation_instance [ expr { (1.0 * $generation_interval_years)/( $females * $offspring ) } ] set mutation_instance2 [ expr { (1.0 * $geologic_interval)/ $mutation_instance } ] set side6 $mutation_instance set side7 $mutation_instance set side8 $mutation_instance2 } proc fillup {aa bb cc dd ee ff gg hh} { .frame.entry1 insert 0 "$aa" .frame.entry2 insert 0 "$bb" .frame.entry3 insert 0 "$cc" .frame.entry4 insert 0 "$dd" .frame.entry5 insert 0 "$ee" .frame.entry6 insert 0 "$ff" .frame.entry7 insert 0 "$gg" .frame.entry8 insert 0 "$hh" } proc clearx {} { foreach i {1 2 3 4 5 6 7 8 } { .frame.entry$i delete 0 end } } proc reportx {} { global answer2 global side1 side2 side3 side4 side5 global side6 side7 side8 global testcase_number global wavelength wavelength2 global wavelength6 wavelength10 global wavelengthsq surfacearea global megafrequency console eval {.console config -bg palegreen} console eval {.console config -font {fixed 20 bold}} console eval {wm geometry . 40x20} console eval {wm title . " Biological Mutation Rate Report V2, screen grab and paste from console 2 to texteditor"} console eval {. configure -background orange -highlightcolor brown -relief raised -border 30} console show; puts "%|table $testcase_number |printed in| tcl format|% " puts "&| quantity| value| comment, if any|& " puts "&| $testcase_number :|testcase_number | |&" puts "&| $side1 :|mutation rate years (1/N): | |&" puts "&| $side2 :|number of females: | |& " puts "&| $side3 :|offspring per female: | |& " puts "&| $side4 :|geologic interval years: | |&" puts "&| $side5 :|mutation years: | |&" puts "&| $side6 :|mutation years: | |&" puts "&| $side7 :|mutation years: | |&" puts "&| $side8 :|mutations per geologic interval: | |&" } frame .buttons -bg aquamarine4 ::ttk::button .calculator -text "Solve" -command { set side8 0 ; calculate } ::ttk::button .test2 -text "Testcase1" -command {clearx;fillup 25E6 5000. 5. 1.7E6 1000. 1000. 1000. 1700. } ::ttk::button .test3 -text "Testcase2" -command {clearx;fillup 20E6 7000. 5. 0.6E6 1000. 570. 570. 1050. } ::ttk::button .test4 -text "Testcase3" -command {clearx;fillup 10E6 9000. 5. 0.8E6 1000. 222. 222. 3600. } ::ttk::button .clearallx -text clear -command {clearx } ::ttk::button .about -text about -command {about} ::ttk::button .self_help -text self_help -command { self_help } ::ttk::button .cons -text report -command { reportx } ::ttk::button .exit -text exit -command {exit} pack .calculator -in .buttons -side top -padx 10 -pady 5 pack .clearallx .cons .self_help .about .exit .test4 .test3 .test2 -side bottom -in .buttons grid .frame .buttons -sticky ns -pady {0 10} . configure -background aquamarine4 -highlightcolor brown -relief raised -border 30 wm title . "Biological Mutation Rate Calculator V2" ====== ---- ---- ---- **Hidden Comments Section** <> Please include your wiki MONIKER and date in your comment with the same courtesy that I will give you. Thanks, [gold] 12Jan2019 ---- <> Numerical Analysis | Toys | Calculator | Mathematics| Example| Toys and Games | Games | Application | GUI ---- <> Development | Concept| Algorithm | Biology ----