1. Software Designing Interface – user friendly (think about MSoffice) –using menu, form, toolbars … –as simple as possible –using default setting, but allow advanced user to change the settings. –language: Visual Basic, VC++, Web-Based (Microsoft.net, JavaScript), Visual Basic for Application…

2. Software Designing Program Design –Understand your problem and get all the formulas –Try to make it extendable –Try to make it more functional –Split the job into small, independent pieces, each can be tested separately –Write each functions –Testing, Revised it, Testing …

3. Interval Mapping and Composite Interval Mapping Program Language: VBA built in PowerPoint Program Design –Interface –Simulation data –Analysis (IM, CIM) –Permutation Test –Using graphics to display profiles –Save results

4. IM and CIM – Interface Design Design user forms Drag and Drop controls into the form Write code corresponding the controls

5. IM and CIM – Simulate Data Simulate Markers –Joint probability give one marker –Random number of polynomial distribution Simulate Trait –Joint probability of a QTL allele given two markers –Normal random number

6. Joint Probability Public Sub SetJointProb1(GeneticDesign As Integer) ' Set Jopint Probablity for One Point Analysis If GeneticDesign = 2 Then 'backcross jprob1(1) = 1 / 2 ‘Qq jprob1(2) = 1 / 2 ‘qq cumprob1(1) = 1 / 2 ‘cumulate probability cumprob1(2) = 1 End If If GeneticDesign = 3 Then 'F2 jprob1(1) = 1 / 4 ‘QQ jprob1(2) = 1 / 2 ‘Qq jprob1(3) = 1 / 4 ‘qq cumprob1(1) = 1 / 4 ‘cumulate probability cumprob1(2) = 3 / 4 cumprob1(3) = 1 End If End Sub

7. Joint Probability Public Sub SetJointProb2(r, GeneticDesign) ' Set Jopint Probablity for Two Point Analysis ' r is recomenant fraction between the two marker If GeneticDesign = 2 Then 'backcross jprob2(1, 1) = (1 - r) / 2 ' Prob(Qq | Mm ) jprob2(1, 2) = r / 2 ' Prob(qq | Mm ) jprob2(2, 1) = r / 2 ' Prob(Qq | mm ) jprob2(2, 2) = (1 - r) / 2 ' Prob(qq | mm ) cprob2(1, 1) = (1 - r) ‘cumulative probability cprob2(1, 2) = r cprob2(2, 1) = r cprob2(2, 2) = (1 - r) End If

8. Joint Probability Public Sub SetJointProb3(a, b, GeneticDesign As Integer) ' Set Jopint Probablity for Three Point Analysis ' a is recomenant fraction between marker1 and qtl ' b is recomenant fraction between qtl and marker2 If GeneticDesign = 2 Then 'backcross jprob3(1, 1) = (1 - a) * (1 - b) / 2 ' Prob(Qq | Mm, Nn ) 2*0+0+1=1 jprob3(1, 2) = a * b / 2 ' Prob(qq | Mm, Nn ) mrk=(0,0) jprob3(2, 1) = (1 - a) * b / 2 ' Prob(Qq | Mm, nn ) 2*0+1+1=2 jprob3(2, 2) = a * (1 - b) / 2 ' Prob(qq | Mm, nn ) mrk=(0,1) jprob3(3, 1) = a * (1 - b) / 2 ' Prob(Qq | mm, Nn ) 2*1+0+1=3 jprob3(3, 2) = (1 - a) * b / 2 ' Prob(qq | mm, Nn ) mrk=(1,0) jprob3(4, 1) = a * b / 2 ' Prob(Qq | mm, nn ) 2*1+1+1=4 jprob3(4, 2) = (1 - a) * (1 - b) / 2 ' Prob(qq | mm, nn ) mrk=(1,1)

9. Simulate Markers Public Sub simulatemarkerandtrait(ByVal N, ByVal cumdist As String, ByVal smu As String, ByVal s2, ByVal qtl, ByVal GeneticDesign As Integer, ByVal MapFunction As Integer) chrom = Split(trimemptyline(cumdist), VBA.Chr(13) + VBA.Chr(10)) qtls = Split(trimemptyline(qtl), VBA.Chr(13) + VBA.Chr(10)) numofchroms = UBound(chrom) + 1 ………………. Subroutines called in this simulation program –trimemptyline –SetJointProb1, SetJointProb2, SetJointProb3 –splitmutoeffect –SGNC: random normal See the real code.

10. Analysis - CIM Subroutines used: –trimemptyline –SetJointProb1, SetJointProb2, SetJointProb3 –formXmatrix: form control matrix X based on ControlMethod –matrixprod: A’*B –truematrixprod: A*B –SAMIDS: inverse of A and determinant of A See the real code.

11. L(y,M|  ) =  i=1 n  k=1 g [  k|i f k (y i )] log L(y,M|  ) =  i=1 n log[  k=1 g  k|i f k (y i )] g=2 for BC, 3 for F2 f k (y i ) = 1/[(2  ) ½  ]exp[- ½ (y-  k ) 2 ],  k =  g k +X i B k=1, …,g  k|i =  k|i f 1 (y i )/[  k=1 g  k|i f 1 (y i )] (1) B =  k=1 g  k (X´X) -1 X´(Y-  g k ) (2)  g k =  i=1 n  k|i (y i -X i B)/  i=1 n  k|i (3)  2 = 1/n  i=1 n  k=1 g  k|i (y i -X i B -  g k ) 2 (4) Y = {y i } nx1,  k = {  k|i } nx1

12. Save to Word File Private Sub CommandButton3_Click() Dim tmp As Long Dim wap As Word.Application Set wap = New Word.Application wap.Visible = False wap.Documents.Open VBA.CurDir$ + "\CIMRes.doc" tmp = wap.Documents("CIMRes.doc").Range().End wap.Documents("CIMRes.doc").Range(tmp - 1, tmp - 1).InsertBreak (wdPageBreak) tmp = wap.Documents("CIMRes.doc").Range().End wap.Documents("CIMRes.doc").Range(tmp - 1, tmp - 1) = gettruepars Slide24.Shapes("Object 6").OLEFormat.Object.Application.Chart.ChartArea.Copy tmp = wap.Documents("CIMRes.doc").Range().End wap.Documents("CIMRes.doc").Range(tmp - 1, tmp - 1).Paste wap.Documents("CIMRes.doc").Save wap.Documents("CIMRes.doc").Close Set wap = Nothing End Sub