1. COMP 6703 Project A GUI Interface to the Gene Microarray Data Analysis Program SigMotif. Student: Ye Luo (u3972395) Clients: Professor Susan Wilson and Dr Kristine Hardy Supervisor: Dr Peter Strazdins Time: 2006 Semester One

2. Background 1. Microarray experiments generate huge data sets Microarray is an orderly arrangement of gene samples.

3. Gene Microarray "1"" Id""Score""Ratio""Human""Mouse""Rat" "Name" "2""305677_A""0.754102827479603""1.28401227454259" "ENSESTG00000047336""NA""NA""NA" "3""813714_A""0.692246894535161""1.59285273685750" "ENSG00000003402""ENSMUSG00000026031" "ENSRNOG00000012473""CFLAR" "4""230261_A""0.665698686323784""1.61538048354537" "ENSG00000006451""ENSMUSG00000008859" "ENSRNOG00000013454""RALA" "5""488061_A""0.118463671125342""3.81975136034479" "ENSG00000010438""ENSMUSG00000036938" "ENSRNOG00000013655""PRSS3"

4. 2. No available software that combines the visualization and analysis of microarray data with that of biochemical networks (regulatory, interaction, metabolic).

5. SigMotif Description A gene microarray data analysis program is developed by an escience student Kristine Hardy last year. It is built on the best of open-source analysis software R. why use R ? R is an open source statistical computing environment controlled by an interpreted programming language. R provides good method and functions for easy manipulation of statistical tests and graphs. Some extension packages such as widgetTools provide GUI interface to R program

6. SigMotif System Component R RWidgetTools SigMotif

7. Systems Component R a programming environment for data analysis and graphics R Widget Tools an useful package for R that develops a GUI interface. SigMotif a gene microarray data analysis program

8. Input and Output data of SigMotif INPUT 1. List of motifs with description 2. Rat motif lists (Up, Down, Unchanged) 3. Human motif lists (Up, Down, Unchanged) 4. Mouse motif lists (Up, Down, Unchanged) 5. Significance/Homology lists (Up, Down, Unchanged) 6. Significance/Homology lists for comparison treatment

9. OUTPUT 1. Lists of significant motifs for different conditions 2. Graph of the significance values of given motifs for different conditions 3. Graphs of the conservation values of given motifs for different conditions 4. Lists of the motifs with the highest conservation values for a comparison treatment

10. Drawbacks in SigMotif GUI Interface SigMotif program is unstable. SigMotif program often crashes. The main reason: GUI Interface is not robust. Other problems:. GUI Interface is not flexible and aesthetic.. Layout of GUI interface objects is unreasonable.. GUI Interface does not agree with users’ common customs

14. New GUI Requirement. Keeping the current design style GUI Interface is composed of several dialogues. Reasonable arrangement of different widget objects on GUI panel. Important Improvements The redundant dialogues

15. New GUI requirement cons The redundant widget objects The fixed buttons Error checking Feedback message The length of text entry ……

16. New GUI Interface Modeling There are two different methods to be used to develop new GUI Interface 1. WXPython under Python environment 2. R Tcl/Tk under R environment

17. SigMotif with WXPython Python WXPython RPy SigMotif

18. System Component 1. Python. a dynamic object-oriented programming language. strong support for integration with other language and tools 2. WXPython. a GUI toolkit for the Python programming language 3. RPy. a Python interface to the R programming language. manage all kinds of R objects and execute arbitrary R functions

19. SigMotif with R Tcl/Tk R R Tcl/Tk SigMotif

20. System Component 1.R. a statistical computing environment. provide good method and functions for easy manipulation of statistical tests and graphs 2. R Tcl/Tk. a extension package connecting R to graphical toolboxes that can be used for developing menus and dialog boxes

21. The flowchart of the New GUI interface Step0 Make or Load experiment Step1 Load gene or motif lists Step4 the Menu Step3 Save Exp Data Step5 Get Exp Step6 List significant motifs Step2 Make homolog tables Step10 Make Network Step7 Graph significant motifs Step8 List conserved motifs Step9 Graph conserved motifs

22. Program Implementation wxPython under Python environment Software Packages Installation. Python. wxPython. R. RPy. Extensions including NumPy and Mark Hommand’s Important the software version number matching

23. Program Implementation R Tcl/Tk under R environment Software packages installation. R. R Tcl/Tk The R Tcl/Tk can be built under the R library directory

24. Basic steps of building a GUI dialogue 1. Load the R Tcl/Tk package under R environment 2. Define an R environment object for saving all intermediate data files and final output data files 3. Create a new top-level window 4. Define widget objects 5. Use command tkgrid to specify the layout 6. Bind events to functions and generate events

25. Implementation Problems New program version with wxPython 1. The appearance is beautiful 2. calling complicated R functions from python is difficult. 3. the program is unstable different input data files stop and even crash! 4. RPy object conversion

26. Testing Expected Output Data. Using the standard input data files provided by former designer and client Dr. K Hardy. There are totally 13 different.txt files. The expected Output Data list of significant motifs list of conserved motifs graph of significant motifs graph of conserved motifs

29. Robustness Performance 1. only one single input data lists loading dialogue 2. freely transform among different GUI dialogues 3. delete the redundant widget objects 4. improved layout of widget objects on top-level window 5. feedback message 6. environment variable

34. Conclusion and Future Work 1. wxPython is a good toolkit for developing GUI interface 2. How to resolve the interaction between R and Python? RPy??? 3. R Tcl/Tk is good. But a huge multi-line R program the layout method 4. Requirement analysis Step10 GUI is too complicated too many widget objects text label of the widget objects