TkLife is a simple drawing tool. Also, TkLife is a generator of complex patterns
simulating birth, life and death of cells. Finally, TkLife can be used to
visualize any kind of numerical data generating so called heat plots. As well as
it can be used for bioinformatics purpose to visualize multiple DNA sequence
TkLife manipulates by 64 different colors on interactive canvas. TkLife canvas is represented by a grid. Each cell of this grid can be painted to a different color.
Originally, each cell on canvas has so called "empty" state and colored into black with white outline. If cell is painted, or activated, then outline has the same color scheme as cell's fill color. There are three modes to operate the program: drawing mode, "TkLife mode", and "BioMode". Drawing mode is a simple drawing tool. By mouse click user can paint cells on canvas into 64 different colors. Results of painting can be saved as a text file. Tklife mode simulates birth, growth and death of cells by rules defined in the source code of the program. These rules are described in the paragraph "TkLife Rules" of this document. TkLife mode is a kind of entertainment. Generated patterns are never the same. To activate TkLife mode click on "New" and then "Start" buttons. Do not click on "Start" button if you just busy with manual painting. Immediately results of your painting will be automatically "mutated" by unpredictable way. However, if you do it with purpose you may get some fun.
If you run TkLife in "BioMode", it is possible to analyze and visualize DNA sequences corresponding to ORFs (Open Reading Frames). 64 different colors can represent 64 different triplets. Each color corresponds to a particular genetic codon or amino acid. There are 64 different triplets formed by combination of four nucleotides A, G, C and T. Total number of amino acids corresponding to codons is 20 because genetic code is redundant. Each codon is distinguishable by a color specific to this codon.
TkLife can generate heat plots using numerical data from tab-delimited text files. Files with extension *.tklife are considered as a native TkLife format. Files with extension *.num_tab are treated as a numerical data. Different dialogs and data processing will take place depending of a particular file extension.
To run TkLife in drawing mode start the program and then click on "New" button. New blank canvas should appear. User can change size of canvas as well as size of cells from main control panel prior clicking on "New" button. It is possible to select 64 different colors from main program window and paint by left mouse click cells on canvas. To restore cell color to original "empty" state hold SHIFT key and click on left mouse button. Right mouse click will show color info about painted cell. Using middle mouse button you can drag (move) cells on canvas. It is possible to save results of painting in file with extension *.tklife as well as load saved results of previous work.
NETWORKING DRAWING MODE
Two TkLife programs running on two different computers can interact one with each other via network sockets. To activate networking mode you need to start SERVERS on both TkLife programs as well as connections via CLIENTS. Mouse click events (painting) will be synchronized on both canvases.
DECOMPOSING OF IMAGES
Accompanying Python script Image2TkLife_003.py converts JPEG images into TkLife file format. User can specify JPEG input file, TkLife output file and the number of pixels (or cells) on TkLife canvas. Output is readable by TkLife program. Read more about Image2TkLife_003.py usage and example outputs on the Decomposed_Art.html web page.
It is possible to visualize Poincare transformation/recurrence on TkLife canvas. To run one round of Poincare iteration click on the left mouse button holding Shift key (or activate Poincare iteration using the Right mouse button). Mouse pointer must be over the "" control area during activation. The algorithm of transformation is described at: http://www.sciencenews.org/ in the article "Scrambled Grids" by Ivars Peterson.
TkLife control panel to activate Poincare iteration is displayed below:
Example input files in TkLife format to visualize Poincare transformation/recurrence:
Poincare transformation/recurrence works slow if the number of nodes is greater than 1000 (for example,
if you are using a grid 30 x 35 or greater). It was designed for visualization purpose. "Save as file"
function does not save a current iteration, it saves the original state. It is possible to save each
iteration in temporary file, default name of temporary file is "temp_pc_iteration_#.tklife" where "#"
is a number of iteration.
some exercises with prime numbers and Poincare transformation - 64 x 48 grid
and 64 x 96 grid
GENERATION OF REPETITIVE PATTERNS
Open new blank canvas by click on "New" button. Point mouse over the color selection box (upper left). By "Shift + Right Mouse Click" repetitive patterns will be generated. Currently 16 different rules (patterns) are available via color select boxes:
0_0_0 0_0_5 0_0_a 0_0_f
0_5_0 0_5_5 0_5_a 0_5_f
0_a_0 0_a_5 0_a_a 0_a_f
0_f_0 0_f_5 0_f_a 0_f_f
Those patterns may be useful for further Poincare transformations.
64 different colors are formed by combination of "0", "5", "a" and "f" hexadecimal values. For example:
"#00f" is blue
"#0f0" is green
"#f00" is red
"#f0f" is purple
"#ff0" is yellow
"#0ff" is cyan
"#fff" is white
"#555" is gray
Total number of all possible combinations for four different values is 64. Values "0", "5", "a" and "f" reflect different level of saturation of particular color components (red, green or blue).
By clicking on "New" and then on "Start" buttons TkLife mode will be activated. During each iteration randomly chosen cell on canvas will be selected and processed according to following rules:
If it is a time for "Mutation" then randomly chosen color will be assigned for that cell. That cell will became painted or activated. Time for mutation is determined by "Mutation Value" (15 by default). It means mutation takes place one time per 15 iterations. Try to change mutation value from 1 to 100, for example, to check how it affects patterns formation. If there is no time for mutation then cell (if it is already painted) will be processed by another algorithm:
If four cells: above, below, on the left and on the right are already painted then their color will be changed to color of the middle cell (so called CROSS TRANSITION):
###################### # # # A X # # DXB -> XXX # # C X # # # # CROSS TRANSITION # ######################
If selected cell is a center of small square (3 x 3) and four corner cells of the square are activated then they painted into color of selected cell. Cells above, below, on the left and on the right have to be painted as selected cell for this condition (so called SQUARE TRANSITION):
###################### # # # AXB XXX # # XXX -> XXX # # DXC XXX # # # # SQUARE TRANSITION # ######################
If selected cell is a center of a large square (5 x 5) and the square has uniform color then death of inner cells may happen if the DEATH status chosen as true. If DEATH status is false then nothing should happen. Green DEATH box corresponds to FALSE state (default), RED to TRUE DEATH state. To change the state click on DEATH box. Upon death inner cells became inactivated (black color with white outline).
###################### # # # XXXXX XXXXX # # XXXXX X---X # # XXXXX -> X---X # # XXXXX X---X # # XXXXX XXXXX # # # # DEATH TRANSITION # ######################
It is possible to stop (pause) animation and save current pattern in file with extension *.tklife. Also, it is possible to restore previously saved pattern from file in TkLife format and continue animation.
If you run TkLife in "BioMode" color values are associated with DNA nucleotides. At the same time values "0", "5", "a" and "f" correspond to nucleotides "A", "G", "C" and "T" respectively. For example:
"#00f" is "AAT" - blue
"#00a" is "AAC"
"#005" is "AAG" - dark blue
"#000" is "AAA" - black
"#ff0" is "TTA" - yellow
"#fa5" is "TCG"
"#f50" is "TGA"
"#fff" is "TTT" - white
Check Amino Acids and Codon Usage web page to see color scheme for all 64 triplets.
"Empty" state or so called "gap" in a sequence alignment coded as "---". User can to run the script "DNA_to_TkLife_03.tcl" to transform DNA alignment into TkLife style input file.
User needs to run custom scripts (or scripts provided with TkLife) to transform DNA sequences into color coding tab-delimited file. Current version of TkLife provides the script to transform sequence alignment at DNA level into TkLife "color" input file. Sequence alignment should be in FASTA format. See the provided example for a subset of Elongation factor sequences. To run TkLife in BioMode you need to start the program in command line with argument "BIO". Or uncomment #set biomode "TRUE" on the end of source code.
Download example files to run TkLife in BioMode:
x-ef2-NCBI.fasta eleven Elongation Factor 2 DNA sequences downloaded from NCBI
x-ef2-dna-one-line.fasta the same sequences with modified header
x-ef2-prot.fasta Translated into protein sequences (first frame)
x-ef2-prot.pir.fasta Protein alignment in FASTA format (by ClustalW)
x-ef2-dna.fasta.alignment DNA alignment derived from protein alignment
x-ef2-dna-one-line.fasta.alignment Modified (one line per sequence) version of the x-ef2-dna.fasta.alignment file
x-ef2-dna.tklife TkLife file format corresponding to x-ef2-dna.fasta.alignment file
DNA_to_TkLife_05.tcl Tcl/Tk script to transform DNA alignment into TkLife file format
DNA_to_TkLife_07.tcl Tcl/Tk script to transform DNA alignment into TkLife file format (this version will generate "*.tab_data" file format)
Note: You need to download only x-ef2-dna.tklife file to view it with TkLife program. Other files are here to show how it was derived. Custom scripts to process DNA data by similar way are available upon request.
TKLIFE DATA MODE
Example of usage in the DATA MODE. File with climate data (average month temperature) from http://www.worldclimate.com for 10 cities temperature_wc.sorted was converted into "TkLife" format using tcl script Data_to_TkLife_03.tcl. temperature_wc.tab_data was used as input for TkLife (file extension *.tab_data is critical). The graphical output is here:
INPUT AND OUTPUT FILES
Program is very flexible to user's input. Imagination is a limitation what user can display using TkLife. It is possible to display simple drawing or visualize any kind of numeric data. TkLife input file is a tab delimited file with color values for each cell of the grid. So, user's data should be transformed into *.tklife format to be digested by this program. Files with extension *.num_tab are treated as a numerical data and conversion into native TkLife format is not required.
Output files can be in five different formats. Each file format user can specify by file extension. For example, file extension *.tklife will generate "TkLife" tab delimited file with "RGB" values for each cell. File extension *.xpm will produce XPM file which can be re-opened by drawing program (GIMP, for example). File extension *.ps will generate file in PostScript format. File extension *.html will generate web page with the table which looks like an image. However it is not a real image, it is an html table where each cell represented as a tile. Combination of these tiles creates illusion of real image. You can check examples of HTML tables generated by TkLife here (will be opened in a new window). File extension *.fasta will generate file which looks like FASTA file with DNA sequences. However, only *.tklife file format (and *.tab_data or *.num_tab in the DATA mode) can be used as input files.
TkLife is written in Tcl/Tk. In order to run it you need to install Tcl/Tk interpreter. Tcl/Tk toolkit is freely available at tcl.activestate.com
TkLife_012_V248Final.tcl TkLife current version 248 (source code)
TkLife_012_V248Final.exe Windows users can download executables. In this case you do not need to install Tcl/Tk interpreter.
tk_life_color_matrix.tklife Example input file generated by "TkLife" mode
tk_life_paint_matrix.tklife Example input file generated by "Paint" mode
palette.tar.gz Set of 64 tiles - regular PNG images (you need it if you save TkLife images as HTML table)
palette_magic.tar.gz Set of 64 tiles - animated GIF images (you need it if you save TkLife images as HTML table)
amino_acids.tar.gz In order to run TkLife in "BioMode" you need to download amino acids images and place them into directory where you run TkLife program
email to: firstname.lastname@example.org Alexander Kozik
last modified January 24 2006