An automation for making tiles and applying standard error correction techniques for DNA self-assembly
XTile produces input files for The Xgrow Simulator to simulate growth of DNA Tiles
How it Works Page for XTile version 1.0
Before you begin: some essential points:-
1. The inputs/outputs on each face are to be given from left to right order.
2. Currently only four gate operations are allowed.
AND gate, is represented by "." (dot) between the operands (e.g. "a.b" represents a AND b).
OR gate is represented by "+" (plus) between the operands (e.g.. "a+b" represents a OR b).
NOT gate is represented by "~" (tilde) before the operand (e.g. "~a" represents NOT a).
XOR gate is represented by "^" (circumflex accent) between the operands (e.g. "a^b" represents a XOR b).
3. More than one inputs to a face can be given, by separating then with "," i.e. commas.
(e.g. "a.b,a+b,~a" represents a AND b, a OR b, NOT a as inputs/outputs on a face).
4. If more than two operands are used in a single input/output, then brackets must be used to cluster two operands and an operator. (e.g. "a.(b+c)" represents a AND (b OR c) ).
5. Do take care in using NOT gate, as it is a gate too, and can't be placed next to another gate operator without using brackets.
So if you wish to write a AND (NOT b) then give the input as "a.(~b)".
6. Do take care in entering glues for the frame tiles.
There you either choose the glues from the glue table given (the glue number representing the binary combination you wish to use in a particular frame tile) or even enter some of your own glues (by entering glue numbers not present in the glue table).
',' i.e. comma separates glues and ';' i.e. semicolon separates frame tiles. With NO semicolon in the ending.
So if you wish to enter these three as frame tiles, when glue no. 3 is not given in the table: then enter 3,0,0,3;1,3,0,3;3,0,3,1 as the frame glues.
7.Error handling has not been implemented till now. So if you don't follow the directions, errors and exceptions are surely expected.
What is XTile ?
XTile, as its name suggests is primarily developed to assist in creation of ".tiles" files which are executed in Xgrow simulator, to simulate solutions to many a problems. As an additional help, it also integrates within itself functionality to apply basic error correction techniques on the created ".tiles" file. All you need to supply to it is the design of the computational tile (which is the most basic requirement for giving a solution to a problem ), and then choose the glues for frame tiles as per your problem requirements.
example : To enter these three as frame tiles, when glue no. 3 is not given in the table: then enter 3,0,0,3;1,3,0,3;3,0,3,1 as the frame glues. Then click on 'Submit frame glues'
Step 2: Check all the inputs you entered for the four faces, and then click on 'Click to confirm'.
Step 5: The '.tiles' file code will be displayed in the lower window. You need to select the entire code and paste it in an editor, then save it with a name of your choice.
[basic .tiles generator]
[basic .tiles generator with proofread and snake error correction schemes application functionality]
[compact error correction schemes application standalones]
Contact us at firstname.lastname@example.org
Developed by: Anshul Chaurasia, Sudhanshu Dwivedi, Prateek Jain.
©2009.Self-Assembly Group, (a part of Laboratory of Natural Information Processing )
Step 1: Describe the design of the computation tile by entering the inputs/outputs on all four faces of the tile.
example : we wanted to enter "a+b" on north face, "a" on east face, "b" on south face and "a^b" on west face. So we enter as shown above and then click on the 'Submit inputs' button.
example : we wanted to enter "a+b" and "a^b"on north face, "a" and "b" on east face, "c" and "d" on south face and "c+d" and "c.d" on west face. So we enter as shown alongside and then click on the 'Submit inputs' button.