GSoC Gupta Lab
Xtile
Self assembly is a process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. It has been predicted that in future self assembly will become an important engineering discipline by combining the fields of bio molecular computation, nano technology and medicine. However error control is a key challenge in realizing the potential of self assembly. Recently many authors have proposed several combinatorial error correction schemes to control errors which have a close analogy with the coding theory such as Winfree's [1] [2] proofreading scheme and its generalizations by Chen and Goel and compact scheme of Reif, Sahu and Yin [3] . XTile is an error correction computational tool that can be used to create input files to the Xgrow simulator [4] of Winfree by providing the design logic of the tiles and it also allows the user to apply proofreading, snake and compact error correction schemes.
Software Homepage
(Click the logo)
Xtile generates input to the E. Winfree's Xgrow simluator at Caltech.
Prerequisites: DNA computing, DNA tile assembly, error correction.
Programming Skills: Java, Python, c++, c .
Road Map:
References:
1. Winfree, E., & Bekbolatov, R. (2003). Proofreading tile sets: Error correction for algorithmic self-assembly. In DNA computing (pp. 126-144). Springer Berlin Heidelberg.
2. Winfree, E. (2006). Self-healing tile sets. In Nanotechnology: science and computation (pp. 55-78). Springer Berlin Heidelberg.
3. Reif, J. H., Sahu, S., & Yin, P. (2006). Compact error-resilient computational DNA tilings. In Nanotechnology: science and computation (pp. 79-103). Springer Berlin Heidelberg.
4. Winfree, E., Schulman, R., & Evans, C. (2003). The xgrow simulator. URL http://www. dna. caltech. edu/Xgrow.
5. Chaurasia, A., Dwivedi, S., Jain, P., & Gupta, M. K. (2009). XTile: An Error-Correction Package for DNA Self-Assembly. arXiv preprint arXiv:0908.2744.
Key Developers
1. Anshul Chaurasia
2. Sudhanshu Dwivedi
3. Prateek Jain
Copyright © 2015- Dixita Limbachiya
2. Winfree, E. (2006). Self-healing tile sets. In Nanotechnology: science and computation (pp. 55-78). Springer Berlin Heidelberg.
3. Reif, J. H., Sahu, S., & Yin, P. (2006). Compact error-resilient computational DNA tilings. In Nanotechnology: science and computation (pp. 79-103). Springer Berlin Heidelberg.
4. Winfree, E., Schulman, R., & Evans, C. (2003). The xgrow simulator. URL http://www. dna. caltech. edu/Xgrow.
5. Chaurasia, A., Dwivedi, S., Jain, P., & Gupta, M. K. (2009). XTile: An Error-Correction Package for DNA Self-Assembly. arXiv preprint arXiv:0908.2744.
2. Sudhanshu Dwivedi
3. Prateek Jain