IT - 468 Resources
Please check this page quite frequently for updated resources.
Suggested Softwares
The Xgrow tile set simulator at http://www.dna.caltech.edu/Xgrow/
The Xtile software at http://www.guptalab.org/xtile
The ISU TAS software at http://www.cs.iastate.edu/~lnsa/software.html
The CadNano software at http://cadnano.org/
The Sarse software at http://www.cdna.dk/index.php/software.html
The Tiamat software at http://yanlab.asu.edu/Resources.html
The Strand Discplacement software of Microsoft Research at http://research.microsoft.com/en-us/projects/dna/
The Genetic Engineering of Cells Simulator software at http://research.microsoft.com/en-us/projects/gec/
The Seesaw Compiler at http://www.dna.caltech.edu/SeesawCompiler/
The Chemical Compiler at http://cctbio.ece.umn.edu/chem-compiler/chem-compiler.pl
The Bio-DSP Compiler at http://cctbio.ece.umn.edu/biocompiler/biocompiler.pl
The Nanorex at http://www.nanoengineer-1.com/content/
Suggested Books
There is no specific text book but the following books will be helpful. We will provide many additional material such as videos, handouts etc during the course.
- Cathy Lazere, Dennis Shasha, Natural Computing: DNA, Quantum Bits, and the Future of Smart Machines, W W Norton & Co Inc, 2010, ISBN 0393336832, 9780393336832
- Martyn Amos, Theoretical and Experimental DNA Computation, 2005, Springer,
ISBN 3-540-65773-8
- Gheorge Paun, Grzegorz Rozenberg and Arto Salomaa, DNA Computing-New
Computing Paradigms, 1998, Springer, ISBN 3-540-64196-3
- Sudheer Sahu and John H. Reif, DNA based self assembly and Nan robotics, 2008
- Cris Calude and Gheorghe Paun, Computing with Cells and Atoms: An
Introduction to Quantum, DNA and Membrane Computing, 2000, CRC
- Zoya Ignatova, Israel Martinez-Perez and Karl-Heinz Zimmermann, DNA
Computing Models, Springer, 2008
- Ehrenfeucht, T. Harju, I. Petre, D.M. Prescott and G. Rozenberg, Computing in
Living Cells: Gene Assembly in ciliates, 2004, Springer
- The Oxford handbook of membrane computing Paun G., Rozenberg G., Salomaa
A., Oxford University Press, Inc., New York, NY, 2010. 696 pp.
- Computing with cells: advances in membrane computing, Frisco P., Oxford
University Press, Inc., New York, NY, 2009. 336 pp.
- Biological Computation (Chapman & Hall/CRC Mathematical & Computational
Biology) by Ehud Lamm and Ron Unger, 2011
- Jian-Qin Liu and Katsunori Shimohara, Biomolecular Computation for
Biotechnology, 2007, ISBN-10: 1-59693-014-4, Artech House
- Rozenberg, Grzegorz; BÃock, Thomas; Kok, Joost N. (Eds.), Handbook of
Natural Computation, Springer, 2010
- Christopher Dwyer and Alvin Lebeck, Introduction to DNA Self-Assembled
Computer Design, December 2007, Artech House Publishers
- John A. Pelesko, Self Assembly: The Science of Things That Put Themselves
Together, May 21, 2007, CRC Press.
- Natalio Krasnogor, Steve Gustafson, David A. Pelta and Jose L. Verdegay,
SYSTEMS SELF-ASSEMBLY, Hardbound, 304 pages, publication date: MAR-
2008 ISBN-13: 978-0-444-52865-0 ISBN-10: 0-444-52865-2, ELSEVIER
- Fundamentals of Natural Computing: Basic Concepts, Algorithms, and
Applications (Chapman & Hall/CRC Computer & Information Science
Series) [Hardcover] Leandro Nunes de Castro (Author)
- Artificial Immune Systems: A New Computational Intelligence
Approach [Paperback] Leandro Nunes de Castro (Author), Jonathan
Timmis (Author)
- Computation in Cells and Tissues: Perspectives and Tools of Thought
R. Paton (Editor), Hamid Bolouri (Editor), W. Michael L. Holcombe (Editor), J.
Howard Parish(Editor), Richard Tateson (Editor)
- Self-organizing Software: From Natural to Artificial Adaptation
Giovanna di Marzo Serugendo (Editor), Marie-Pierre Gleizes (Editor), Anthony
Karageorgos (Editor)
- Computability of the DNA and Cells: Splicing and Membrane
Computing [Hardcover] Andrei Paun (Author)
- Infochemistry: Information Processing at the Nanoscale, Konrad Szacilowski (Author), June 2012, Wiley.
- A New Kind of Science, Stephen Wolfram, 2002, Wolfram Press.
- A Computable Universe: Understanding and Exploring Nature as Computation, Hector Zenil (Author), May 2012, World Scientific.
- The Nature of Computation, Cristopher Moore (Author) and Stephan Mertens (Author), October 2011, Oxford.
- Natural Computing in Computational Finance, Brabazon, Anthony; O'Neill,
Michael; Maringer, Dietmar G. (Eds.) 1st Edition., 2010, 241
Labs/Groups doing work in this area
- The Circuits and Biology Lab at UMN
- Adleman Lab for Molecular Science at USC
- Winfree Lab: DNA and Natural Algorithms Group at Caltech
- Pierce Lab at Caltech
- Bruck Lab: Paradise at Caltech
- Goel Lab at Stanford
- Gupta Lab at DA-IICT
- Whitesides Lab at Harvard
- Kari Lab at UWO, Canada
- Reif Lab at Duke
- Rozenberg's Group
- Calude's Group at New Zealand
- Adamatzky's Group at UK
- Head's Group
- Jonoska's Group
- Seeman Lab
- Hendrik Dietz Lab
- Yamuna Krishnan Lab
- Kurt Gothelf Lab
- William Shih Lab
Companies doing work in this area
- Microsoft Research
- IBM Research
Specific Research Centers doing work in this area
- Leiden Center for Natural Computing
- Wyss Institute at Harvard for Biologically Inspired Engineering
- Center for Biological Circuit Design (CBCD) at Caltech
- J. Craig Venter Institute, USA
- International Center of Unconventional Computing
Conferences in this area
- International meeting on DNA computing and Molecular Programming
- Foundations of Nanoscience: Self-Assembled Architectures and Devices
- International Conference UNCONVENTIONAL COMPUTATION (UC)
Misc. Links
- The P System Page
- BIOMOD:International Biomolecular Design Competition
- International Genetically Engineered Machine (iGEM) competition in synthetic biology
© 2010-2012 Manish K. Gupta