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Revision as of 22:45, 28 September 2011

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

    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.

    1. Cathy Lazere, Dennis Shasha, Natural Computing: DNA, Quantum Bits, and the Future of Smart Machines, W W Norton & Co Inc, 2010, ISBN 0393336832, 9780393336832
    2. Martyn Amos, Theoretical and Experimental DNA Computation, 2005, Springer, ISBN 3-540-65773-8
    3. Gheorge Paun, Grzegorz Rozenberg and Arto Salomaa, DNA Computing-New Computing Paradigms, 1998, Springer, ISBN 3-540-64196-3
    4. Sudheer Sahu and John H. Reif, DNA based self assembly and Nan robotics, 2008
    5. Cris Calude and Gheorghe Paun, Computing with Cells and Atoms: An Introduction to Quantum, DNA and Membrane Computing, 2000, CRC
    6. Zoya Ignatova, Israel Martinez-Perez and Karl-Heinz Zimmermann, DNA Computing Models, Springer, 2008
    7. Ehrenfeucht, T. Harju, I. Petre, D.M. Prescott and G. Rozenberg, Computing in Living Cells: Gene Assembly in ciliates, 2004, Springer
    8. The Oxford handbook of membrane computing Paun G., Rozenberg G., Salomaa A., Oxford University Press, Inc., New York, NY, 2010. 696 pp.
    9. Computing with cells: advances in membrane computing, Frisco P., Oxford University Press, Inc., New York, NY, 2009. 336 pp.
    10. Biological Computation (Chapman & Hall/CRC Mathematical & Computational Biology) by Ehud Lamm and Ron Unger, 2011
    11. Jian-Qin Liu and Katsunori Shimohara, Biomolecular Computation for Biotechnology, 2007, ISBN-10: 1-59693-014-4, Artech House
    12. Rozenberg, Grzegorz; BÃock, Thomas; Kok, Joost N. (Eds.), Handbook of Natural Computation, Springer, 2010
    13. Christopher Dwyer and Alvin Lebeck, Introduction to DNA Self-Assembled Computer Design, December 2007, Artech House Publishers
    14. John A. Pelesko, Self Assembly: The Science of Things That Put Themselves Together, May 21, 2007, CRC Press.
    15. 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
    16. Fundamentals of Natural Computing: Basic Concepts, Algorithms, and Applications (Chapman & Hall/CRC Computer & Information Science Series) [Hardcover] Leandro Nunes de Castro (Author)
    17. Artificial Immune Systems: A New Computational Intelligence Approach [Paperback] Leandro Nunes de Castro (Author), Jonathan Timmis (Author)
    18. 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)
    19. Self-organizing Software: From Natural to Artificial Adaptation Giovanna di Marzo Serugendo (Editor), Marie-Pierre Gleizes (Editor), Anthony Karageorgos (Editor)
    20. Computability of the DNA and Cells: Splicing and Membrane Computing [Hardcover] Andrei Paun (Author)
    21. 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

    1. <a href="http://www.cctbio.ece.umn.edu/wiki/index.php/Main_Page"> The Circuits and Biology Lab at UMN</a>
    2. <a href="http://www.usc.edu/dept/molecular-science/index.html"> Adleman Lab for Molecular Science at USC</a>
    3. <a href="http://www.dna.caltech.edu/~winfree/"> Winfree Lab: DNA and Natural Algorithms Group at Caltech</a>
    4. <a href="http://www.piercelab.caltech.edu/"> Pierce Lab at Caltech</a>
    5. <a href="http://www.paradise.caltech.edu/"> Bruck Lab: Paradise at Caltech</a>
    6. <a href="http://www.stanford.edu/~ashishg/"> Goel Lab at Stanford</a>
    7. <a href="http://www.guptalab.org"> Gupta Lab at DA-IICT</a>
    8. <a href="http://gmwgroup.harvard.edu/research_selfassembly.html"> Whitesides Lab at Harvard </a>
    9. <a href="http://www.csd.uwo.ca/~lila/biocomplab.html"> Kari Lab at UWO, Canada </a>
    10. <a href="http://www.cs.duke.edu/~reif/"> Reif Lab at Duke </a>
    11. <a href="http://www.liacs.nl/~rozenber/"> Rozenberg's Group </a>
    12. <a href="http://www.cs.auckland.ac.nz/~cristian/"> Calude's Group at New Zealand</a>
    13. <a href="http://uncomp.uwe.ac.uk/adamatzky/"> Adamatzky's Group at UK</a>
    14. <a href="http://www.math.binghamton.edu/tom/"> Head's Group </a>
    15. <a href="http://shell.cas.usf.edu/~jonoska/"> Jonoska's Group </a>
    16. <a href="http://seemanlab4.chem.nyu.edu/"> Seeman Lab </a>
    17. <a href="http://bionano.physik.tu-muenchen.de/">Hendrik Dietz Lab</a>
    18. <a href="http://www.ncbs.res.in/index.php?option=com_content&task=view&id=60&Itemid=69">Yamuna Krishnan Lab</a>
    19. <a href="http://www.cdna.dk/index.php/home.html" title="http://www.cdna.au.dk/en">Kurt Gothelf Lab</a>
    20. <a href="http://research2.dfci.harvard.edu/shih/SHIH_LAB/Home.html">William Shih Lab</a>

    Companies doing work in this area

    1. <a href="http://research.microsoft.com/en-us/groups/science/natcomp.aspx"> Microsoft Research</a>
    2. <a href="http://www-03.ibm.com/press/us/en/presskit/21463.wss"> IBM Research</a>

    Specific Research Centers doing work in this area

    1. <a href="http://www.lcnc.nl/index.html"> Leiden Center for Natural Computing</a>
    2. <a href="http://wyss.harvard.edu/">Wyss Institute at Harvard for Biologically Inspired Engineering </a>
    3. <a href="http://www.cbcd.caltech.edu/"> Center for Biological Circuit Design (CBCD) at Caltech </a>
    4. <a href="http://www.jcvi.org/"> J. Craig Venter Institute, USA </a>
    5. <a href="http://uncomp.uwe.ac.uk/">International Center of Unconventional Computing </a>

    Conferences in this area

    1. <a href="http://hagi.is.s.u-tokyo.ac.jp/dna/"> International meeting on DNA computing and Molecular Programming</a>
    2. <a href="http://www.cs.duke.edu/~reif/FNANO/">Foundations of Nanoscience: Self-Assembled Architectures and Devices </a>
    3. <a href="http://www.cs.auckland.ac.nz/CDMTCS//conferences/uc/uc.html">International Conference UNCONVENTIONAL COMPUTATION (UC) </a>

    Misc. Links

    1. <a href="http://ppage.psystems.eu/">The P System Page </a>
    2. <a href="http://biomod.net/">BIOMOD:International Biomolecular Design Competition </a>
    3. <a href="http://ung.igem.org/Main_Page">International Genetically Engineered Machine (iGEM) competition in synthetic biology </a>