@PREAMBLE{ "\newcommand{\noopsort}[1]{}" }

@STRING{CUP = {Cambridge University Press}}

@STRING{OUP = {Oxford University Press}}

@STRING{PUP = {Princeton University Press}}

@STRING{SV = {Springer-Verlag}}

@STRING{AP = {Academic Press}}

@STRING{AMS = {American Mathematical Society}}

%S! fix this citation!

@article{morrison-walker,

    AUTHOR = {David Clark and Scott Morrison and Kevin Walker},

    TITLE = {Fixing the functoriality of Khovanov homology},

     note = {\arxiv{math.GT/0701339}},

}

@misc{kw:tqft,

    AUTHOR = {Walker, Kevin},

    TITLE  = {Topological Quantum Field Theories},

    note    = {draft available at \url{http://canyon23.net/math/tc.pdf}},

}

@article {MR1854636,

    AUTHOR = {Keller, Bernhard},

     TITLE = {Introduction to {$A$}-infinity algebras and modules},

   JOURNAL = {Homology Homotopy Appl.},

  FJOURNAL = {Homology, Homotopy and Applications},

    VOLUME = {3},

      YEAR = {2001},

    NUMBER = {1},

     PAGES = {1--35 (electronic)},

      ISSN = {1512-0139},

   MRCLASS = {18E30 (18D50 18G40 55P43 55U35)},

  MRNUMBER = {MR1854636 (2004a:18008a)},

MRREVIEWER = {Ulrike Tillmann},

      note = {\mathscinet{MR1854636} \arxiv{math.RA/9910179}},

}

@incollection {MR2061854,

    AUTHOR = {McClure, James E. and Smith, Jeffrey H.},

     TITLE = {Operads and cosimplicial objects: an introduction},

 BOOKTITLE = {Axiomatic, enriched and motivic homotopy theory},

    SERIES = {NATO Sci. Ser. II Math. Phys. Chem.},

    VOLUME = {131},

     PAGES = {133--171},

 PUBLISHER = {Kluwer Acad. Publ.},

   ADDRESS = {Dordrecht},

      YEAR = {2004},

   MRCLASS = {55P48 (18D50)},

  MRNUMBER = {MR2061854 (2005b:55018)},

MRREVIEWER = {David Chataur},

      note = {\mathscinet{MR2061854} \arxiv{math.QA/0402117}},

}

@book {MR0420610,

    AUTHOR = {May, J. P.},

     TITLE = {The geometry of iterated loop spaces},

 PUBLISHER = {Springer-Verlag},

   ADDRESS = {Berlin},

      YEAR = {1972},

     PAGES = {viii+175},

   MRCLASS = {55D35},

  MRNUMBER = {MR0420610 (54 \#8623b)},

MRREVIEWER = {J. Stasheff},

      note = {Lectures Notes in Mathematics, Vol. 271 \mathscinet{MR0420610} \href{http://www.math.uchicago.edu/~may/BOOKS/gils.pdf}{available online}},

}

@article {MR0236922,

    AUTHOR = {Boardman, J. M. and Vogt, R. M.},

     TITLE = {Homotopy-everything {$H$}-spaces},

   JOURNAL = {Bull. Amer. Math. Soc.},

  FJOURNAL = {Bulletin of the American Mathematical Society},

    VOLUME = {74},

      YEAR = {1968},

     PAGES = {1117--1122},

      ISSN = {0002-9904},

   MRCLASS = {55.42},

  MRNUMBER = {MR0236922 (38 \#5215)},

MRREVIEWER = {R. J. Milgram},

      note = {\mathscinet{MR0236922} \doi{10.1090/S0002-9904-1968-12070-1}},

}

@book {MR0420609,

    AUTHOR = {Boardman, J. M. and Vogt, R. M.},

     TITLE = {Homotopy invariant algebraic structures on topological spaces},

    SERIES = {Lecture Notes in Mathematics, Vol. 347},

 PUBLISHER = {Springer-Verlag},

   ADDRESS = {Berlin},

      YEAR = {1973},

     PAGES = {x+257},

   MRCLASS = {55D35},

  MRNUMBER = {MR0420609 (54 \#8623a)},

MRREVIEWER = {J. Stasheff},

      note = {\mathscinet{MR0420609}},

}

%The framed little discs operad:

@article {MR1256989,

    AUTHOR = {Getzler, E.},

     TITLE = {Batalin-{V}ilkovisky algebras and two-dimensional topological

              field theories},

   JOURNAL = {Comm. Math. Phys.},

  FJOURNAL = {Communications in Mathematical Physics},

    VOLUME = {159},

      YEAR = {1994},

    NUMBER = {2},

     PAGES = {265--285},

      ISSN = {0010-3616},

     CODEN = {CMPHAY},

   MRCLASS = {81T70 (17B81 55Q99 58Z05 81T40)},

  MRNUMBER = {MR1256989 (95h:81099)},

MRREVIEWER = {J. Stasheff},

      note = {\mathscinet{MR1256989} \euclid{1104254599}},

}

@article {MR1917056,

    AUTHOR = {Bar-Natan, Dror},

     TITLE = {On {K}hovanov's categorification of the {J}ones polynomial},

   JOURNAL = {Algebr. Geom. Topol.},

  FJOURNAL = {Algebraic \& Geometric Topology},

    VOLUME = {2},

      YEAR = {2002},

     PAGES = {337--370 (electronic)},

      ISSN = {1472-2747},

   MRCLASS = {57M27},

  MRNUMBER = {MR1917056 (2003h:57014)},

MRREVIEWER = {Jacob Andrew Rasmussen},

      note = {arXiv:\arxiv{math.QA/0201043}},

}

@incollection {MR2147420,

    AUTHOR = {Bar-Natan, Dror},

     TITLE = {Khovanov homology for knots and links with up to 11 crossings},

 BOOKTITLE = {Advances in topological quantum field theory},

    SERIES = {NATO Sci. Ser. II Math. Phys. Chem.},

    VOLUME = {179},

     PAGES = {167--241},

 PUBLISHER = {Kluwer Acad. Publ.},

   ADDRESS = {Dordrecht},

      YEAR = {2004},

   MRCLASS = {57M27},

  MRNUMBER = {MR2147420 (2006c:57009)},

MRREVIEWER = {Marta M. Asaeda},

}

@article {MR2174270,

    AUTHOR = {Bar-Natan, Dror},

     TITLE = {Khovanov's homology for tangles and cobordisms},

   JOURNAL = {Geom. Topol.},

  FJOURNAL = {Geometry and Topology},

    VOLUME = {9},

      YEAR = {2005},

     PAGES = {1443--1499 (electronic)},

      ISSN = {1465-3060},

   MRCLASS = {57M27 (57M25)},

  MRNUMBER = {MR2174270},

      note = {arXiv:\arxiv{math.GT/0410495}},

}

@article {MR1680395,

    AUTHOR = {Khovanov, Mikhail and Kuperberg, Greg},

     TITLE = {Web bases for {${\rm sl}(3)$} are not dual canonical},

   JOURNAL = {Pacific J. Math.},

  FJOURNAL = {Pacific Journal of Mathematics},

    VOLUME = {188},

      YEAR = {1999},

    NUMBER = {1},

     PAGES = {129--153},

      ISSN = {0030-8730},

     CODEN = {PJMAAI},

   MRCLASS = {17B37 (22E60 57M27 81R05)},

  MRNUMBER = {MR1680395 (2000j:17023a)},

MRREVIEWER = {Robert J. Marsh},

      note = {arXiv:\arxiv{q-alg/9712046}},

}

@article {MR1740682,

    AUTHOR = {Khovanov, Mikhail},

     TITLE = {A categorification of the {J}ones polynomial},

   JOURNAL = {Duke Math. J.},

  FJOURNAL = {Duke Mathematical Journal},

    VOLUME = {101},

      YEAR = {2000},

    NUMBER = {3},

     PAGES = {359--426},

      ISSN = {0012-7094},

     CODEN = {DUMJAO},

   MRCLASS = {57M27 (57R56)},

  MRNUMBER = {MR1740682 (2002j:57025)},

}

@article {MR1928174,

    AUTHOR = {Khovanov, Mikhail},

     TITLE = {A functor-valued invariant of tangles},

   JOURNAL = {Algebr. Geom. Topol.},

  FJOURNAL = {Algebraic \& Geometric Topology},

    VOLUME = {2},

      YEAR = {2002},

     PAGES = {665--741 (electronic)},

      ISSN = {1472-2747},

   MRCLASS = {57M27 (57R56)},

  MRNUMBER = {MR1928174 (2004d:57016)},

MRREVIEWER = {Jacob Andrew Rasmussen},

    note   = {arXiv:\arxiv{math.GT/0103190}},

}

@article {MR2034399,

    AUTHOR = {Khovanov, Mikhail},

     TITLE = {Patterns in knot cohomology. {I}},

   JOURNAL = {Experiment. Math.},

  FJOURNAL = {Experimental Mathematics},

    VOLUME = {12},

      YEAR = {2003},

    NUMBER = {3},

     PAGES = {365--374},

      ISSN = {1058-6458},

   MRCLASS = {57M27 (18G60 57M25 57R56)},

  MRNUMBER = {MR2034399 (2004m:57022)},

MRREVIEWER = {Jacob Andrew Rasmussen},

}

@article {MR2100691,

    AUTHOR = {Khovanov, Mikhail},

     TITLE = {sl(3) link homology},

   JOURNAL = {Algebr. Geom. Topol.},

  FJOURNAL = {Algebraic \& Geometric Topology},

    VOLUME = {4},

      YEAR = {2004},

     PAGES = {1045--1081 (electronic)},

      ISSN = {1472-2747},

   MRCLASS = {57M27 (18G60 57R56)},

  MRNUMBER = {MR2100691 (2005g:57032)},

MRREVIEWER = {Justin Sawon},

      note = {arXiv:\arxiv{math.QA/0304375}},

}

@article {MR2124557,

    AUTHOR = {Khovanov, Mikhail},

     TITLE = {Categorifications of the colored {J}ones polynomial},

   JOURNAL = {J. Knot Theory Ramifications},

  FJOURNAL = {Journal of Knot Theory and its Ramifications},

    VOLUME = {14},

      YEAR = {2005},

    NUMBER = {1},

     PAGES = {111--130},

      ISSN = {0218-2165},

   MRCLASS = {57M27},

  MRNUMBER = {MR2124557 (2006a:57016)},

MRREVIEWER = {Marta M. Asaeda},

}

@article {MR2171235,

    AUTHOR = {Khovanov, Mikhail},

     TITLE = {An invariant of tangle cobordisms},

   JOURNAL = {Trans. Amer. Math. Soc.},

  FJOURNAL = {Transactions of the American Mathematical Society},

    VOLUME = {358},

      YEAR = {2006},

    NUMBER = {1},

     PAGES = {315--327 (electronic)},

      ISSN = {0002-9947},

     CODEN = {TAMTAM},

   MRCLASS = {57Q45},

  MRNUMBER = {MR2171235},

      note = {arXiv:\arxiv{math.GT/0207264}},

}

@misc{math.QA/0401268,

    title = {{Matrix factorizations and link homology}},

    author = {Mikhail Khovanov and Lev Rozansky},

      note = {arXiv:\arxiv{math.QA/0401268}}}

@misc{math.QA/0505056,

    title = {{Matrix factorizations and link homology II}},

    author = {Mikhail Khovanov and Lev Rozansky},

      note = {arXiv:\arxiv{math.QA/0505056}}}

@incollection {MR2048108,

    AUTHOR = {Thurston, Dylan P.},

     TITLE = {The algebra of knotted trivalent graphs and {T}uraev's shadow

              world},

 BOOKTITLE = {Invariants of knots and 3-manifolds (Kyoto, 2001)},

    SERIES = {Geom. Topol. Monogr.},

    VOLUME = {4},

     PAGES = {337--362 (electronic)},

 PUBLISHER = {Geom. Topol. Publ., Coventry},

      YEAR = {2002},

   MRCLASS = {57M25 (57M15 57M20 57Q40)},

  MRNUMBER = {MR2048108 (2005c:57010)},

MRREVIEWER = {Marko Kranjc},

      note = {arXiv:\arxiv{math.GT/0311458}},

}

@article {MR1403861,

    AUTHOR = {Kuperberg, Greg},

     TITLE = {Spiders for rank {$2$} {L}ie algebras},

   JOURNAL = {Comm. Math. Phys.},

  FJOURNAL = {Communications in Mathematical Physics},

    VOLUME = {180},

      YEAR = {1996},

    NUMBER = {1},

     PAGES = {109--151},

      ISSN = {0010-3616},

     CODEN = {CMPHAY},

   MRCLASS = {17B10 (22E60 81R05)},

  MRNUMBER = {MR1403861 (97f:17005)},

MRREVIEWER = {Stefano Capparelli},

      note = {arXiv:\arxiv{q-alg/9712003}},

}

@misc{math.GT/0606318,

    title  = {{Fast Khovanov Homology Computations}},

    author = {Dror Bar-Natan},

    note   = {arXiv:\arxiv{math.GT/0606318}},

    url    = {http://www.math.toronto.edu/~drorbn/papers/FastKh/}

    }

@misc{math.GT/0603347,

    title = {{On the Algebraic Structure of Bar-Natan's Universal

        Geometric Complex and the Geometric Structure of Khovanov

        Link Homology Theories}},

    author = {Gad Naot},

    note   = {arXiv:\arxiv{math.GT/0603347}}}

@misc{math.QA/9909027,

    title = {{Planar algebras, I}},

    author = {Vaughan F. R. Jones},

    note   = {arXiv:\arxiv{math.QA/9909027}}}

@article {MR1217386,

    AUTHOR = {Turaev, V. and Wenzl, H.},

     TITLE = {Quantum invariants of {$3$}-manifolds associated with

              classical simple {L}ie algebras},

   JOURNAL = {Internat. J. Math.},

  FJOURNAL = {International Journal of Mathematics},

    VOLUME = {4},

      YEAR = {1993},

    NUMBER = {2},

     PAGES = {323--358},

      ISSN = {0129-167X},

   MRCLASS = {57M25 (17B37 57N10)},

  MRNUMBER = {MR1217386 (94i:57019)},

MRREVIEWER = {Toshitake Kohno},

}

@article {MR1470857,

    AUTHOR = {Wenzl, Hans},

     TITLE = {{$C\sp *$} tensor categories from quantum groups},

   JOURNAL = {J. Amer. Math. Soc.},

  FJOURNAL = {Journal of the American Mathematical Society},

    VOLUME = {11},

      YEAR = {1998},

    NUMBER = {2},

     PAGES = {261--282},

      ISSN = {0894-0347},

   MRCLASS = {46L89 (17B37 46L05)},

  MRNUMBER = {MR1470857 (98k:46123)},

MRREVIEWER = {Andrzej Sitarz},

    eprint = {\url{http://ftp.ams.org/jams/1998-11-02/S0894-0347-98-00253-7/S0894-0347-98-00253-7.pdf}},

}

@misc{math.GT/0603307,

    title  = {{The universal sl3-link homology}},

    author = {Marco Mackaay and Pedro Vaz},

    note  = {arXiv:\arxiv{math.GT/0603307}}}

 @misc{wiki:Grothendieck-group,

   author = "Wikipedia",

   title = "Grothendieck group --- Wikipedia{,} The Free Encyclopedia",

   year = "2006",

   note = "[\href{http://en.wikipedia.org/w/index.php?title=Grothendieck_group&oldid=52451663}{Online}; accessed 30-June-2006]"

 }

 @misc{wiki:Invariant-basis-number,

   author = "Wikipedia",

   title = "Invariant basis number --- Wikipedia{,} The Free Encyclopedia",

   year = "2006",

   note = "[\href{http://en.wikipedia.org/w/index.php?title=Invariant_basis_number&oldid=85220456}{Online}; accessed 24-December-2006]"

 }

@article {MR1403351,

    AUTHOR = {Etingof, Pavel and Kazhdan, David},

     TITLE = {Quantization of {L}ie bialgebras. {I}},

   JOURNAL = {Selecta Math. (N.S.)},

  FJOURNAL = {Selecta Mathematica. New Series},

    VOLUME = {2},

      YEAR = {1996},

    NUMBER = {1},

     PAGES = {1--41},

      ISSN = {1022-1824},

     CODEN = {SMATF6},

   MRCLASS = {17B37 (16W30 18D20 81R50)},

  MRNUMBER = {MR1403351 (97f:17014)},

MRREVIEWER = {Yu. N. Bespalov},

}

@article {MR1669953,

    AUTHOR = {Etingof, Pavel and Kazhdan, David},

     TITLE = {Quantization of {L}ie bialgebras. {II}},

   JOURNAL = {Selecta Math. (N.S.)},

  FJOURNAL = {Selecta Mathematica. New Series},

    VOLUME = {4},

      YEAR = {1998},

    NUMBER = {2},

     PAGES = {213--231, 233--269},

      ISSN = {1022-1824},

     CODEN = {SMATF6},

   MRCLASS = {17B62 (16W35 17B37 18D20)},

  MRNUMBER = {MR1669953 (2000i:17033)},

MRREVIEWER = {Benjamin David Enriquez},

      note = {arXiv:\arxiv{q-alg/9701038}},

}

@article {MR1771217,

    AUTHOR = {Etingof, Pavel and Kazhdan, David},

     TITLE = {Quantization of {L}ie bialgebras. {IV}. {T}he coinvariant

              construction and the quantum {KZ} equations},

   JOURNAL = {Selecta Math. (N.S.)},

  FJOURNAL = {Selecta Mathematica. New Series},

    VOLUME = {6},

      YEAR = {2000},

    NUMBER = {1},

     PAGES = {79--104},

      ISSN = {1022-1824},

     CODEN = {SMATF6},

   MRCLASS = {17B37 (32G34 81R50)},

  MRNUMBER = {MR1771217 (2002i:17021)},

}

@article {MR1771218,

    AUTHOR = {Etingof, Pavel and Kazhdan, David},

     TITLE = {Quantization of {L}ie bialgebras. {V}. {Q}uantum vertex

              operator algebras},

   JOURNAL = {Selecta Math. (N.S.)},

  FJOURNAL = {Selecta Mathematica. New Series},

    VOLUME = {6},

      YEAR = {2000},

    NUMBER = {1},

     PAGES = {105--130},

      ISSN = {1022-1824},

     CODEN = {SMATF6},

   MRCLASS = {17B37 (17B69 81R50)},

  MRNUMBER = {MR1771218 (2002i:17022)},

}

@article {MR2253455,

    AUTHOR = {Bar-Natan, Dror and Morrison, Scott},

     TITLE = {The {K}aroubi envelope and {L}ee's degeneration of {K}hovanov

              homology},

   JOURNAL = {Algebr. Geom. Topol.},

  FJOURNAL = {Algebraic \& Geometric Topology},

    VOLUME = {6},

      YEAR = {2006},

     PAGES = {1459--1469 (electronic)},

      ISSN = {1472-2747},

   MRCLASS = {57M27 (18E05 57M25)},

  MRNUMBER = {MR2253455},

      note = {arXiv:\arxiv{math.GT/0606542}},

}

@article{math.GT/0206303,

    title = {{An invariant of link cobordisms from Khovanov homology}},

    author = {Magnus Jacobsson},

    journal = {Algebr. Geom. Topol.},

    volume = 4,

    year = 2004,

    pages = {1211--1251},

    note = {arXiv:\arxiv{math.GT/0206303}}}

@misc{math.GT/0610650,

    title = {{Khovanov-Rozansky homology via a canopolis formalism}},

    author = {Ben Webster},

      note = {arXiv:\arxiv{math.GT/0610650}}}

@misc{green-implementation,

    title = {{JavaKh}},

    author= {Jeremey Green},

    note = {\url{http://katlas.math.toronto.edu/wiki/Khovanov_Homology}},

}

@misc{ortiz-navarro,

    title = {{Khovanov Homology and Reidemeister Torsion}},

    author ={Juan Ariel Ortiz-Navarro and Chris Truman},

    note = {a talk at the 2006 Toronto CMS meeting, slides at \url{http://www.math.uiowa.edu/~jortizna/Present-CMS-06.pdf}},

}

@book {MR1438306,

    AUTHOR = {Gelfand, Sergei I. and Manin, Yuri I.},

     TITLE = {Methods of homological algebra},

      NOTE = {Translated from the 1988 Russian original},

 PUBLISHER = {Springer-Verlag},