@misc{
hp:ssp,
   Author = {Alvarez, Guillermo and Keeton, Kim and Merchant, Arif and Riedel, Erik and Wilkes, John},
   Title = {Storage Systems Management},
   Month = {June},
         Year = {2000} }



@article{
hp:three,
   Author = {Amiri, A.},
   Title = {A system for the design of packet-switched communication networks with economic tradeoffs},
   Journal = {Computer Communications},
   Volume = {21},
   Pages = {1670-1680},
      Year = {1998} }



@article{
andersen_ye96,
   Author = {Andersen, E. D. and Ye, Y.},
   Title = {Combining Interior-Point and Pivoting Algorithms for Linear Programming},
   Journal = {Management Science},
   Volume = {42},
   Pages = {1719--1731},
      Year = {1996} }



@techreport{
hp:five,
   Author = {Atamtürk, A.},
   Title = {On capacitated network design cut-set polyhedra},
   Institution = {IEOR Department, University of California at Berkeley},
   Note = {Available at http://ieor.berkeley.edu1 atamturk},
   Month= {December},
      Year = {2000} }



@article{
opt1989,
   Author = {Balakrishnan, A. and Magnanti, T. L. and Wong, R. T.},
   Title = {A Dual-Ascent Procedure for Large-Scale Uncapacitated Network Design},
   Journal = {Operations Research},
   Volume = {37},
   Number = {5},
   Pages = {716-740},
      Year = {1989} }



@article{
hp:six,
   Author = {Barahona, F.},
   Title = {Network design using cut inequalities},
   Journal = {SIAM Journal on Optimization},
   Pages = {823-837},
      Year = {1996} }



@article{
hp:seven,
   Author = {Bienstock, D. and Chopra, S. and Gunluk, O.},
   Title = {Minimum cost capacity installation for multicommodity network flows},
   Journal = {Mathematical Programming},
   Volume = {81},
   Number = {2-1},
   Pages = {177-199},
      Year = {1998} }



@article{
hp:eight,
   Author = {Bienstock, D. and Gunluk, O.},
   Title = {Capacitated network design. Polyhedral structure and computation.},
   Journal = {INFORMS Journal on Computing},
   Volume = {8},
   Pages = {243-259},
      Year = {1996} }



@article{
boland04,
   Author = {Boland, N. and Hamacher, H. W. and Lenzen, F.},
   Title = {Minimizing beam-on time in cancer radiation treatment using multileaf collimators},
   Journal = {Networks},
   Volume = {43},
   Number = {4},
   Pages = {226-240},
      Year = {2004} }



@article{
BF77,
   Author = {Boorstyn, R. B. and Frank, H.},
   Title = {Large-scale network topological optimization},
   Journal = {IEEE Transactions on Communications},
   Volume = {COM-25},
   Pages = {29-47},
      Year = {1977} }



@article{
boyer93,
   Author = {Boyer, A. L. and Bortfeld, T. and Kahler, D. and Starkschall, G. and Waldron, T.},
   Title = {X-Ray Field Compensation with Multileaf Collimation},
   Journal = {International Journal of Radiation Oncology Biology Physics},
   Volume = {27},
   Pages = {208-208},
   Note = {Suppl. 1},
      Year = {1993} }



@techreport{
karen2009,
   Author = {Brownlee, J.N. and Halytskyy, Y. and Jones, N. and Kharuk, A.F. and O'Sullivan, M.J. and Walker, C.G. and Ziedins, I.},
   Title = {Storage Network Planning for KAREN/BeSTGRID},
   Institution = {REAANZ},
      Year = {2009} }



@article{
hubLoc:two,
   Author = {Campbell, J.F.},
   Title = {A survey of hub location},
   Journal = {Studies in Locational Analysis},
   Volume = {6},
   Pages = {31-49},
      Year = {1994} }



@phdthesis{
chen03,
   Author = {Chen, Jessica},
   Title = {Minimising IMRT Treatment Time by Optimal Configuration of Multileaf Collimators},
   School = {University of Auckland},
      Year = {2003} }



@article{
hp:ten,
   Author = {Chopra, S. and Gilboa, I. and Sastry, S. T.},
   Title = {Source sink flows with capacity installation in batches},
   Journal = {Discrete Applied Mathematics},
   Volume = {85},
   Pages = {165-192},
      Year = {1998} }



@article{
hp:eleven,
   Author = {Chu, C.-H. and Premkumar, G. and Chou, C. and Sun, J.},
   Title = {Dynamic degree constrained network design: a genetic algorithm approach},
   Journal = {Proceedings GECCO-99. Genetic and Evolutionary Computation Conference. Eighth International Conference on Genetic Algorithms (ICGA-99) and the Fourth Annual Genetic Programming Conference (GP-99)},
   Volume = {1},
   Pages = {141-148},
      Year = {1999} }



@article{
conder98,
   Author = {Conder, M. D. E. and Walker, C. G.},
   Title = {The infinitude of 7-arc-transitive graphs},
   Journal = {Journal of Algebra},
   Volume = {208},
   Number = {2},
   Pages = {619-629},
      Year = {1998} }



@article{
conder98a,
   Author = {Conder, M. D. E. and Walker, C. G.},
   Title = {Vertex-transitive non-Cayley graphs with arbitrarily large vertex-stabilizer},
   Journal = {Journal of Algebraic Combinatorics},
   Volume = {8},
   Number = {1},
   Pages = {29-38},
      Year = {1998} }



@article{
dai99,
   Author = {Dai, Jian-Rong and Hu, Yi-Min},
   Title = {Intensity-modulation radiotherapy using independent collimators: An algorithm study},
   Journal = {Medical Physics},
   Volume = {26},
   Number = {12},
   Pages = {2562-2570},
   Keywords = {radiation therapy
simulated annealing
intensity modulation
dosimetry
linear accelerators},
   Year = {1999} }



@article{
das03,
   Author = {Das, Shiva and Cullip, Timothy and Tracton, Gregg and Chang, Sha and Marks, Lawrence and Anscher, Mitchell and Rosenman, Julian},
   Title = {Beam orientation selection for intensity-modulated radiation therapy based on target equivalent uniform dose maximization},
   Journal = {International Journal of Radiation Oncology Biology Physics},
   Volume = {55},
   Number = {1},
   Pages = {215-224},
   Abstract = {Purpose: To develop an automated beam-orientation selection procedure for intensity-modulated radiotherapy (IMRT), and to determine if a small number of beams picked by this automated procedure can yield results comparable to a large number of manually placed orientations. Methods and Materials: The automated beam selection procedure maximizes an unconstrained objective function composed of target equivalent uniform dose (EUD) and critical structure dose-volume histogram (DVH) constraints. Beam orientations are selected from a large feasible set of directions through a series of alternating fluence optimization and orientation alteration steps, until convergence to a stable orientation set. The fluence optimization step adjusts fluences to maximize the objective function. The orientation alteration step substitutes beams in the orientation set currently under consideration with beams of the parent set in the immediate angular vicinity; the altered orientation set is deemed current if it produces a higher objective function value in the fluence optimization step. Results and Conclusions: It is demonstrated, for prostate IMRT planning, that a modest number of appropriately selected beam orientations (3 or 5) can provide dose distributions as satisfactory as those produced by a large number of unselected equispaced orientations. Such selected beam orientations can reduce overall treatment time, thus making IMRT more clinically practical. &copy; 2003 Elsevier Science Inc.},
   Keywords = {Radiation
Radiotherapy
Particle beams},
   Year = {2003} }



@article{
hp:twelve,
   Author = {Deo, N. and Hakimi, S.L.},
   Title = {The shortest generalized Hamiltonian tree},
   Journal = {Proceedings of the 6th Annual Allerton Conference},
   Pages = {879-888},
      Year = {1968} }



@article{
ehrgott03,
   Author = {Ehrgott, M. and Johnston, R.},
   Title = {Optimisation of beam directions in intensity modulated radiation therapy planning},
   Journal = {OR Spectrum},
   Volume = {25},
   Number = {2},
   Pages = {251-264},
      Year = {2003} }



@article{
evans97,
   Author = {Evans, Philip M. and Hansen, Vibeke N. and Swindell, William},
   Title = {The optimum intensities for multiple static multileaf collimator field compensation},
   Journal = {Medical Physics},
   Volume = {24},
   Number = {7},
   Pages = {1147-1156},
   Keywords = {radiation therapy
X-ray apparatus},
   Year = {1997} }



@article{
hp:fourteen,
   Author = {Fetterolf, P.C. and Anandalingam, G.},
   Title = {A Lagrangian relaxation technique for optimizing interconnection of local area networks},
   Journal = {Operations Research},
   Volume = {40},
   Pages = {678-688},
      Year = {1992} }



@book{
ampl2002,
   Author = {Fourer, Robert and Gay, David and Kernighan, Brian},
   Title = {AMPL: A Modeling Language for Mathematical Programming},
   Publisher = {{Duxbury Press}},
   Abstract = {{AMPL is a language for large-scale optimization and mathematical programming problems in production, distribution, blending, scheduling, and many other applications. Combining familiar algebraic notation and a powerful interactive command environment, AMPL makes it easy to create models, use a wide variety of solvers, and examine solutions. Though flexible and convenient for rapid prototyping and development of models, AMPL also offers the speed and generality needed for repeated large-scale production runs. This book, written by the creators of AMPL, is a complete guide for modelers at all levels of experience. It begins with a tutorial on widely used linear programming models, and presents all of AMPL's features for linear programming with extensive examples. Additional chapters cover network, nonlinear, piecewise-linear, and integer programming; database and spreadsheet interactions; and command scripts. Most chapters include exercises. Download free versions of AMPL and several solvers from www.ampl.com for experimentation, evaluation, and education. The Web site also lists vendors of the commercial version of AMPL and numerous solvers.}},
      Year = {2002} }



@inproceedings{
DIP,
   Author = {Galati, Matt and Ralphs, Ted K.},
   Title = {A Framework for Decomposition in Integer Programming},
   BookTitle = {INFORMS Annual COnference},
   Address= {San Diego},
      Year = {2009} }



@article{
galvin93,
   Author = {Galvin, J. M. and Chen, X. G. and Smith, R. M.},
   Title = {Combining Multileaf Fields to Modulate Fluence Distributions},
   Journal = {International Journal of Radiation Oncology Biology Physics},
   Volume = {27},
   Number = {3},
   Pages = {697-705},
      Year = {1993} }



@book{
hp:fifteen,
   Author = {Garey, M.R. and Johnson, D. S.},
   Title = {Computers and intractability: A guide to the theory of NP-completeness},
   Publisher = {W. H Freeman and Company},
   Address = {San Francisco, CA},
      Year = {1979} }



@article{
hp:sixteen,
   Author = {Gavish, B.},
   Title = {A general model for the topological design of computer networks},
   Journal = {IEEE Global Telecommunications Conference},
   Volume = {3},
   Pages = {1584-1588},
      Year = {1986} }



@article{
hp:seventeen,
   Author = {Gavish, B.},
   Title = {Topological design of computer communication networks - the overall design problem},
   Journal = {European Journal of Operational Research},
   Volume = {58},
   Pages = {149-172},
      Year = {1992} }



@article{
SANVEs,
   Author = {Glider, J. S. and Fuente, C. F. and Scales, W. J.},
   Title = {The software architecture of a SAN storage control system},
   Journal = {IBM Systems Journal},
   Volume = {42},
   Number = {2},
   Pages = {232-249},
      Year = {2003} }



@article{
haas98,
   Author = {Haas, O.C.L. and Burnham, K.J. and Mills, J.A.},
   Title = {Optimization of beam orientation in radiotherapy using planar geometry},
   Journal = {Physics in Medicine and Biology},
   Volume = {43},
   Number = {8},
   Pages = {2179-2193},
   Abstract = {This paper proposes a new geometrical formulation of the coplanar beam orientation problem combined with a hybrid multiobjective genetic algorithm.  The approach is demonstrated by optimizing the beam orientation in two dimensions, with the objectives being formulated using planar geometry.  The traditional formulation of the objectives associated with the organs at risk has been modified to account for the use of complex dose delivery techniques such as beam intensity modulation.  The new algorithm attempts to replicate the approach of a treatment planner whilst reducing the amount of computation required. Hybrid genetic search operators have been developed to improve the performance of the genetic algorithm by exploiting problem-specific features.  The multiobjective genetic algorithm is formulated around the concept of Pareto optimality which enables the algorithm to search in parallel for different objectives. When the approach is applied without constraining the number of beams, the solution produces an indication of the minimum number of beams required.  It is also possible to obtain non-dominated solutions for various numbers of beams, thereby giving the clinicians a choice in terms of the number of beams as well as in the orientation of these beams.},
      Year = {1998} }



@misc{
hamacher03,
   Author = {Hamacher, H. W. and Ahuja, R. K.},
   Title = {Minimizing beam-on time in radiation treatment using network flows},
   Note = {Preprint},
         Year = {2003} }



@article{
hamacher02,
   Author = {Hamacher, H.W. and Kufer, K.-H.},
   Title = {Inverse radiation therapy planning - A multiple objective optimization approach},
   Journal = {Discrete Applied Mathematics},
   Volume = {118},
   Number = {1-2},
   Pages = {145-161},
   Abstract = {For some decades, radiation therapy has been proved successful in cancer treatment. It is the major task of clinical radiation treatment planning to realize, on the one hand, a high level dose of radiation in the cancer tissue in order to obtain maximum tumor control. On the other hand, it is obvious that it is absolutely necessary to keep the unavoidable radiation in the tissue outside the tumor, particularly in organs at risk, as low as possible. No doubt, these two objectives of treatment planning - high level dose in the tumor, low radiation outside the tumor - have a basically contradictory nature. Thus, there is need to compromise between overdosing the organs at risk and underdosing the target volume. Differing from the currently used time consuming interactive approach between dosimetrists and physicians, we consider the radiation therapy planning problem as a multiple objective linear programming problem and build a data base of relatively few efficient solutions representing the set of Pareto solutions. This data base can be easily scanned by physicians looking for an adequate treatment plan with the aid of an appropriate online tool. The paper includes a report on first numerical experiments and a list of further research topics which is hoped to stimulate interest of the OR community in a subject, where OR methods can make a difference for many individual's lives. &copy; 2002 Elsevier Science B.V. All rights reserved.},
      Year = {2002} }



@article{
hp:nineteen,
   Author = {Herrmann, J.W. and Ioannou, G. and Minis, I. and Proth, J.M.},
   Title = {A dual ascent approach to the fixed-charge capacitated network design problem},
   Journal = {European Journal of Operational Research},
   Volume = {95},
   Pages = {476-90},
      Year = {1996} }



@article{
holder03,
   Author = {Holder, Allen},
   Title = {Designing Radiotherapy Plans with Elastic Constraints and Interior Point Methods},
   Journal = {Health Care Management Science},
   Volume = {6},
   Number = {1},
   Pages = {5-16},
      Year = {2003} }



@article{
hp:twenty,
   Author = {Holmberg, K. and Yuan, Di},
   Title = {A Lagrangean heuristic based branch-and-bound method for the capacitated network design problem},
   Journal = {Proceedings of International Symposium on Operations Research},
   Pages = {78-83},
      Year = {1996} }



@article{
holmes94,
   Author = {Holmes, T. and Mackie, T. R.},
   Title = {A comparison of three inverse treatment planning algorithms},
   Journal = {Physics in Medicine and Biology},
   Number = {1},
   Pages = {91-106},
   Abstract = {Three published inverse treatment planning algorithms for physical optimization of external beam radiotherapy are compared. All three algorithms attempt to minimize a quadratic objective function of the dose distribution. It is shown that the algorithms are based on the common framework of Newton's method of multidimensional function minimization. The approximations used within this framework to obtain the different algorithms are described. The use of these algorithms requires that the number of weights of elemental dose distributions be equal to the number of sample points taken in the dose volume. The primary factor in determining how the algorithms are implemented is the dose computation model. Two of the algorithms use pencil beam dose models and therefore directly optimize individual pencil beam weights, whereas the third algorithm is implemented to optimize groups of pencil beams, each group converging upon a common point. All dose computation models assume that the irradiated medium is homogeneous. It is shown that the two different implementations produce similar results for the simple optimization problem of conforming dose to a convex target shape. Complex optimization problems consisting of nonconvex target shapes and dose limiting structures are shown to require a pencil beam optimization method.},
      Year = {1994} }



@book{
cplex2007,
   Author = {ILOG},
   Title = {ILOG AMPL CPLEX System Version 11.0 User's Guide},
   Publisher = {ILOG},
      Year = {2007} }



@article{
karmarkar84,
   Author = {Karmarkar, N.},
   Title = {A New Polynomial Time Algorithm for Linear Programming},
   Journal = {Combinatorica},
   Volume = {4},
   Pages = {373-395},
      Year = {1984} }



@article{
hp:twentyone,
   Author = {Kleinburg, J. M},
   Title = {Single source unsplittable flow},
   Journal = {Proceedings of the 37th Annual IEEE Symposium on Foundations of Computer Science},
   Pages = {68-77},
      Year = {1996} }



@article{
hubLoc:one,
   Author = {Klincewicz, J.G.},
   Title = {Hub location in backbone/tributary network design: a review},
   Journal = {Location Science},
   Volume = {6},
   Pages = {307-335},
      Year = {1998} }



@article{
kolmonen98,
   Author = {Kolmonen, Pekka and Tervo, Jouko and Lahtinen, Tapani},
   Title = {Use of the Cimmino algorithm and continuous approximation for the dose deposition kernel in the inverse problem of radiation treatment planning},
   Journal = {Physics in Medicine and Biology},
   Number = {9},
   Pages = {2539-2554},
   Abstract = {An approximate continuous data fitting model for the dose deposition kernel was developed. The model uses a discrete Fourier transform to interpolate dose values in patient space and intensity distribution in treatment space. The continuous kernel was applied to the inverse problem of radiation treatment planning. In the problem a prescribed dose distribution was to be created using intensity modulation of several fields. The Cimmino algorithm suitable for solving large systems of inequalities was adapted. Upper and lower dose constraints for planning target volume (PTV) and organs at risk (OAR) can be implemented into the algorithm. Using continuous and discrete kernels an intensity modulation was computed in a two-dimensional phantom with a PTV and low-dose region, and in the real three-dimensional patient planning. Intensity modulations obtained using continuous and discrete kernels were in good agreement.},
      Year = {1998} }



@article{
lee97,
   Author = {Lee, Shinhak and Cho, Paul S. and II, Robert J. Marks and Oh, Seho},
   Title = {Conformal radiotherapy computation by the method of alternating projections onto convex sets},
   Journal = {Physics in Medicine and Biology},
   Number = {6},
   Pages = {1065-1086},
   Abstract = {Synthesis of beam profiles for a given dose prescription is a central problem in radiotherapy. Care must be taken in the beam design to expose the tumour volume at a high level, to avoid significant irradiation of critical organs, and to minimize exposure of all other tissue. Use of the synthesis procedure known as alternating projections onto convex sets (POCS) is shown to be a viable approach to beam design. POCS is a powerful tool for signal and image restoration and synthesis. Convex sets of signals obeying desired constraint sets are first specified. Then, by repeated projections onto these sets, convergence is to a signal obeying all desired constraints if the constraint sets have a finite intersection. In this paper we apply the method of POCS to conformal radiotherapy dose computation. The performance of the method is shown through three representative examples.},
      Year = {1997} }



@misc{
geoff_coke,
   Author = {Leyland, G. and Kraines, S. and Akatsuka, T. and Molyneaux, A. K. and Favrat, D. and Komiyama., H.},
   Title = {Minimising transport and investment costs in the coke industry in Shanxi province, China},
   Note = {In preparation},
         Year = {2002} }



@article{
hp:twentytwo,
   Author = {Magnanti, T. L. and Mirchandani, P. and Vachani, R.},
   Title = {Modeling and solving the capacitated network loading problem},
   Journal = {Operations Research},
   Volume = {43},
   Pages = {142-157},
      Year = {1995} }



@article{
magnanti95,
   Author = {Magnanti, Thomas L. and Mirchandani, Prakash and Vachani, Rita},
   Title = {Modeling and solving the two-facility capacitated network loading problem},
   Journal = {Operations Research},
   Volume = {43},
   Number = {1},
   Pages = {142},
      Year = {1995} }





@inproceedings{
graph,
   Author = {Mirchandi, P. and Simchi-Levi, D.},
   Title = {Handbook of Graph Theory},
   Publisher = {CRC Press},
   Pages = {1117-1139},
      Year = {2004} }





@article{
MASCOTSSim,
   Author = {Molero, Xavier and Silla, Federico and Santonja, Vicente and Duato, José},
   Title = {Modeling and simulation of storage area networks},
   Journal = {Modeling, Analysis and Simulation of Computer and Telecommunication Systems, 2000. Proceedings. 8th International Symposium on},
   Pages = {307-314},
      Year = {2000} }



@article{
SANevolution,
   Author = {Morris, R. J. T. and Truskowski, B. J.},
   Title = {The evolution of storage systems},
   Journal = {IBM Systems Journal},
   Volume = {42},
   Number = {2},
   Pages = {205-217},
      Year = {2003} }



@techreport{
minos1998,
   Author = {Murtagh, Bruce A. and Saunders, Michael A.},
   Title = {MINOS 5.5 User's Guide},
      Year = {1998} }



@article{
hp:twentyfive,
   Author = {Narula, S.C. and Ho, C.A.},
   Title = {Degree-constrained minimum spanning tree},
   Journal = {Computers and Operations Research},
   Volume = {7},
   Pages = {239-49},
      Year = {1980} }



@techreport{
gurobi2010,
   Author = {Optimization, Gurobi},
   Title = {Gurobi Optimizer Reference Manual},
      Year = {2010} }



@phdthesis{
mo_masters95,
   Author = {O'Sullivan, Michael},
   Title = {Scheduling and Loading of Fleet Operations},
   School = {University of Auckland},
      Year = {1995} }



@techreport{
mo_minos97,
   Author = {O'Sullivan, Michael},
   Title = {Linking MINOS and MATLAB},
   Institution = {Systems Optimization Laboratory, Management Science and Engineering, Stanford University},
      Year = {1997} }



@phdthesis{
mo_phd2002,
   Author = {O'Sullivan, Michael},
   Title = {New Methods for Dynamic Programming over an Infinite Time Horizon},
   School = {Stanford University},
      Year = {2002} }



@techreport{
ow05,
   Author = {O'Sullivan, Michael and Walker, Cameron},
   Title = {A Mixed-Integer Approach to Storage Area Network Design using Generic Network Components},
   Institution = {Department of Engineering Science, University of Auckland, New Zealand},
      Year = {2005} }



@inproceedings{
mo_ictsm09,
   Author = {O'Sullivan, Michael and Walker, Cameron},
   Title = {Bi-Criterion Design of Core-Edge Storage Area Networks},
   BookTitle = {International Conference on Telecommunication Systems Management},
   Address= {Monterey},
   Publisher = {2009 International Conference on Telecommunications Systems - Modeling and Analysis},
      Year = {2009} }



@techreport{
os2006,
   Author = {O'Sullivan, M.J. and Saunders, M.A.},
   Title = {Stabilizing policy improvement for large-scale infinite-horizon dynamic programming},
   Institution = {Systems Optimization Laboratory, Management Science and Engineering Department, Stanford University},
      Year = {2006} }



@article{
os2010,
   Author = {O'Sullivan, M.J. and Saunders, M.A.},
   Title = {Stabilizing Policy Improvement for Large-Scale Infinite-Horizon Dynamic Programming},
   Journal = {SIAM Journal on Matrix Analysis and Applications},
   Volume = {31},
   Number = {2},
   Pages = {434-459},
      Year = {2010} }



@misc{
sponge,
   Author = {O'Sullivan, Michael J. and Walker, Cameron G.},
   Title = {The {S}ponge {R}oll {P}roduction {P}roblem},
   Note = {Case study within the online teaching TWiki (Department of Engineering Science, University of Auckland), \url{http://twiki.esc.auckland.ac.nz/twiki/bin/view/OpsRes/SpongeRollProductionProblem}},
         Year = {2008} }



@inproceedings{
owa2003,
   Author = {O'Sullivan, M.J. and Walker, C.G. and J., Allard},
   Title = {Improving Optimal Storage Area Network Design},
   BookTitle = {ORSNZ},
   Address= {Hamilton, New Zealand},
   Publisher = {Proceedings of ORSNZ 38th Anual Conference},
   Pages = {119-128},
      Year = {2003} }



@inproceedings{
owot2003,
   Author = {O'Sullivan, M.J. and Walker, C.G. and O'Sullivan, M.L. and Thompson, T.D.},
   Title = {Optimal Fibre-Optic Cable Layout using Integer Programming},
   BookTitle = {ORSNZ},
   Address= {Hamilton, New Zealand},
   Publisher = {Proceedings of 38th ORSNZ Anual Conference},
   Pages = {205-214},
      Year = {2003} }



@techreport{
owot2004,
   Author = {O'Sullivan, M.J. and Walker, C.G. and O'Sullivan, M.L. and Thompson, T.D.},
   Title = {Protecting Telecommunications Networks: Toward a Minimum-Cost Solution},
   Institution = {Department of Engineering Science, University of Auckland},
      Year = {2004} }



@inproceedings{
ows2004,
   Author = {O'Sullivan, M.J. and Walker, C.G. and Shum, H.},
   Title = {Minimizing Total Treatment in IMRT using Multileaf Collimators},
   BookTitle = {ICOTA 6},
   Address= {Ballarat, Australia},
   Publisher = {Proceedings of The Sixth International Conference on Optimization: Techniques and Applications},
      Year = {2004} }



@article{
2007284390,
   Author = {O'Sullivan, M.J.
Walker, C.G. and O'Sullivan, M.L. and Thompson, T.D. and Philpott, A.B.},
   Title = {Protecting local access telecommunications networks: Toward a minimum-cost solution},
   Journal = {Telecommunication Systems},
   Volume = {33},
   Pages = {353-376},
      Year = {2006} }



@misc{
opl1999,
   Author = {Pascal Van, Hentenryck and Laurent, Michel and Philippe, Laborie and Wim, Nuijten and Jerome, Rogerie},
   Title = {Combinatorial Optimization in OPL Studio},
   Publisher = {Springer-Verlag},
   Note = {651190
1-15},
         Year = {1999} }



@techreport{
hp:twentysix,
   Author = {Peh, Li-Shiuan},
   Title = {The Appia topology solver: implementation},
   Institution = {Hewlett-Packard Laboratories},
   Note = {http://www.hpl.hp.com/SSP/papers/\#Appia},
   Month= {September},
      Year = {1998} }



@article{
pugachev01a,
   Author = {Pugachev, Andrei and Li, Jonathan G. and Boyer, Arthur L. and Hancock, Steven L. and Le, Quynh-Thu and Donaldson, Sarah S. and Xing, Lei},
   Title = {Role of beam orientation optimization in intensity-modulated radiation therapy},
   Journal = {International Journal of Radiation Oncology Biology Physics},
   Volume = {50},
   Number = {2},
   Pages = {551-560},
   Abstract = {Purpose: To investigate the role of beam orientation optimization in intensity-modulated radiation therapy (IMRT) and to examine the potential benefits of noncoplanar intensity-modulated beams. Methods and Materials: A beam orientation optimization algorithm was implemented. For this purpose, system variables were divided into two groups: beam position (gantry and table angles) and beam profile (beamlet weights). Simulated annealing was used for beam orientation optimization and the simultaneous iterative inverse treatment planning algorithm (SIITP) for beam intensity profile optimization. Three clinical cases were studied: a localized prostate cancer, a nasopharyngeal cancer, and a paraspinal tumor. Nine fields were used for all treatments. For each case, 3 types of treatment plan optimization were performed: (1) beam intensity profiles were optimized for 9 equiangular spaced coplanar beams; (2) orientations and intensity profiles were optimized for 9 coplanar beams; (3) orientations and intensity profiles were optimized for 9 noncoplanar beams. Results: For the localized prostate case, all 3 types of optimization described above resulted in dose distributions of a similar quality. For the nasopharynx case, optimized noncoplanar beams provided a significant gain in the gross tumor volume coverage. For the paraspinal case, orientation optimization using noncoplanar beams resulted in better kidney sparing and improved gross tumor volume coverage. Conclusion: The sensitivity of an IMRT treatment plan with respect to the selection of beam orientations varies from site to site. For some cases, the choice of beam orientations is important even when the number of beams is as large as 9. Noncoplanar beams provide an additional degree of freedom for IMRT treatment optimization and may allow for notable improvement in the quality of some complicated plans. Copyright &copy; 2001 Elsevier Science Inc.},
   Keywords = {Tumors
Oncology
Simulated annealing
Algorithms
Radiotherapy},
   Year = {2001} }



@article{
pugachev01,
   Author = {Pugachev, A. and Xing, L.},
   Title = {Pseudo beam's-eye-view as applied to beam orientation selection in intensity-modulated radiation therapy},
   Journal = {International Journal of Radiation Oncology Biology Physics},
   Volume = {51},
   Number = {5},
   Pages = {1361-1370},
   Abstract = {Purpose: To introduce the concept of pseudo beam's-eye-view (pBEV), to establish a framework for computer-assisted beam orientation selection in intensity-modulated radiation therapy (IMRT), and to evaluate the utility of the proposed technique. Methods and Materials: To facilitate the selection of beam orientations for IMRT treatment planning, a scoring of beam direction was introduced. The score function was based on the maximum target dose deliverable by the beam without exceeding the tolerance doses of the critical structures. For the score function calculation, the beam portal at given gantry and couch angles was divided into a grid of beamlets. Each beamlet crossing the target was assigned the maximum intensity that could be used without exceeding the dose tolerances of the organs at risk (OARs) and normal tissue. Thereafter, a score was assigned to the beam according to the target dose delivered. The beams for the treatment were selected among those with the highest scores. In a sense, this technique is similar to the beam's-eye-view approach used in conventional radiation therapy, except that the evaluation by a human is replaced by a score function, and beam modulation is taken into account. Results: The pBEV technique was tested on two clinical cases: a paraspinal treatment and a nasopharyngeal cancer with both coplanar and noncoplanar beam configurations. The plans generated under the guidance of pBEV for the paraspinal treatment offered superior target dose uniformity and reduced OAR doses. For the nasopharyngeal cancer case, it was also found that the pBEV-selected coplanar and noncoplanar beams significantly improved the target coverage without compromising the sparing of the OARs. Conclusions: The pBEV technique developed in this work provides a comprehensive tool for beam orientation selection in IMRT. It is especially valuable for complicated cases, where the target is surrounded by several sensitive structures and where it is difficult to select a set of good beam orientations. The pBEV technique has considerable potential for simplifying the IMRT treatment planning process and for maximizing the technical capacity of IMRT. &copy; 2001 Elsevier Science Inc.},
   Keywords = {Oncology
Medical imaging
Dosimetry
Tumors
Radiotherapy},
   Year = {2001} }



@article{
que99,
   Author = {Que, W.},
   Title = {Comparison of algorithms for multileaf collimator field segmentation},
   Journal = {Medical Physics},
   Volume = {26},
   Number = {11},
   Pages = {2390-2396},
      Year = {1999} }




@article{
2007317216,
   Author = {Reynolds, H.M. and Walker, C.G. and Dunbar, P.R. and O'Sullivan, M.J. and Uren, R.F. and Thompson, J.F. and Smith, N.P.},
   Title = {Functional anatomy of the lymphatics draining the skin via a detailed statistical analysis},
   Journal = {Journal of Anatomy},
   Volume = {-},
   Pages = {-},
      Year = {2009} }



@article{
xpressmp2009,
   Author = {Richard, Laundy and Michael, Perregaard and Gabriel, Tavares and Horia, Tipi and Alkis, Vazacopoulos},
   Title = {Solving Hard Mixed-Integer Programming Problems with Xpress-MP: A MIPLIB 2003 Case Study},
   Journal = {INFORMS J. on Computing},
   Volume = {21},
   Number = {2},
   Pages = {304-313},
   Note = {1538328},
      Year = {2009} }



@article{
rowbottom01,
   Author = {Rowbottom, Carl Graham and Nutting, Christopher Martin and Webb, Steve},
   Title = {Beam-orientation optimization of intensity-modulated radiotherapy: clinical application to parotid gland tumours},
   Journal = {Radiotherapy and Oncology},
   Volume = {59},
   Number = {2},
   Pages = {169-177},
      Year = {2001} }



@article{
siochi99,
   Author = {Siochi, R. A. C.},
   Title = {Minimizing static intensity modulation delivery time using an intensity solid paradigm},
   Journal = {International Journal of Radiation Oncology Biology Physics},
   Volume = {43},
   Number = {3},
   Pages = {671-680},
      Year = {1999} }



@article{
hubLoc:three,
   Author = {Skorin-Kapov, D. and Skorin-Kapov, J.},
   Title = {On hub location models},
   Journal = {Journal of Computing and Information Technology},
   Volume = {3},
   Pages = {183-192},
      Year = {1995} }



@phdthesis{
DS07,
   Author = {Soni, D.},
   Title = {Dakshai's Thesis},
   School = {University of Auckland, Auckland, NZ},
      Year = {2007} }



@article{
spirou98,
   Author = {Spirou, Spiridon V. and Chui, Chen-Shou},
   Title = {A gradient inverse planning algorithm with dose-volume constraints},
   Journal = {Medical Physics},
   Volume = {25},
   Number = {3},
   Pages = {321-333},
   Keywords = {dosimetry
radiation therapy
lung
conjugate gradient methods
least mean squares methods
medical computing},
   Year = {1998} }



@article{
hp:twentyseven,
   Author = {Sridhar, V. and Park, J.S.},
   Title = {Benders-and-cut algorithm for fixed-charge capacitated network design problem},
   Journal = {European Journal of Operational Research},
   Volume = {125},
   Pages = {622-32},
      Year = {2000} }



@article{
stein97,
   Author = {Stein, Jorg and Mohan, Radhe and Wang, Xiao-Hong and Bortfeld, Thomas and Wu, Qiuwen and Preiser, Konrad and Ling, C. Clifton and Schlegel, Wolfgang},
   Title = {Number and orientations of beams in intensity-modulated  radiation treatments},
   Journal = {Medical Physics},
   Volume = {24},
   Number = {2},
   Pages = {149-160},
   Keywords = {radiation therapy
dosimetry},
   Year = {1997} }



@phdthesis{
santk02,
   Author = {Strand, S.},
   Title = {Storage Area Networks and SANTK},
   School = {University of Minnesota, Minnesota, USA},
      Year = {2002} }



@article{
tervo00,
   Author = {Tervo, J. and Kolmonen, P.},
   Title = {Model for the control of a multileaf collimator in radiation therapy treatment planning},
   Journal = {Inverse Problems},
   Volume = {16},
   Number = {6},
   Pages = {1875-1895},
   Abstract = {A new approach for inverse treatment planning in radiation therapy with the multileaf collimator (MLC) technique is presented. The application of the MLC technique requires an algorithm for the computation of the positions or velocities of leaves as a function of time such that the prescribed dose in the patient space is obtained. The conventional method is to first determine the intensity distribution in the treatment space by applying some inverse treatment techniques. Then an MLC control algorithm which generates the determined intensity distribution is required. In this paper an MLC control algorithm not requiring an intensity distribution as an intermediate step is expressed. The algorithm uses the MLC leaf positions and delivery times (in multiple static treatments) directly in inverse treatment planning. The method is implemented to multiple static treatments but a modification to dynamical MLC techniques is possible. The numerical test is based on the search for a feasible solution but also the optimization (object function) based approach is formulated. The related feasible problem consists of a high-dimensional system of algebraic (in-) equations. It is solved by an iterative row action projection method. The applied algorithm is well suited and computationally robust for high-dimensional feasible problems.},
   Keywords = {Radiotherapy
Linear algebra
Inverse problems
Algorithms
Mathematical models
Optical collimators},
   Year = {2000} }



@article{
vaidya90,
   Author = {Vaidya, P. M.},
   Title = {An Algorithm for Linear Programming which Requires {$O(((m + n)n^2 + (m+n)^{1.5}n)L)$} Arithmetic Operations},
   Journal = {Mathematical Programming},
   Volume = {47},
   Pages = {175-201},
      Year = {1990} }



@techreport{
2005078214,
   Author = {Voessner, Siegfried and O'Sullivan, Michael and Kausch, U.},
   Title = {Improving the Efficiency of Genetic Algorithms for Linearly Constrained Optimization},
   Institution = {Department of Engineering Science, University of Auckland},
      Year = {2003} }



@inproceedings{
mo_qw99,
   Author = {Voessner, Siegfried and O'Sullivan, Michael and Wegener, Joachim},
   Title = {Genetic Algorithm with Cluster Analysis for Software Testing},
   BookTitle = {12th International Software Quality Week 1999 Conference},
   Address= {San Jose, California, USA},
      Year = {1999} }



@techreport{
woe05,
   Author = {Walker, Cameron and O'Sullivan, Michael and Elangasinghe, Mihiriyani},
   Title = {Evaluation of Core-Edge Storage Area Network Designs using Simulation},
   Institution = {Department of Engineering Science, University of Auckland, New Zealand},
      Year = {2005} }



@article{
wmdo2009,
   Author = {Walker, C.G. and MacKenzie, M.L. and Donovan, C. and O'Sullivan, M.J.},
   Title = {SALSA - A Spatially Adaptive Smoothing Algorithm},
   Journal = {Journal of Computational and Graphical Statistics},
   Volume = {-},
   Pages = {-},
      Year = {2009} }



@article{
wo2010,
   Author = {Walker, Cameron G. and O’Sullivan, Michael J.},
   Title = {Core-Edge Design of Storage Area Networks - a Single-edge formulation with problem-specific cuts},
   Journal = {Computers and Operations Research},
   Volume = {37},
   Number = {5},
   Pages = {916-926},
      Year = {2010} }



@inproceedings{
wo2004,
   Author = {Walker, C.G. and O'Sullivan, M.J.},
   Title = {Experiments with the Equally-Weighted Bi-Criteria Knapsack Problem},
   BookTitle = {ORSNZ},
   Address= {Auckland, New Zealand},
   Publisher = {Proceedings of 39th Anual Conference},
   Pages = {198-207},
      Year = {2004} }



@misc{
coke,
   Author = {Walker, Cameron G. and O'Sullivan, Michael J.},
   Title = {The {C}oke {S}upply {C}hain {P}roblem},
   Note = {Case study within the online teaching TWiki (Department of Engineering Science, University of Auckland), \url{http://twiki.esc.auckland.ac.nz/twiki/bin/view/OpsRes/CokeSupplyChain}},
         Year = {2008} }



@inproceedings{
wog2005,
   Author = {Walker, C.G. and O'Sullivan, M.J. and Gordon, M.},
   Title = {Determining Knot Location for Regression Splines using Optimisation},
   BookTitle = {ORSNZ},
   Address= {Wellington, New Zealand},
   Publisher = {ORSNZ 40th Annual Conference Proceedings},
      Year = {2005} }



@techreport{
2007315473,
   Author = {Walker, C.G. and O'Sullivan, M.J. and Miller, E.},
   Title = {Using Optimization to improve Storage Area Network Design},
   Institution = {Department of Engineering Science, University of Auckland},
      Year = {2009} }



@article{
wot2007,
   Author = {Walker, C.G. and O'Sullivan, M.J. and Thompson, T.D.},
   Title = {A Mixed-Integer Approach to Core-Edge Design of Storage Area Networks},
   Journal = {Computers and Operations Research},
   Volume = {34},
   Number = {10},
   Pages = {2976-3000},
      Year = {2007} }



@misc{
SANSim,
   Author = {Wang, Chao-Yang and Zhou, Feng and Zhu, Yao-Long and Chong, Chong Tow and Hou, Bo and Xi, Wei-Ya},
   Title = {Simulation of Fibre Channel Storage Area Network Using SANSim},
   Month = {September},
         Year = {2003} }



@article{
ip:fast02,
   Author = {Ward, Julie and O'Sullivan, Michael and Shahoumian, Troy and Wilkes, John},
   Title = {Appia: automatic storage area network design},
   Journal = {Conference on File and Storage Technology (FAST'02)},
   Pages = {203-217},
      Year = {2002} }



@article{
hptech03,
   Author = {Ward, Julie and O'Sullivan, Michael and Shahoumian, Troy and Wilkes, John and Wu, Ren and Beyer, Dirk},
   Title = {Appia and the HP SAN Designer: automatic storage area network fabric design},
   Journal = {Hewlett-Packard Technical Conference 2003},
      Year = {2003} }



@article{
webb98,
   Author = {Webb, S.},
   Title = {Configuration options for intensity-modulated radiation therapy using multiple static fields shaped by a multileaf collimator. II: Constraints and limitations on 2D modulation},
   Journal = {Physics in Medicine and Biology},
   Volume = {43},
   Number = {6},
   Pages = {1481-1495},
      Year = {1998} }



@article{
w01,
   Author = {Webster, John},
   Title = {The overwhelming importance of storage},
   Journal = {Storage Networking World Online},
      Year = {2001} }



@inproceedings{
mo_es98,
   Author = {Wegner, Joachim and Voessner, Siegfried and O'Sullivan, Michael},
   Title = {Testing Temporal Correctness of Real Time Systems},
   BookTitle = {EuroSTAR 1998 Conference},
   Address= {Munich, Germany},
      Year = {1998} }



@inproceedings{
ceph,
   Author = {Weil, Sage and Brandt, Scott A. and Miller, Ethan L. and Long, Darrell D. E. and Maltzahn, Carlos},
   Title = {Ceph: A Scalable, High-Performance Distributed File System},
   BookTitle = {Proceedings of the 7th Conference on Operating Systems Design and Implementation (OSDI '06)},
      Year = {2006} }



@article{
wu00,
   Author = {Wu, Qiuwen and Mohan, Radhe},
   Title = {Algorithms and functionality of an intensity modulated radiotherapy optimization system},
   Journal = {Medical Physics},
   Volume = {27},
   Number = {4},
   Pages = {701-711},
   Keywords = {radiation therapy
dosimetry
optimisation
tumours
lung
brain
biological organs},
   Year = {2000} }



@article{
wu01,
   Author = {Wu, X. G. and Zhu, Y. P.},
   Title = {An optimization method for importance factors and beam weights based on genetic algorithms for radiotherapy treatment planning},
   Journal = {Physics in Medicine and Biology},
   Volume = {46},
   Number = {4},
   Pages = {1085-1099},
      Year = {2001} }



@article{
xia98,
   Author = {Xia, P. and Verhey, L. J.},
   Title = {Multileaf collimator leaf sequencing algorithm for intensity modulated beams with multiple static segments},
   Journal = {Medical Physics},
   Volume = {25},
   Number = {8},
   Pages = {1424-1434},
      Year = {1998} }



@article{
xiao03,
   Author = {Xiao, Y. and Michalski, D. and Galvin, J.M. and Censor, Y.},
   Title = {The Least-Intensity Feasible Solution for Aperture-Based Inverse Planning in Radiation Therapy},
   Journal = {Annals of Operations Research},
   Volume = {119},
   Number = {1-4},
   Pages = {183-203},
      Year = {2003} }



@article{
yu95,
   Author = {Yu, C. X. and Symons, M. J. and Du, M. N. and Martinez, A. A. and Wong, J. W.},
   Title = {A Method for Implementing Dynamic Photon-Beam Intensity Modulation Using Independent Jaws and a Multileaf Collimator},
   Journal = {Physics in Medicine and Biology},
   Volume = {40},
   Number = {5},
   Pages = {769-787},
      Year = {1995} }



@article{
yu95a,
   Author = {Yu, C. X. and Yan, D. and Du, M. N. and Zhou, S. and Verhey, L. J.},
   Title = {Optimization of leaf positions when shaping a radiation field with a multileaf collimator},
   Journal = {Physics in Medicine and Biology},
   Number = {2},
   Pages = {305-308},
   Abstract = {Computer-controlled multileaf collimators are receiving increasing acceptance for clinical use in radiation therapy due to their efficiency in shaping radiation fields. Because of the physical leaf width of the multileaf collimator, a smooth field contour prescribed by a physician is approximated by a staircase-shaped field boundary. The point of intersection with the prescribed field contour determines the error of the approximation and may affect the outcome of the treatment. This article provides analytically optimized solutions for leaf positioning based on two different geometric object functions.},
      Year = {1995} }




%@misc{
%pulp,
%   Author = {Mitchell, S. and Kean, A. and A.Mason and O'Sullivan, M. and Phillips, A.},
%   Title = {Optimization with PuLP},
%   Note = {http://www.coin-or.org/PuLP/},
%         Year = {2009} }





@ARTICLE{
coin_or,
   Author = {Lougee-Heimer, R.},
   Title = {The {Common Optimization Interface for Operations Research}},
   Journal = {IBM Journal of Research and Development},
   Volume = {47},
   Number = {1},
   Pages = {57-66},
      Year = {2003} }

@ELECTRONIC{ pulp,
	TITLE  = "{PuLP}",
	URL    = "http://www.coin-or.org/PuLP/",
	AUTHOR = "Mitchell, S. A. and Roy, J.S.",
}

@MANUAL{ python,
	title = "Python Reference Manual",
	author = "Guido {van Rossum}",
	organization = "CWI Report",
	edition = "{CS-R9525}",
	month = "May",
	year = "1995",
	url = "http://www.cwi.nl/ftp/CWIreports/AA/CS-R9525.ps.Z"
}

@ARTICLE{
agg_mir2001,
   Author = {Marchand, H. and Wolsey, L. A.},
   Title = {Aggregation and Mixed Integer Rounding to Solve {MIP}s},
   Journal = {Oper. Res.},
   Volume = {49},
   Number = {3},
   Pages = {363-371},
   Note = {769096},
      Year = {2001} }
      
@INCOLLECTION{
decomp04,
   Author = {Ralphs, T. K. and Galati, M. V.},
   Title = {Decomposition in Integer Programming},
   BookTitle = {Integer Programming: Theory and Practice},
   Editor = {Karlof, J},
   Publisher = {CRC Press},
      Year = {2005} }
      
 
@ARTICLE{
DWDecomp00,
 author = {Vanderbeck, Fran\c{c}ois},
 title = {On {Dantzig-Wolfe} Decomposition in Integer Programming and ways to Perform Branching in a Branch-and-Price Algorithm},
 journal = {Oper. Res.},
 volume = {48},
 issue = {1},
 year = {2000},
 pages = {111--128},
}
