Publications using Octave

Articles

Pre-prints

• Preprint arXiv:1108.3206v2 Modeling and frequency domain analysis of nonlinear compliant joints for a passive dynamic swimmer
• Technical Report UBLCS-2012-02 Queueing Networks Analysis with the qnetworks Toolbox
• Preprint arXiv:1109.0397 Auction-Based Resource Allocation in Digital Ecosystems (Scripts used in the paper)
• Technical Report UBLCS-2011-04 Dynamic Power Management for QoS-Aware Applications (Scripts and data files used in the paper)
• Preprint arXiv:1104.5392 A Framework for QoS-aware Execution of Workflows over the Cloud, to appear in proc. CLOSER 2012 (Script used in the paper)
• Technical Report UBLCS-2010-12 Dynamic Scalability for Next Generation Gaming Infrastructures, to appear in ACM Computers in Entertainment (Script used in the paper)

2012

• GNU Octave and reproducible research GNU Octave and reproducible research
• Comput. Methods Appl. Mech. Engrg., 2012, Multiscale Modeling and Simulation of Organic Solar Cells (Also available at arXiv)
• 12th Int. Conf. on Adaptive Behaviour (2012). Synthesis and Adaptation of Effective Motor Synergies for the Solution of Reaching Tasks. (package used for this publication)
• Communications in Computational Physics System reduction using an LQR-inspired version of Optimal Replacement Variables
• Journal of Computational and Applied Mathematics A Test Set for stiff Initial Value Problem Solvers in the open source software R: Package deTestSet
• Biophysical Journal Locomotion control of Caenorhabditis elegans through confinement
• Behavior Research Methods OpenSesame: An open-source, graphical experiment builder for the social sciences
• Journal of Neural Engineering Stimulus specificity of a steady-state visual-evoked potential-based brain-computer interface
• Nuclear Fusion Detection of geodesic acoustic mode oscillations, using multiple signal classification analysis of Doppler backscattering signal on Tore Supra
• Simulation Modelling Practice and Theory Development and implementation of hydro turbine and governor models in a free and open source software package
• Journal of Biomechanical Engineering Syrinx fluid transport: Modeling pressure-wave-induced flux across the spinal pial membrane
• Biochemistry Testing the nearest neighbor model for canonical RNA base pairs: Revision of GU parameters
• Journal of Chemical Theory and Computation Construction of the free energy landscape of peptide aggregation from molecular dynamics simulations
• Modern Physics Letters B Dynamics on multilayered hyperbranched fractals through continuous time random walks
• IEEE Nuclear Science Symposium Conference Record Dose-free monitoring of radiotherapy treatments with scattered photons: First experimental results at a 6-MV Linac
• Journal of Physics: Conference Series Integration of a neuroimaging processing pipeline into a pan-canadian computing grid
• Journal of Nanomaterials Design and construction of a one-dimensional DNA track for an artificial molecular motor
• Computing in Science and Engineering Applications of computational science: Data-intensive computing for student projects
• Computer Physics Communications Numerical tools to validate stationary points of so (8) -gauged N = 8 D = 4 supergravity
• Advances in OptoElectronics Fundamental issues in manufacturing photovoltaic modules beyond the current generation of materials
• IEEE Transactions on Fuzzy Systems Zadehs extension principle for continuous functions of non-interactive variables: A parallel optimization approach
• Methods in Enzymology Open source tools for fluorescent imaging
• Computer Physics Communications An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells

2011

• Phys. Rev. E 83, 066707 (2011), Exploiting the passive dynamics of a compliant leg to develop gait transitions
• Journal of Fluid Mechanics, volume 681, (2011), pp. 622-638. Perturbations of the coupled Jeffery-Stokes equations.
• International Journal for Numerical Methods in Fluids, 65(11-12):1407–1422, 2011 Isogeometric analysis: Stable elements for the 2d stokes equation.
• Numerical Algorithms, 56(1):107–127, January 2011, A parameter robust Petrov-Galerkin scheme for advection-diffusion-reaction equations.
• Advances in Engineering Software, 42(12):1020–1034, 2011, Geopdes: A research tool for IsoGeometric Analysis of PDEs. (Octave package used discussed in this publication)
• Int. J. of Performability Engineering, 7(5):479–492, 2011 PARSY: Performance-Aware Reconfiguration of Software Systems
• IEEE Trans. Antennas and Propagation, 59(6):2047-2057, 2011, Demonstration of a Dual-Polarized Phased-Array Feed.

• IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum p2 Matlab: Productive parallel matlab for the exascale
• Physics of Fluids Relaminarisation of Re τ = 100 channel flow with globally stabilising linear feedback control
• Journal of Machine Learning Research Lightweight implementations of probabilistic programming languages via transformational compilation
• Proceedings of the ASME Design Engineering Technical Conference uBlasCL: Architecture agnostic massively parallel Linear Algebra system
• SEKE 2011 - Proceedings of the 23rd International Conference on Software Engineering and Knowledge Engineering [ SC-xScript: An embedded script language for scientific computation in embedded systems]
• Proceedings - 2011 IEEE Electronics, Robotics and Automotive Mechanics Conference, CERMA 2011 Analysis of AVI files for mice behavior experiments in the Morris water maze
• Earthquake and Structures Reconstruction of missing response data for identification of higher modes
• Advances in Engineering Software GeoPDEs: A research tool for Isogeometric Analysis of PDEs
• 2011 IEEE International Conference on Robotics and Biomimetics, ROBIO 2011 From walking to running a natural transition in the SLIP model using the hopping gait
• Applied Bionics and Biomechanics Teletactile system based on mechanical properties estimation
• Proceedings of the National Academy of Sciences of the United States of America Mean-field modeling of thalamocortical dynamics and a model-driven approach to EEG analysis
• Nucleic Acids Research A quantitative model of nucleosome dynamics
• ACM Transactions on Graphics Steady affine motions and morphs
• Wiener Medizinische Wochenschrift Role of optimization criterion in static asymmetric analysis of lumbar spine load
• Journal of Composite Materials Micro-mechanical prediction of UD laminates behavior under combined compression up to failure: Influence of matrix degradation
• Proceedings - 2011 IEEE International Symposium on Assembly and Manufacturing, ISAM 2011 Importance sampling based on adaptive principal component analysis
• International Journal for Numerical Methods in Engineering RK-Slim: Embedded Runge-Kutta without the excess baggage
• Journal of Neuroscience Methods Calcium signals: Analysis in time and frequency domains
• IFIP Advances in Information and Communication Technology Architecture of a Pan-European framework for integrated soil water erosion assessment
• Proceedings - Annual Workshop on Interaction between Compilers and Computer Architectures, INTERACT MATLAB parallelization through scalarization
• 2011 Promotion and Innovation with New Technologies in Engineering Education, FINTDI 2011, Conference Proceedings A review of teaching power system harmonics
• Physical Review E - Statistical, Nonlinear, and Soft Matter Physics Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals
• Communications in Computer and Information Science Analysis of time measurements in network systems using decomposition on subprocesses
• Proceedings of the ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI) Automatic compilation of MATLAB programs for synergistic execution on heterogeneous processors
• Journal of Aerospace Engineering Experiments and cohesive zone model parameters for T650/AFR-PE-4/FM680-1 at high temperatures
• Proceedings of the IEEE Enabling accurate cross-layer PHY/MAC/NET simulation studies of vehicular communication networks
• Journal of Mathematics and Music A few more words about James Tenney: Dissonant counterpoint and statistical feedback
• Applied Optics On the importance of path for phase unwrapping in synthetic aperture radar interferometry
• Physical Review E - Statistical, Nonlinear, and Soft Matter Physics Exploiting the passive dynamics of a compliant leg to develop gait transitions
• BMC Systems Biology Automated Bayesian model development for frequency detection in biological time series
• Journal of Wind Engineering and Industrial Aerodynamics Fractional spectral moments for digital simulation of multivariate wind velocity fields
• Advances in Applied Probability Approximation of bounds on mixed-level orthogonal arrays
• IEEE Transactions on Antennas and Propagation Demonstration of a dual-polarized phased-array feed
• Electrochimica Acta Reducing error and measurement time in impedance spectroscopy using model based optimal experimental design
• Biomacromolecules Infrared linear dichroism spectroscopy on amyloid fibrils aligned by molecular combing
• Chemical Science Conformational states of nucleic acid-peptide complexes monitored by acoustic wave propagation and molecular dynamics simulation
• Journal of the Acoustical Society of America Estimating the control parameters of an articulatory model from electromagnetic articulograph data
• Fuzzy Sets and Systems Decision tree based fuzzy classifier of 1H magnetic resonance spectra from cerebrospinal fluid samples
• Computational Management Science Shape-based scenario generation using copulas
• 2011 4th IFIP International Conference on New Technologies, Mobility and Security, NTMS 2011 - Proceedings Adaptive fuzzy-MAC for power reduction in Wireless Sensor Networks
• Communications in Computational Physics Reduction of linear systems of ODEs with optimal replacement variables
• Optics Express Longitudinal mode multistability in Ring and Fabry-Pérot lasers: The effect of Spatial Hole Burning
• Journal of Chemical Physics Photoelectron imaging of several 5d and 6p Rydberg states Xe 2 and improving the Xe 2 + I(12g) potential
• Chemical Physics Letters Analysis of motion features for molecular dynamics simulation of proteins
• Journal of Physical Chemistry B In silico predictions of the temperature-dependent viscosities and electrical conductivities of functionalized and nonfunctionalized ionic liquids
• Journal of Molecular Biology Probing designability via a generalized model of helical bundle geometry

2010

• Wireless Networks, Vol. 16, No. 2, pp. 355-365, February 2010, Allocating data for broadcasting over wireless channels subject to transmission errors
• Int. J. Numer. Anal. Model., 7(4):444–461, 2010, Interior layers in a reaction–diffusion equation with a discontinuous diffusion coefficient
• Comput. Methods Appl. Mech. Engrg., 199:1722–1732, 2010, Analytical and numerical study of photocurrent transients in organic polymer solar cells (Octave package used to perform the computations)
• Proc. European Performance Engineering Workshop (EPEW), Bertinoro, Italy, sep 2010, Performance-Aware Reconfiguration of Software Systems (Octave script used to perform the computations and produce the plots)
• Proc. Analythical Stochastic Modelling Techniques and Applications (ASMTA'10), Cardiff, UK, jun 2010, The qnetworks Toolbox: A Software Package for Queueing Networks Analysis
• 5th Int. Conf. on Comparing Design in Nature with Science and Engineering (2010). Magneto-mechanical actuation model for fin-based locomotionHTML.

• Algebraic and Geometric Topology Symmetric homology of algebras
• ICFC 2010 ICNC 2010 - Proceedings of the International Conference on Fuzzy Computation and International Conference on Neural Computation [ Development of a fuzzy calculator for continuous functions of non-interactive fuzzy variables]
• Journal of Computational and Applied Mathematics Modeling of an insurance system and its large deviations analysis
• 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC'10 Real-time Experiment Interface for biological control applications
• INFORMS Journal on Computing A heuristic for nonlinear global optimization
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Probabilistic semantics and program analysis
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Performance aware reconfiguration of software systems
• Biotechnology, Agronomy and Society and Environment Comparison of two drying models applied to corn drying in fluidized bed [Comparaison d'un modèle empirique et d'un modèle physique de séchage de grains de maïs en lit fluidisé]
• Spectroscopy Letters Quantitative infrared spectroscopy in the undergraduate laboratory via multivariate mixture analysis of a simulated analgesic
• European Radiology Longitudinal study of a mouse model of chronic pulmonary inflammation using breath hold gated micro-CT
• Chemical Physics A classical Master equation approach to modeling an artificial protein motor
• ACM Transactions on Mathematical Software Increasing the reliability of adaptive quadrature using explicit interpolants
• Computer Applications in Engineering Education Teaching differential equations in different environments: A first approach
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) The qnetworks toolbox: A software package for queueing networks analysis
• Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences Stochastically forced water waves in a circular basin
• Performance Evaluation Review RSIO: Automatic user interaction detection and scheduling
• Journal of High Energy Physics Quasinormal modes of massive charged avor branes
• Langmuir Viscoelastic modeling with interfacial slip of a protein monolayer electrode-adsorbed on an acoustic wave biosensor
• Journal of Biological Chemistry Biochemical basis of the interaction between cystic fibrosis transmembrane conductance regulator and immunoglobulin-like repeats of filamin
• Computers and Chemical Engineering Data smoothing and numerical differentiation by a regularization method
• Physical Review A - Atomic, Molecular, and Optical Physics Resonant trapping in the transport of a matter-wave soliton through a quantum well
• High Pressure Research Raman spectroscopy of triolein under high pressures
• Journal of Physics A: Mathematical and Theoretical Relaxation dynamics of perturbed regular hyperbranched fractals
• Bulletin of the Polish Academy of Sciences: Technical Sciences Extending scientific computing system with structural quantum programming capabilities
• Communications in Computational Physics Simulation of spherulite growth using a comprehensive approach to modeling the first-order isotropic/smectic-a mesophase transition
• Computational Statistics and Data Analysis Grapham: Graphical models with adaptive random walk Metropolis algorithms
• Autonomous Robots HERB: A home exploring robotic butler
• International Journal of Electrical Engineering Education Experience with PSAT (Power System Analysis Toolbox) as free and open-source software for power system education and research

2009

• Proceedings of APSIS, Charleston, SC (US), June 2009, Accuracy limits of in-room localisation using RSSI
• J. Comput. Phys., 228:770–1789, 2009, Quantum corrected drift–diffusion models: Solution fixed point map and finite element approximation
• Proceedings of BAIL, Limerick, 2008, volume 69 of LNCSE, 2009, A patched mesh method for singularly perturbed reaction-diffusion equations
• Proceedings of BAIL, Limerick, 2008, volume 69 of LNCSE, 2009, Singularly perturbed reaction-diffusion problem with a boundary turning point
• Proceedings of the 2008 ECMI conference, London, volume 15 of Mathematics in Industry, 2009, Patches of finite elements for singularly-perturbed diffusion reaction equations with discontinuous coefficients
• Journal of Physical Chemistry B Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis
• IEEE Transactions on Semiconductor Manufacturing A novel approach to analyze and model feature size effects in CMP
• Performance Evaluation System-theoretical algorithmic solution to waiting times in semi-Markov queues
• Computer Languages, Systems and Structures jLab: Integrating a scripting interpreter with Java technology for flexible and efficient scientific computation
• Journal of Geophysical Research B: Solid Earth NW Australian intraplate seismicity and stress regime
• Journal of Chemometrics A comparison of nine PLS1 algorithms
• Measurement Science and Technology Determining membrane permeability of giant phospholipid vesicles from a series of videomicroscopy images
• Mathematical Methods of Statistics A Bayesian approach to the estimation of maps between Riemannian manifolds. II: Examples
• Physical Review Special Topics - Accelerators and Beams Tracking studies of the Compact Linear Collider collimation system
• Biological Cybernetics Predictive feedback in human simulated pendulum balancing
• Bulletin of the Russian Academy of Sciences: Physics Regions of excessive flux of PeV cosmic rays
• Computing in Science and Engineering Scientific scripting for the java platform with jlab
• International Journal of Control Constrained intermittent model predictive control
• Journal of Chromatography A Suppressing the charged coupled device noise in univariate thin-layer videoscans: A comparison of several algorithms
• ACM Transactions on Mathematical Software Algorithm 892: DISPMODULE, a Fortran 95 module for pretty-printing matrices
• Stochastic Processes and their Applications Importance sampling for a Markov modulated queuing network

2008

• Proceedings of the 79th GAMM meeting, volume 8 of Proc. Appl. Math. Mech. PAMM, pages 10061 – 10064, 2008, Dynamical iteration schemes for multiscale simulation in nanoelectronics
• Proceedings of the 79th GAMM meeting, volume 8 of Proc. Appl. Math. Mech. (PAMM), pages 10065–10068, 2008, Dynamical iteration schemes for coupled simulation in nanoelectronics
• Journal of Biological Chemistry Monitoring light-induced structural changes of channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy
• Journal of Applied Physics Electro-optical modeling of bulk heterojunction solar cells
• Clinical and Experimental Ophthalmology Fourier analysis of digital retinal images in estimation of cataract severity
• Numerische Mathematik Approximating optimization problems over convex functions
• Medical Engineering and Physics Cervical spine biomechanics following implantation of a disc prosthesis
• IEEE Power and Energy Society 2008 General Meeting: Conversion and Delivery of Electrical Energy in the 21st Century, PES Towards a common model for studying critical infrastructure interdependencies
• 3rd International Symposium on Wireless Pervasive Computing, ISWPC 2008, Proceedings A novel low-complexity algorithm for linear MMSE MIMO receivers
• Studies in Computational Intelligence Visualization and interactive exploration of large, multidimensional data sets
• Studies in Computational Intelligence A versatile surrogate-assisted memetic algorithm for optimization of computationally expensive functions and its engineering applications
• IEEE Transactions on Education An open source power system virtual laboratory: The PSAT case and experience
• Applied Mechanics Reviews A review of H∞ robust control of piezoelectric smart structures
• IEEE Transactions on Biomedical Engineering Image analysis for microelectronic retinal prosthesis
• Composite Structures Finite element modeling and optimization of load transfer in multi-fastener joints using structural elements

2007

• Water Science and Technology Kinetics of autothermal thermophilic aerobic digestion - Application and extension of Activated Sludge Model No 1 at thermophilic temperatures
• Western North American Naturalist Moistened seeds increase rodent trap success
• EUROMICRO 2007 - Proceedings of the 33rd EUROMICRO Conference on Software Engineering and Advanced Applications, SEAA 2007 GridIJ - A dynamic grid service architecture for scientific image processing
• IEEE International Conference on Intelligent Robots and Systems Kernel-based visual servoing
• 2007 IEEE Power Engineering Society General Meeting, PES Application of the PSAT, an open source software, for educational and research purposes
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Abstract interpretation for worst and average case analysis
• Proceedings - IEEE International Conference on Cluster Computing, ICCC Performance analysis of a user-level memory server
• Proceedings of the Institution of Mechanical Engineers. Part I: Journal of Systems and Control Engineering An adaptive learning algorithm for controlling a two-degree-of-freedom serial ball-and-socket actuator
• Lecture Notes in Control and Information Sciences A nonlinear model predictive control framework as free software: Outlook and progress report
• Collection of Technical Papers - 2007 AIAA InfoTech at Aerospace Conference Airfoil shape optimization by minimization of an expensive and discontinuous black-box function
• Periodica Polytechnica: Chemical Engineering Connection between oxygen uptake rate and carbon dioxide evolution rate in aerobic thermophilic sludge digestion
• Journal of Fluid Mechanics Instability of the buoyancy layer on an evenly heated vertical wall
• Electronic Notes in Theoretical Computer Science On Probabilistic Techniques for Data Flow Analysis
• Collection of Technical Papers - AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference T650/AFR-PE-4/FM680-1 mode I critical energy release rate at high temperatures: Experiments and numerical models
• Phytochemistry Design of substrate label for steady state flux measurements in plant systems using the metabolic network of Brassica napus embryos
• IET Software Scientific programming with Java classes supported with a scripting interpreter
• Genetics Adaptation of a quantitative trait to a moving optimum
• Water Environment Research Application of activated sludge model no. 3 for the modeling of organic matter biodegradation at thermophilic temperatures
• Computational Statistics Excel :: COM :: R
• IEEE Transactions on Power Delivery Effects of sampling rate and ADC width on the accuracy of amplitude and phase measurements in power-quality monitoring
• Bulletin of the Russian Academy of Sciences: Physics Search for sources of cosmic rays in the region of the knee: Part II

2006

• Chemometrics and Intelligent Laboratory Systems How octave can replace Matlab in chemometrics
• 41st International Universities Power Engineering Conference, UPEC 2006, Conference Procedings System requirements of real time continuous data acquisition for power quality monitoring
• e-Science 2006 - Second IEEE International Conference on e-Science and Grid Computing Grid services toolkit for process data processing
• Chemometrics and Intelligent Laboratory Systems Superresolution of hyperspectral images
• Computer Applications in Engineering Education A Web-based tool for control engineering teaching
• ANZIAM Journal Drainage after total knee replacement
• Protein Engineering, Design and Selection Consensus guided mutagenesis of Renilla luciferase yields enhanced stability and light output
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) SCE toolboxes for the development of high-level parallel applications
• Space Science Reviews End-to-end modeling of the solar terrestrial system
• Publications of the Astronomical Society of Japan [ Milliarcsecond-scale spectral properties and jet motions in M 87]
• Nucleic Acids Research Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I
• Physiological Measurement Uses and abuses of EIDORS: An extensible software base for EIT
• International Journal for Numerical and Analytical Methods in Geomechanics Review of validation of the discontinuous deformation analysis (DDA) method
• Physical Review A - Atomic, Molecular, and Optical Physics Maximizing nearest-neighbor entanglement in finitely correlated qubit chains
• Transportation Science Solving noisy, large-scale fixed-point problems and systems of nonlinear equations

2005

• Collection of Technical Papers - AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference Comprehensive rotorcraft analysis: Past, present, and future
• Journal of Geophysical Research A: Space Physics Analysis and visualization of space science model output and data with CISM-DX
• Applied Catalysis A: General Simplified kinetic models of methanol oxidation on silver
• Automatica Data compression for estimation of the physical parameters of stable and unstable linear systems
• IEEE Transactions on Power Systems An open source power system analysis toolbox
• BMC Bioinformatics Computing expectation values for RNA motifs using discrete convolutions
• IEEE Transactions on Signal Processing Design of discrete coefficient FIR filters by a fast entropy-directed deterministic annealing algorithm

2004

• Proceedings of the International Conference on Automation Technology for Off-road Equipment, ATOE 2004 [ RTK-GPS based autonomous crawler wagon control]
• Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science) Data analysis of microarrays using SciCraft
• Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) Self-adaptive scouting-autonomous experimentation for systems biology
• Journal of Engineering Mechanics Time integration in discontinuous deformation analysis

2003

• Physical Review Special Topics - Accelerators and Beams Calibration of the Fermilab Booster ionization profile monitor
• SAR and QSAR in Environmental Research Zherlock: An open source data analysis software

2002

• Journal of Magnetic Resonance Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR

Books

• GNU Octave Manual Version 3, ISBN 0-9546120-6-X
• Scientific Computing with MATLAB and Octave, ISBN 978-3-642-12429-7
• Numerical Methods for the Life Scientist, ISBN 978-3-642-20819-5
• GNU Octave Beginners Guide, ISBN 1849513325