Tuesday, August 29, 2006

ADCPtools - acoustic doppler current profiler data processing
AFDesign - designing analog and digital filters
AIRES - automatic integration of reusable embedded software
Air-Sea - air-sea flux estimates in oceanography
Animation - developing scientific animations
ARfit - estimation of parameters and eigenmodes of multivariate autoregressive methods
ARMASA - power spectrum estimation
AR-Toolkit - computer vision tracking
Auditory - auditory models
b4m - interval arithmetic
Bayes Net - inference and learning for directed graphical models
Binaural Modeling - calculating binaural cross-correlograms of sound
Bode Step - design of control systems with maximized feedback
Bootstrap - for resampling, hypothesis testing and confidence interval estimation
BrainStorm - MEG and EEG data visualization and processing
BSTEX - equation viewer
CALFEM - interactive program for teaching the finite element method
Calibr - for calibrating CCD cameras
Camera Calibration
Captain - non-stationary time series analysis and forecasting
CHMMBOX - for coupled hidden Markov modeling using maximum likelihood EM
Classification - supervised and unsupervised classification algorithms
CLOSID
Cluster - for analysis of Gaussian mixture models for data set clustering
Clustering - cluster analysis
ClusterPack - cluster analysis
COLEA - speech analysis
CompEcon - solving problems in economics and finance
Complex - for estimating temporal and spatial signal complexities
Computational Statistics
Coral - seismic waveform analysis
DACE - kriging approximations to computer models
DAIHM - data assimilation in hydrological and hydrodynamic models
Data Visualization
DBT - radar array processing
DDE-BIFTOOL - bifurcation analysis of delay differential equations
Denoise - for removing noise from signals
DiffMan - solving differential equations on manifolds
Dimensional Analysis -
DIPimage - scientific image processing
Direct - Laplace transform inversion via the direct integration method
DirectSD - analysis and design of computer controlled systems with process-oriented models
DMsuite - differentiation matrix suite
DMTTEQ - design and test time domain equalizer design methods
DrawFilt - drawing digital and analog filters
DSFWAV - spline interpolation with Dean wave solutions
DWT - discrete wavelet transforms
EasyKrig
Econometrics
EEGLAB
EigTool - graphical tool for nonsymmetric eigenproblems
EMSC - separating light scattering and absorbance by extended multiplicative signal correction
Engineering Vibration
FastICA - fixed-point algorithm for ICA and projection pursuit
FDC - flight dynamics and control
FDtools - fractional delay filter design
FlexICA - for independent components analysis
FMBPC - fuzzy model-based predictive control
ForWaRD - Fourier-wavelet regularized deconvolution
FracLab - fractal analysis for signal processing
FSBOX - stepwise forward and backward selection of features using linear regression
GABLE - geometric algebra tutorial
GAOT - genetic algorithm optimization
Garch - estimating and diagnosing heteroskedasticity in time series models
GCE Data - managing, analyzing and displaying data and metadata stored using the GCE data structure specification
GCSV - growing cell structure visualization
GEMANOVA - fitting multilinear ANOVA models
Genetic Algorithm
Geodetic - geodetic calculations
GHSOM - growing hierarchical self-organizing map
glmlab - general linear models
GPIB - wrapper for GPIB library from National Instrument
GTM - generative topographic mapping, a model for density modeling and data visualization
GVF - gradient vector flow for finding 3-D object boundaries
HFRadarmap - converts HF radar data from radial current vectors to total vectors
HFRC - importing, processing and manipulating HF radar data
Hilbert - Hilbert transform by the rational eigenfunction expansion method
HMM - hidden Markov models
HMMBOX - for hidden Markov modeling using maximum likelihood EM
HUTear - auditory modeling
ICALAB - signal and image processing using ICA and higher order statistics
Imputation - analysis of incomplete datasets
IPEM - perception based musical analysis
JMatLink - Matlab Java classes
Kalman - Bayesian Kalman filter
Kalman Filter - filtering, smoothing and parameter estimation (using EM) for linear dynamical systems
KALMTOOL - state estimation of nonlinear systems
Kautz - Kautz filter design
Kriging
LDestimate - estimation of scaling exponents
LDPC - low density parity check codes
LISQ - wavelet lifting scheme on quincunx grids
LKER - Laguerre kernel estimation tool
LMAM-OLMAM - Levenberg Marquardt with Adaptive Momentum algorithm for training feedforward neural networks
Low-Field NMR - for exponential fitting, phase correction of quadrature data and slicing
LPSVM - Newton method for LP support vector machine for machine learning problems
LSDPTOOL - robust control system design using the loop shaping design procedure
LS-SVMlab
LSVM - Lagrangian support vector machine for machine learning problems
Lyngby - functional neuroimaging
MARBOX - for multivariate autogressive modeling and cross-spectral estimation
MatArray - analysis of microarray data
Matrix Computation - constructing test matrices, computing matrix factorizations, visualizing matrices, and direct search optimization
MCAT - Monte Carlo analysis
MDP - Markov decision processes
MESHPART - graph and mesh partioning methods
MILES - maximum likelihood fitting using ordinary least squares algorithms
MIMO - multidimensional code synthesis
Missing - functions for handling missing data values
M_Map - geographic mapping tools
MODCONS - multi-objective control system design
MOEA - multi-objective evolutionary algorithms
MS - estimation of multiscaling exponents
Multiblock - analysis and regression on several data blocks simultaneously
Multiscale Shape Analysis
Music Analysis - feature extraction from raw audio signals for content-based music retrieval
MWM - multifractal wavelet model
NetCDF
Netlab - neural network algorithms
NiDAQ - data acquisition using the NiDAQ library
NEDM - nonlinear economic dynamic models
NMM - numerical methods in Matlab text
NNCTRL - design and simulation of control systems based on neural networks
NNSYSID - neural net based identification of nonlinear dynamic systems
NSVM - newton support vector machine for solving machine learning problems
NURBS - non-uniform rational B-splines
N-way - analysis of multiway data with multilinear models
OpenFEM - finite element development
PCNN - pulse coupled neural networks
Peruna - signal processing and analysis
PhiVis - probabilistic hierarchical interactive visualization, i.e. functions for visual analysis of multivariate continuous data
Planar Manipulator - simulation of n-DOF planar manipulators
PRTools - pattern recognition
psignifit - testing hyptheses about psychometric functions
PSVM - proximal support vector machine for solving machine learning problems
Psychophysics - vision research
PyrTools - multi-scale image processing
RBF - radial basis function neural networks
RBN - simulation of synchronous and asynchronous random boolean networks
ReBEL - sigma-point Kalman filters
Regression - basic multivariate data analysis and regression
Regularization Tools
Regularization Tools XP
Restore Tools
Robot - robotics functions, e.g. kinematics, dynamics and trajectory generation
Robust Calibration - robust calibration in stats
RRMT - rainfall-runoff modelling
SAM - structure and motion
Schwarz-Christoffel - computation of conformal maps to polygonally bounded regions
SDH - smoothed data histogram
SeaGrid - orthogonal grid maker
SEA-MAT - oceanographic analysis
SLS - sparse least squares
SolvOpt - solver for local optimization problems
SOM - self-organizing map
SOSTOOLS - solving sums of squares (SOS) optimization problems
Spatial and Geometric Analysis
Spatial Regression
Spatial Statistics
Spectral Methods
SPM - statistical parametric mapping
SSVM - smooth support vector machine for solving machine learning problems
STATBAG - for linear regression, feature selection, generation of data, and significance testing
StatBox - statistical routines
Statistical Pattern Recognition - pattern recognition methods
Stixbox - statistics
SVM - implements support vector machines
SVM Classifier
Symbolic Robot Dynamics
TEMPLAR - wavelet-based template learning and pattern classification
TextClust - model-based document clustering
TextureSynth - analyzing and synthesizing visual textures
TfMin - continous 3-D minimum time orbit transfer around Earth
Time-Frequency - analyzing non-stationary signals using time-frequency distributions
Tree-Ring - tasks in tree-ring analysis
TSA - uni- and multivariate, stationary and non-stationary time series analysis
TSTOOL - nonlinear time series analysis
T_Tide - harmonic analysis of tides
UTVtools - computing and modifying rank-revealing URV and UTV decompositions
Uvi_Wave - wavelet analysis
varimax - orthogonal rotation of EOFs
VBHMM - variation Bayesian hidden Markov models
VBMFA - variational Bayesian mixtures of factor analyzers
VMT - VRML Molecule Toolbox, for animating results from molecular dynamics experiments
VOICEBOX
VRMLplot - generates interactive VRML 2.0 graphs and animations
VSVtools - computing and modifying symmetric rank-revealing decompositions
WAFO - wave analysis for fatique and oceanography
WarpTB - frequency-warped signal processing
WAVEKIT - wavelet analysis
WaveLab - wavelet analysis
Weeks - Laplace transform inversion via the Weeks method
WetCDF - NetCDF interface
WHMT - wavelet-domain hidden Markov tree models
WInHD - Wavelet-based inverse halftoning via deconvolution
WSCT - weighted sequences clustering toolkit
XMLTree - XML parser
YAADA - analyze single particle mass spectrum data
ZMAP - quantitative seismicity analysis

Membrane Simulation: Cell Division

Evolution of cell population in a lymph node section

Evolution of lattice structure (Lymph node section). Pink cells are Th2, light blue are Th1, light red are naïve T cells, dark red are Th0, green represents naïve B cells with a few activated ones, dark blue colour is for macrophages. The surface represented is 1,7mm x 1,7mm master's thesis work. Keywords: immunology, system biology, arthritis, collagen induced arthritis, computer models, simulations. lymphocyte, T cell, B cell, agent based model, individual based model. Nicolas Rapin / medical inflammation research Lund 26 sec - Jun 2, 2005 membres.lycos.fr

Drosophilia

Recent advances in microscopy and in fluorescence labeling of proteins allow the observation of complex biological processes in living organisms. This movie shows the early stages of embryonic development of a fruit fly egg, which is half a millimeter in size. In the first part of the movie, the observation of fluorescently labeled histones (proteins that help packaging the chromosomes into a compact nucleoprotein structure in the cell) reveals the dynamics of the mitotic divisions of the nuclei that occur in the egg during the first two hours of development. Following the synchronous nuclear divisions, cellular membranes form and cell movements initiate a process called gastrulation, during which cells invaginate in the embryo to form tissue layers and organs following a genetically determined developmental program. Early steps of gastrulation are shown in the second part of the movie through fluorescence labeling of membrane proteins. As suggested in the movie by the biophysicist writing down differential reaction-diffusion equations on a blackboard, the ability to observe these kinds of processes at the molecular level and in real time has opened new venues in modern biology, by applying tools from mathematics and physics to understand complex biological processes in a quantitative manner. Jean-Baptiste Boule, Matthieu Coppey, and Thomas G 52 sec - May 13, 2006 www.princeton.edu