Curator Dashboard

Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

A software package for numerical computation providing a powerful computing environment for engineering and scientific applications. It includes hundreds of mathematical functions and has a high level programming language allowing access to advanced data structures, 2D and 3D graphical functions.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

A neural simulator which models integrate-and-fire neurons with conductance-based synapses. NCS supports simulations for larger models and also supports real-time neurorobotics applications. Two versions of NCS are available: NCS 5, which is based on CPU cluster; and NCS 6, a multi-box, multi-GPU version. NCS 5 models integrate-and-fire neurons with conductance-based synapses using two clusters: four SUN 4600 machines and 208 Opteron cores. NCS 6 is a neural simulator for heterogeneous clusters of both CPUs and GPUS.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

Software tool for simulating heterogeneous networks composed of different model neurons and synapses. CSIM simulates networks containing up to a few thousand neurons and up to the order of 1.000.000 synapses. It is capable of supporting different levels of modeling and has an object oriented design. A user manual is available on the site.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

Software toolbox able to perform electrophysiological experiments using simple stimulation protocols and more complex paradigms, such as dynamic clamp or hybrid networks.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

A video tracking system designed for high-throughput behavioral experiments. LimeLight can track up to 4 arenas at once and can collect images at up to 30 frames per second for one animal or up to 8 frames per second when tracking 4 arenas at once. The tracking system has 2 different hardware configurations: the 1-camera system can be used to record 1 to 4 animals at once, while for multiple animals, each one is placed in a separate arena in one quadrant of the image. The software contains productivity features such as flexible arena setup, user-defined behavior scoring, stimulus control, and various analytical functions for quantifying behavior. The program is designed for experiments such as Open Field, Plus Maze, Radial Arm Maze, Zero Maze, Novel Object Recognition, Conditioned Place Preference, and Barnes Maze.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A software tool that combines biomechanical simulation and biologically realistic neural networks to create realistic models of, and perform tests on, biomechanical workings. AnimatLab was primarily designed to model and test the operation of neural circuits that might produce behavior patterns observed in an intact animal. Users can create an animalistic or robotic body and place it in a virtual environment with physics that are accurate and realistic. Users can then design a nervous system that controls the behavior of the body within the physically realistic environment. Various models for different types of actions, builds, and movements are available.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

3D modeling, animation, and rendering software which allows users to create custom tools and share design projects. 3ds Max contains various tools and templates for rendering and and editing, including tools for graph construction, project collaboration, and complex topography creation.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

StatSoft's flagship product line is the STATISTICA suite of analytics software products and solutions. STATISTICA provides the most comprehensive array of data analysis, data management, data visualization, and data mining procedures. Its techniques include the widest selection of predictive modeling, clustering, classification, and exploratory techniques in one software platform.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A software program used to control G:BOX hardware, specifically to capture and process images. While viewing images in real time, GeneSnap controls the illumination and exposure length of the lens, as well as the focussing, zooming and iris setting of a motorized lens.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

ZEN - ZEISS Efficient Navigation – is the single user interface you will see on all light microscopy imaging systems from Carl Zeiss. ZEN microscope software leads you simply and quickly to the result. At all times you see which options the system is making available to you and which step is appropriate to take next. Use ZEN imaging software to achieve scientific success: nothing diverts you from your goal - to document your results and reproduce them at any time.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

In vivo imaging software which facilitates workflow for in vivo optical, X-ray and microCT image acquisition, analysis and data organization., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software designed to automatically realign brain images for easier cross patient examination regardless of age, disease or head position. It positions and aligns anatomy-related sagittal, coronal and axial slices using anatomical landmarks.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

Software that processes neural data at run-time to control the implant's electrical stimulation functionality for the Braincon brain-computer interface (BCI). Braincon Platform Software is a general, flexible and verifiable BCI software architecture with a filter pipeline for low-latency multi-threaded processing of neuronal signals.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

A spatial statistics program which provides tools for crime mapping and analyzing crime incident locations. CrimeStat is organized into five sections: data setup, which arranges and organizes the location data; spatial description, which performs analyses such spatial distribution, spatial autocorrelation, and distance and hot spot analysis; spatial modeling, which performs a number of analyses such as Bayesian journey to crime analysis and space-time analysis; crime travel demand modeling, which detects crime patterns and correlations over time and space; and CrimeStat libraries, which are component objects that include all of the routines that were developed through version 2.0 of the regular CrimeStat program.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

Software which controls all operations in the experimental setup, data acquisition and monitoring, and data analysis stages of the Bio-Rad Opticon 2 system. In the experimental setup stage, setup and programming operations are accessed from the Master File window. The master file consists of a plate file, which specifies the parameters of the plate, and a protocol file, which specifies the experimental conditions. After a plate and a protocol setup have been created or selected, a run can be initiated, which begins the data acquisition and monitoring stage. Data collection can be monitored during the run by viewing a plot of fluorescence intensity vs. cycle number. In the data analysis stage, data can be analyzed using the Quantitation, Melting Curve, and/or Analysis windows. The window used depends on the type of data being collected.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje