Curator Dashboard

A software to calculate molecular descriptors and fingerprints. The descriptors and fingerprints are calculated using The Chemistry Development Kit with additional descriptors and fingerprints such as atom type electrotopological state descriptors, Crippen's logP and MR, extended topochemical atom (ETA) descriptors, and McGowan volume.

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• SciCrunch
• 11 years ago - submitted by Gergo Barta

Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A suite of programs for recording and analyzing signals from intracellular electrophysiology experiments. A list of the latest software is available from the website. The programs work with common electrophysiological laboratory interface units, including: Cambridge Electronic Design 1401 / 1401plus / Micro1401 / Power 1401; Axon Instruments Digidata 1200 or 1320/22, 1440, 1550, 1550A; Instrutech ITC16 or ITC-18; National Instruments multifunction interface cards; Biologic VP500; Tecella patch clamps; and Heka EPC-9, EPC-10.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

An ImageJ plugin used for analyzing 2D time-lapse images or stacks. The plugin can be used to add a predefined ROI (Auto ROI) through mouse clicks. After selecting the object to be defined, an ROI is added on the image and in ROI Manager.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A software toolbox which provides MATLAB functions, apps, and a Simulink block for analyzing, designing, and simulating fuzzy logic systems. Fuzzy Logic Toolbox allows users to model complex system behaviors using simple logic rules, and then implement these rules in a user-designed fuzzy inference system. Functions are provided for many common methods, including fuzzy clustering and adaptive neurofuzzy learning. The toolbox can be used as a stand-alone fuzzy inference engine or in connection with Simulink. Different versions of the software are available for specific fuzzy inference systems.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

BrainVoyager QX is a highly optimized and user friendly software package for the analysis and visualization of functional and structural magnetic resonance imaging data sets. The program runs on all major computer platforms including Windows (XP/7/8/8.1), Linux (e.g. RedHat, SUSE) and Mac OS X (10.8 or higher).

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software tool for plasmid and sequence editing, annotating and drawing plasmid sequences. Used to view circular or linear maps of DNA sequences. Users can perform virtual digests whereby they select predefined DNA ladder, or specify their own, and visualize theoretical DNA fragments. Used to highlight restriction sites in editing window, accurately reflect Dam/Dcm blocking of enzyme sites, highlighting and drawing graphic maps using feature annotations from genbank and embl files, highlighting text using pre-defined and custom feature libraries, and directly BLASTing selected sequence at NCBI or Wormbase. Runs across Windows, OS X, and Linux/Unix.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software suite of sequence analysis and design tools that help manage, view, analyze, transform, share, and publicize various types of molecular biology data within one analysis environment. Users can analyze and compare sequences, design cloning and other vector related experiments, and curate and organize data and collections. Different classes for different user and experimental focuses are available.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.

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• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Neurosimulation software that links sophisticated model development with behavior. The software package provides a framework that can be expanded using standard KDE (K Desktop Environment) parts and plugins to incorporate a variety of different projects, like visual system, auditory system or memory system. KInNeSS contains two fully developed project environments: one for generic input and another for spatial navigation tasks. The option of creating a new project environment is provided for advanced users. A user manual and tutorials/examples are provided as part of documentation.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

An event-based neuronal network simulator designed to handle large, complicated neuronal networks. The software is capable of creating realistic and accurate neuronal models in terms of neuronal dynamics and spike timing. ERNST is written in Java.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

Simulation software which creates spiking cell models using either a time-driven strategy or an event-driven strategy based on look-up tables. EDLUT serves as a tool for studying the computational principles of neural systems to reveal how different functionalities of the brain and central nervous system are based on cell and topology properties.

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• SciCrunch
• 11 years ago - submitted by Jamie Li

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