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http://ipython.org/notebook.html
A web application and interactive computational environment where users can combine code execution, rich text, mathematics, plots, and rich media. IPython Notebook consists of two parts, the web application and plain texts. The Ipython Notebook web application is used for interactive authoring of literate computations, in which explanatory text, mathematics, computations, and rich media output may be combined. Input and output are stored in persistent cells that may be edited in-place. The plain text documents, called notebooks, record and distribute the results of the rich computations. Saved files in the notebook can be put under version control and shared with colleagues.
Proper citation: IPython Notebook (RRID:SCR_013984) Copy
A public health center and research institution affiliated with Vanderbilt University.
Proper citation: Vanderbilt University Medical Center; Tennessee; USA (RRID:SCR_014046) Copy
http://www.cytobank.org/index.html
A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.
Proper citation: Cytobank (RRID:SCR_014043) Copy
A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems.
Proper citation: BioPSE (RRID:SCR_014044) Copy
A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available.
Proper citation: StatCrunch (RRID:SCR_013992) Copy
A web application which performs Python data analysis. Users can create IPython notebooks to hold uploaded data and use various tools to describe, analyze, and visualize the data. Notebooks, data, and Anaconda environments can be shared as "bundles" with other users, who can edit and download them.
Proper citation: Wakari (RRID:SCR_013995) Copy
A public health center and research institution affiliated with McGill University.
Proper citation: McGill University Health Centre; Quebec; Canada (RRID:SCR_014048) Copy
Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.
Proper citation: ChEMBL (RRID:SCR_014042) Copy
http://www.nitrc.org/projects/iterdrwsp/
Software which aims to better estimate the neuronal activation of an individual using the results of an independent component analysis (ICA) method applied to a temporally concatenated group of functional magnetic resonance imaging (fMRI) data (i.e., Tc-GICA method). This approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs (i.e., minimally overlapping SPs) based on L(1)-norm minimization.
Proper citation: Iterative dual-regression with sparse prior (RRID:SCR_014128) Copy
http://actimetrics.com/products/limelight/
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.
Proper citation: Limelight (RRID:SCR_014254) Copy
http://www.nitrc.org/projects/l-neuron
A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth.
Proper citation: L-Neuron (RRID:SCR_014132) Copy
http://www.nitrc.org/projects/lwdp/
A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing.
Proper citation: Lightweight Data Pipeline (RRID:SCR_014135) Copy
http://www.lsm.tugraz.at/csim/
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.
Proper citation: CSIM (RRID:SCR_014256) Copy
http://www.cse.unr.edu/brain/ncs
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.
Proper citation: NeoCortical Simulator (RRID:SCR_014257) Copy
http://www.nitrc.org/projects/neuritetracer
A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons.
Proper citation: NeuriteTracer (RRID:SCR_014146) Copy
http://www.nitrc.org/projects/bvqxtools
A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab.
Proper citation: NeuroElf (RRID:SCR_014147) Copy
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.
Proper citation: COPASI (RRID:SCR_014260) Copy
http://www.cyana.org/wiki/index.php/Main_Page
Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution.
Proper citation: CYANA (RRID:SCR_014229) Copy
https://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html
Software package for NMR spectra acquisition, processing, and data analysis. Features include: deconvolution/spectrum simulation/iteration; comprehensive functionalities for processing, displaying and analyzing one and multi-dimensional spectra; and user customization. A full list of features is available on the website.
Proper citation: TopSpin (RRID:SCR_014227) Copy
http://www.nitrc.org/projects/exposition/
An R package for descriptive (i.e., fixed-effects) multivariate analysis with singular value decomposition.
Proper citation: ExPosition Packages (RRID:SCR_014107) Copy
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