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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://journalysis.org

A database where researchers can read and post reviews of publishing experiences with scientific journals. When writing comments, reviewers are adivsed to provide facts where possible, be specific, be honest, check the review, and offer constructive criticism when writing a negative report. Journalysis collates submitted reviews and data for each journal and provides useful summary information (metrics). Authors wanting to find out more about specific journals can search its databases and find the best journal for their next manuscript submission. Journals can use these reviews and metrics to demonstrate high publishing standards, or to improve standards where reviews may be negative.

Proper citation: Journalysis (RRID:SCR_014015) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cmind_py_2014/

A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project.

Proper citation: CMIND PY (RRID:SCR_014097) Copy   

•   Source: SciCrunch Registry

http://www.usefulscience.org

A collection of concise summaries of scientific articles that link back to the physical article. Users can contribute resources to the site and may choose to provide a summary; if they do not, Useful Science will do so. Summaries are then tagged with the appropriate topic. Topics that relate to everday life such as health, fitness, nutrition, and sleep are the main focus of the site.

Proper citation: Useful Science (RRID:SCR_013968) Copy   

•   Source: SciCrunch Registry

https://www.plos.org/article-level-metrics

A portal which provides access to article level metrics, PLOS news, and videos and presentations. PLOS ALMs provides altmetrics for every article published in PLOS. Researchers can stay up-to-date with their published work and share information about the impact of their publications with collaborators, funders, institutions, and the research community at large.

Proper citation: PLOS Article-Level Metrics (RRID:SCR_014022) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://copasi.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/home/sparky/

A graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. Sparky displays NMR spectra, the peaks of which users may pick, assign, and integrate using a graphical interface. Users can work with any number of 2, 3 or 4 dimensional spectra simultaneously. Spectra for input to Sparky can be produced with processing programs NMRPipe, Felix, VNMR, XWinNMR or UXNMR. Output consists of text peak lists showing assignments, chemical shifts, volumes, line widths, etc.

Proper citation: Sparky (RRID:SCR_014228) Copy   

•   Source: SciCrunch Registry

http://www.scilifelab.se

A Swedish national center of research for molecular biosciences with a focus on health and environmental research. Researchers from Sweden can use both the technology and the expertise provided by SciLifeLab. Swedish researchers typically pay only for reagents and other consumables. Users from commercial companies pay the actual costs of the analyses performed. SciLifeLab also provides educational courses, seminars, and programs for PhD students, postdocs, investigators and other employees within all Swedish universities.

Proper citation: SciLifeLab (RRID:SCR_014078) Copy   

•   Source: SciCrunch Registry

https://svi.nl/HuygensSoftware

A set of fluorescence microscope image processing packages which perform image restoration, interactive analysis, and volume visualization of 2D and 3D multi channel microscopy images or time series. The restoration is based on different deconvolution algorithms, that permit the recovery of objects from images that are degraded by blurring and noise. Tutorials and documentation are available on the website.

Proper citation: Huygens Software (RRID:SCR_014237) Copy   

•   Source: SciCrunch Registry

http://www.creative-peptides.com/Peptide-synthesis.html

A reagent manufacturer which provides custom peptide APIs and custom peptide synthesis services. These products and services include high throughput peptide library/array synthesis, high quality bulk API peptides, bioactive catalog peptides, and cosmetic peptides.

Proper citation: Peptide Synthesis (RRID:SCR_014070) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/aca_rc

A large scale functional connectivity data mining software package which enables large-scale seed-based analysis and brain-behavior analysis. It can examine a large number of seed regions with minimal user input. ACA has a brain-behavior analysis component to delineate associations among imaging biomarkers and one or more behavioral variables.

Proper citation: Advanced Connectivity Analysis (ACA) (RRID:SCR_014195) Copy   

•   Source: SciCrunch Registry

http://dbm.neuro.uni-jena.de/vbm/

A collection of extensions to the segmentation algorithm of SPM2, SPM5, and SPM8 to provide voxel-based morphometry. The toolboxes are named according to the SPM version. The software is available to the scientific community under the terms of the GNU General Public License. VBM subpages can be accessed from the VBM website.

Proper citation: VBM toolbox (RRID:SCR_014196) Copy   

•   Source: SciCrunch Registry

http://www.malvern.com/en/products/technology/nanoparticle-tracking-analysis/

Software which utilizes the properties of both light scattering and Brownian motion to obtain the particle size distribution of samples in liquid suspension. The Nanoparticle Tracking Analysis software tracks many particles individually and calculates their hydrodynamic diameters using the Stokes Einstein equation.

Proper citation: Nanoparticle Tracking Analysis (RRID:SCR_014239) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/biomag_group/

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 11, 2015. A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG).

Proper citation: Biomag Discussion Group on Yahoo (RRID:SCR_014089) Copy   

•   Source: SciCrunch Registry