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https://collage.elsevier.com

A web application which provides the framework for collaborative preparation and publication of computational experiments that can back executable papers. The Collage environment enables researchers to embed chunks of executable code and data into scientific publications and facilitate repeated execution of such codes on underlying computing and data storage resources. Executable papers made with Collage can be embedded into a web site.

Proper citation: Collage Authoring Environment (RRID:SCR_014008) Copy   

•   Source: SciCrunch Registry
  

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.runmycode.org

A database and storage service resource which allows users to create, view, share, and download information from companion websites. RunMyCode allows users to create companion websites for their scientific publications. Users can share and download computer code and data from companion websites made with RunMyCode. Any software and data format is compatible with RunMyCode.

Proper citation: RunMyCode (RRID:SCR_014011) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://academickarma.org

A peer review management system which encourages timely and high quality peer review by using a credit system. Reviewers complete reviews using a general webform on academickarma.org, and if that review is submited to an editor within ten days, the reviewer is awarded a certain amount of points (karma credits). The author and editor both receive the review. Editors can use Academic Karma to identify specialized reviewers for future reference. A reviewer's personal profile, which includes the amount of karma credits they've received, is connected to their ORCID account and publication record for an overview of the reviewer's work.

Proper citation: Academic Karma (RRID:SCR_014017) Copy   

•   Source: SciCrunch Registry
  

http://www.journalreviewer.org

A database which allows researchers to view and comment on the logistics of scientific journals' review processes. JournalReviewer collects and aggregates feedback from users who have submitted manuscripts to journals in order to provide information for others considering journal submissions. Statistics such as turnaround rate, review length and quality, journal recommendations, and desk reject plausabilities are compiled from commentors' ratings.

Proper citation: JournalReviewer (RRID:SCR_014014) 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://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   

•   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.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   

•   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
  

http://www.plumanalytics.com

A service resource which provides researchers with metrics around usage, captures, social media, citations, and mentions from various online research outlets. Plum Analytics pulls information from reserch outlets such as journal articles, books, videos, presentations, conference proceedings, datasets, and source code. Plum Analytics also collects metrics for labs, departments, and other research groups. PlumX is a product of Plum Analytics.

Proper citation: Plum Analytics (RRID:SCR_014023) 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://chgv.org/GenicIntolerance/

A gene-based score intended to help in the interpretation of human sequence data. The score is designed to rank genes in terms of whether they have more or less common functional genetic variation relative to the genome wide expectation given the amount of apparently neutral variation the gene has. A gene with a positive score has more common functional variation, and a gene with a negative score has less and is referred to as intolerant.

Proper citation: Residual Variation Intolerance Score (RVIS) (RRID:SCR_013850) Copy   

•   Source: SciCrunch Registry
  

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https://www.kaggle.com

A group resource which connects organizations to data scientists who produce accurate predictive models. Kaggle uses competition to incentivize data scientists to create the most accurate and precise predictive models for an organization’s sets of data. The data scientist or team of data scientists who creates the best model is awarded a prize and the organization receives the predictive model.

Proper citation: Kaggle (RRID:SCR_013852) 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
  

https://www.innocentive.com

A global network group resource which provides crowdsourcing services for “innovation solutions.” InnoCentive utilizes an innovation framework, called Challenge Drive Innovation, which is based on leveraging open innovation and crowdsourcing. Software tools are available for idea management, innovation management, and external crowdsourcing programs and competitions.

Proper citation: InnoCentive (RRID:SCR_013851) 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.slideshare.net

A collaboration tool which allows users to upload and share presentations, infographics, documents, videos, PDFs, and webinars. Individual slideshows are available for download and are easily uploaded to other websites and blogs.

Proper citation: SlideShare (RRID:SCR_013818) Copy   

•   Source: SciCrunch Registry