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http://alleninstitute.github.io/dipde/

Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.

Proper citation: DiPDE (RRID:SCR_015822) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sanworks

Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.

Proper citation: Bpod (RRID:SCR_015943) Copy   

•   Source: SciCrunch Registry
  

http://www.genetherapyreview.com/gene-therapy-research

The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.

Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy   

•   Source: SciCrunch Registry
  

http://www.fsm.ethz.ch/publications-list/software.html

Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.

Proper citation: FiberApp (RRID:SCR_015826) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ABCD-STUDY/geocoding

Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.

Proper citation: geocoding (RRID:SCR_016007) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/SC3.html

Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.

Proper citation: SC3 (RRID:SCR_015953) Copy   

•   Source: SciCrunch Registry
  

https://github.com/haotianteng/Chiron

Software basecaller for Oxford Nanopore Technologies' sequencers.

Proper citation: Chiron (RRID:SCR_015950) Copy   

•   Source: SciCrunch Registry
  

http://www.hermit-reasoner.com/

Algorithm for a reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more.

Proper citation: HermiT OWL Reasoner (RRID:SCR_016006) Copy   

•   Source: SciCrunch Registry
  

http://digestivediseasescenters.org/content/ddrc-emory-university-overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Center for pathobiology research development.

Proper citation: Emory Epithelial Pathobiology Research Development Center (RRID:SCR_015916) Copy   

•   Source: SciCrunch Registry
  

https://www.olympus-lifescience.com/en/microscopes/inverted/ix53/

Equipment that is a microscope for routine inverted microscopic analysis. Its features include pre-centered phase contrast, relief contrast, and UIS2 DIC optics for visualization across all magnifications for both thin and thick specimens.

Proper citation: Olympus IX-53 (RRID:SCR_015801) Copy   

•   Source: SciCrunch Registry
  

https://www.thermofisher.com/order/catalog/product/4444202

Software for high-throughput gene expression and genotyping analysis for use with the Applied Biosystems® 7900HT Fast Real Time PCR System. It features automation software tools to fully automate high-throughput applications for gene expression and SNP genotyping.

Proper citation: Sequence Detector System (RRID:SCR_015806) Copy   

•   Source: SciCrunch Registry
  

https://www.thermofisher.com/order/catalog/product/ND-3300

Fluorospectrometer for broad spectrum fluorescence analysis. It uses as little as 1 μL of sample volume and lowers the mass detection limit more than an order of magnitude.

Proper citation: NanoDrop 3300 Fluorospectrometer (RRID:SCR_015804) Copy   

•   Source: SciCrunch Registry
  

https://www.thermofisher.com/order/catalog/product/4376600

Equipment and software system that is a real-time thermal cycler for intuitive data analysis of polymerase chain reactions. It comes with analysis software, instrument control software, and a LED-based 4-color optical recording feature.

Proper citation: Thermo Fisher: StepOnePlus Real-Time PCR System (RRID:SCR_015805) Copy   

•   Source: SciCrunch Registry
  

https://github.com/DDTBOX/DDTBOX

Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.

Proper citation: Decision Decoding Toolbox (RRID:SCR_015978) Copy   

•   Source: SciCrunch Registry
  

https://nxr.northwestern.edu/digital-rat

Software for a 2D elastic beam model that can be used to model quasistatic bending of the vibrissa to compute forces and bending moments at the base. Elastica2D is part of the Digital Rat software project that that aims to enable morphologically and mechanically accurate modelling of the rat head and vibrissal (whisker) array.

Proper citation: Elastica2D (RRID:SCR_015858) Copy   

•   Source: SciCrunch Registry
  

https://www.quantumbiologyinstitute.org/

Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions.

Proper citation: Quantum Biology Institute (RRID:SCR_015855) Copy   

•   Source: SciCrunch Registry
  

https://sdrc.stanford.edu/

University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University.

Proper citation: Stanford Diabetes Research Center (RRID:SCR_015856) Copy   

•   Source: SciCrunch Registry
  

http://www.ctotstudies.org

Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients.

Proper citation: Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) Copy   

•   Source: SciCrunch Registry
  

http://www.ctotc.org

Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients.

Proper citation: Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cmayer/BaitFisher-package

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

Proper citation: Baitfisher (RRID:SCR_015985) Copy   

•   Source: SciCrunch Registry