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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://purl.bioontology.org/ontology/HUPSON
Ontology as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles.
Proper citation: Human Physiology Simulation Ontology (RRID:SCR_010340) Copy
http://purl.bioontology.org/ontology/LOINC
Ontology of logical observation identifier names and codes (LOINC); Version 2.26; January 2, 2009
Proper citation: Logical Observation Identifier Names and Codes (RRID:SCR_010341) Copy
http://purl.bioontology.org/ontology/REPO
Ontology for livestock reproductive traits and phenotypes
Proper citation: Reproductive Trait and Phenotype Ontology (RRID:SCR_006245) Copy
http://purl.bioontology.org/ontology/DCM
DICOM Controlled Terminology (PS3.16 2013 Annex D)
Proper citation: DICOM Controlled Terminology (RRID:SCR_010302) Copy
http://purl.bioontology.org/ontology/DIAGONT
A computational diagnostic ontology containing 91 elements, including classes and sub-classes, which are required to conduct SR-MA (Systematic Review - Meta Analysis) for diagnostic studies, that will assist in standardized reporting of diagnostic articles. They also report high percentage of agreement among five observers as a result of the inter-observer agreement that they conducted among them to tag 13 articles using the diagnostic ontology. Moreover, they extend their existing repository CERR-N (Center of Excellence in Research Reporting in Neurosurgery) to include diagnostic studies.
Proper citation: Diagnostic Ontology (RRID:SCR_010307) Copy
http://purl.bioontology.org/ontology/BP-METADATA
Ontology that represents the structure that BioPortal uses to represent all of its metadata (ontology details, mappings, notes, reviews, views)
Proper citation: BioPortal Metadata Ontology (RRID:SCR_010167) Copy
https://www.amazon.com/How-Brain-Works-Mark-Dubin/dp/0632044411
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Is the Brain (Like) a Computer is an e-book written by Prof. Mark Dubin. It consists of the following: Introduction. Why do we consider the relationship of brains and computers and what does this have to do with consciousness? What's a Brain Made Of? A thought experiment. Test Drive a Turing Machine. A theoretical approach. Interim Summary. Many of the main pages have links to additional information. When you click on one of those links a NEW page will open ON TOP of the page you are clicking from. This convention is adopted so that you can look at the additional information and then easily return to the main page you got there from.
Proper citation: Is the Brain (Like) a Computer (RRID:SCR_008809) Copy
http://purl.bioontology.org/ontology/TMO
A high level patient-centric ontology for the pharmaceutical industry. The ontology should enable silos in discovery research, hypothesis management, experimental studies, compounds, formulation, drug development, market size, competitive data, population data, etc. to be brought together. This would enable scientists to answer new questions, and to answer existing scientific questions more quickly. This will help pharmaceutical companies to model patient-centric information, which is essential for the tailoring of drugs, and for early detection of compounds that may have sub-optimal safety profiles. The ontology should link to existing publicly available domain ontologies.
Proper citation: Translational Medicine Ontology (RRID:SCR_010439) Copy
https://github.com/SciCrunch/NIF-Ontology/tree/neurons/ttl
An ontology for describing the complex phenotypes of neurons.
Proper citation: Neuron Phenotype Ontology (RRID:SCR_017403) Copy
https://github.com/GuyButcher/alpha-helix-coordinate-frame-simulation
Source code for alpha-helix simulation framework written in Matlab. Specifically tested on Talin-1 Rod Domain.
Proper citation: alpha helix coordinate frame simulation (RRID:SCR_019320) Copy
https://github.com/mtu-most/linear-actuator
Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system.
Proper citation: linear actuator (RRID:SCR_021613) Copy
https://github.com/KravitzLab/ROBucket
Software tool as ROBucket source code.
Proper citation: Rodent Operant Bucket (RRID:SCR_021610) Copy
https://github.com/jf-lab/chendoscope
Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems.
Proper citation: chendoscope (RRID:SCR_021616) Copy
https://github.com/jamieboyd/AutoHeadFix
Software Python code for automated control of behavioural apparatus and imaging for mice in home cage environment.Part of Homecage Task Training and Mesoscale Imaging system.
Proper citation: AutoHeadFix (RRID:SCR_021617) Copy
https://github.com/HUST-NingKang-Lab/Meta-Prism-2.0
Software tool as microbial community sample search method based on smart pair wise sample comparison without compromising accuracy. Used as microbial communities similarites calculation and comparison tool.
Proper citation: Meta-Prism (RRID:SCR_021836) Copy
https://murphylab.med.ubc.ca/automated-homecages/
Software tool as part of Automated Home Cage Functional Imaging system.
Proper citation: Automated Home-Cage Functional Imaging (RRID:SCR_021607) Copy
https://github.com/dublon/scintillate
Open source graphical viewer for time series calcium imaging evaluation and pre-processing.
Proper citation: Scintillate (RRID:SCR_021531) Copy
https://github.com/agneslandemard/naturalsounds_analysis
Software tool as source code for analyzing functional ultrasound data.
Proper citation: naturalsounds analysis (RRID:SCR_021793) Copy
https://github.com/ribeiro-lab/flyPAD-fpga
FPGA code for running main board of flyPAD. Code written in VHDL using Quartus 2 web edition software.
Proper citation: flyPAD (RRID:SCR_021522) Copy
https://github.com/tedinburgh/sepsis3-amsterdamumcdb
Repository contains files for implementing the Sepsis-3 definition in the freely-accessible Amsterdam University Medical Centers Database.
Proper citation: sepsis3-amsterdamumcdb (RRID:SCR_022042) Copy
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