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https://github.com/BackofenLab/RNAProt

Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction.

Proper citation: RNAProt (RRID:SCR_021218) Copy   

•   Source: SciCrunch Registry

https://evidencegraph.github.io/EVI/index.html

Evidence Graph Ontology extends core concepts from W3C Provenance Ontology PROV-O to describe evidence for correctness of findings in biomedical publications. Semantic data model in EVI is expressed using OWL2 Web Ontology Language.

Proper citation: Evidence Graph Ontology (RRID:SCR_021225) Copy   

•   Source: SciCrunch Registry

http://api.brain-map.org/api/v2/structure_graph_download/1.json

Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree.

Proper citation: Allen Mouse Reference Atlas Ontology (RRID:SCR_021000) Copy   

•   Source: SciCrunch Registry

http://imj.com.au/sgs/

Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output.

Proper citation: Sustainable Grazing System Pasture Model (RRID:SCR_021854) Copy   

•   Source: SciCrunch Registry

http://www.plafornea.com.ar/

Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos.

Proper citation: PlaForNEA (RRID:SCR_022027) Copy   

•   Source: SciCrunch Registry

https://simulabeta.sourceforge.io/

Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model.

Proper citation: SimulaBeta (RRID:SCR_021900) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MAMO

Ontology that is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.

Proper citation: Mathematical Modelling Ontology (RRID:SCR_000910) Copy   

•   Source: SciCrunch Registry

http://interactome.org/index.php/Main_Page

This Wiki page provides information about Interactome of various species. An interactome of a species provides an important clues on how to interpret metabolic pathways of constituent enzymes and global protein network, which facilitates in turn to understand the mechanism responsible for the cellular functions.

Proper citation: Interactome Wiki (RRID:SCR_000750) Copy   

•   Source: SciCrunch Registry

http://opensim.stanford.edu

OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration. The underlying software is written in ANSI C++, and the graphical user interface (GUI) is written in Java. OpenSim technology makes it possible to develop customized controllers, analyses, contact models, and muscle models among other things. These plugins can be shared without the need to alter or compile source code. Users can analyze existing models and simulations and develop new models and simulations from within the GUI.

Proper citation: OpenSim (RRID:SCR_002683) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/DOT/resources/tmcimg/

Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available.

Proper citation: Monte Carlo Simulation Software: tMCimg (RRID:SCR_002588) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/annotation-ontology/

Provides vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web.

Proper citation: Annotation Ontology (RRID:SCR_002862) Copy   

•   Source: SciCrunch Registry

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

Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images.

Proper citation: TumorSim (RRID:SCR_002604) Copy   

•   Source: SciCrunch Registry

https://github.com/OSS-Lab/ChemChaste

Software tool for simulating spatially inhomogenous biochemical reaction diffusion systems for modelling cell environment feedbacks. Simulation software for spatially organised biochemical systems.

Proper citation: ChemChaste (RRID:SCR_022208) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/pbsim/

Software that simulates PacBio reads by using either a model-based or sampling-based simulation.

Proper citation: PBSIM (RRID:SCR_002512) Copy   

•   Source: SciCrunch Registry

http://biologicstylus.sourceforge.net/

Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python

Proper citation: Biologic Stylus (RRID:SCR_002991) Copy   

•   Source: SciCrunch Registry

http://www.ncbcs.org/biositemaps/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO).

Proper citation: Biomedical Resource Ontology (RRID:SCR_004443) Copy   

•   Source: SciCrunch Registry

http://hymao.org

A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)

Proper citation: Hymenoptera Anatomy Ontology (RRID:SCR_003340) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NIFCELL

Ontology for cell types from NIFSTD

Proper citation: NIF Cell Ontology (RRID:SCR_003977) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/MS

A structured controlled vocabulary for the annotation of mass spectrometry experiments.

Proper citation: Mass Spectrometry Ontology (RRID:SCR_003579) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/REXO

An application ontology for the domain of gene expression regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.

Proper citation: Regulation of Gene Expression Ontolology (RRID:SCR_006124) Copy   

•   Source: SciCrunch Registry