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https://zenodo.org/record/167621
Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation.
Proper citation: BeatBox (RRID:SCR_015780) Copy
Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response.
Proper citation: o²S²PARC (RRID:SCR_018997) Copy
https://www.bio-rad.com/en-us/product/ze5-cell-analyzer?ID=OC62Q015
BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals.
Proper citation: Bio-Rad: ZE5 Cell Analyzer (RRID:SCR_019712) Copy
https://github.com/mlinderm/npsv
Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline.
Proper citation: NPSV (RRID:SCR_020984) Copy
https://github.com/dmnfarrell/epitopepredict
Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported.
Proper citation: epitopepredict (RRID:SCR_019221) Copy
http://metagenomics.iiserb.ac.in/mp3/
Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MP3 tool (RRID:SCR_019282) Copy
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
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
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
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
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
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
https://github.com/SpineML/SpineML_2_BRAHMS
Simulation software which can execute neural network models specified in the SpineML format (an extension of the INCF's NineML). It is used as the canonical simulator backend by SpineCreator and translates the SpineML specification of the model into object code and a SystemML specification of the network.
Proper citation: SpineML_2_BRAHMS (RRID:SCR_015640) Copy
https://github.com/cerebis/sim3C/tree/0.1
Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities.
Proper citation: Sim3C (RRID:SCR_015772) Copy
Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
Proper citation: Aevol (RRID:SCR_015966) Copy
http://abacus.gene.ucl.ac.uk/software/indelible/
Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.
Proper citation: Indelible (RRID:SCR_016163) Copy
Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models.
Proper citation: Vensim (RRID:SCR_016394) Copy
http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf
Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution.
Proper citation: Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) Copy
https://haddock.science.uu.nl/dna/dna.php
DNA structure modelling server. Web server for generating custom 3D structural models of DNA with control over local and global conformation.
Proper citation: 3D DART (RRID:SCR_017588) Copy
https://rayyan.qcri.org/welcome
Software tool for screening papers for systematic reviews. Web and mobile app to help to expedite initial screening of abstracts and titles using process of semi automation while incorporating high level of usability.
Proper citation: Rayyan QCRI (RRID:SCR_017584) Copy
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