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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
Realistic simulated MEG datasets ranging from basic sensory to oscillatory sets that mimic functional connectivity; as well as basic visual, auditory, and somatosensory empirical sets. The simulated sets were created for the purpose of testing analysis algorithms across the different MEG systems when the truth is known. MEG baseline recordings were obtained from 5 healthy participants, using three MEG systems: VSM/CTF Omega, Elekta Neuromag Vectorview, 4-D Magnes 3600. Simulated signals were embedded within the CTF and Neuromag 306 baseline recordings (4-D to be added). Participant MRIs are available. Averaged simulation files are available as netcdf files. Neuromag 306 averaged simulations are also available in fif format. Also available: single trials of data where the simulated signal is jittered about a mean value, continuous fif files where the simulated signal is marked by a trigger, and simulations with oscillations added to mimic functional connectivity.
Proper citation: MEGSIM (RRID:SCR_002420) Copy
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
http://www.frontiersin.org/10.3389/conf.fninf.2013.09.00111/event_abstract
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. ASP.NET AJAX .NET 4, Telerik controls enabled application designed to be used with the books presented, papers and web content to help with the acceleration of learning and software development for the neurosciences. All content developed at The Cromwell Workshop is intended to accelerate the implementation of biomedical knowledge, help with EEG clinical certifications and provide the opportunity for students, software developers, neuroscientists, neurologists and neurosurgeons to collaborate globally with knowledge content. e-NeoTutor relies on a subscription model to build software components in multiple languages and access book material. Tutor designed to complement free online course content in neuroscience, work with the Society of Neuroscience, The Human Connectome Project and assist researchers with CNIM certification, biomedical informatics, neuroinformatics and neuroscience training programs.
Proper citation: eNeoTutor (RRID:SCR_001590) Copy
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
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
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
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
https://huttenhower.sph.harvard.edu/picrust/
Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases.
Proper citation: PICRUSt2 (RRID:SCR_022647) Copy
https://www.antibodysociety.org/the-airr-community/
Research driven group that is organizing and coordinating stakeholders in use of next generation sequencing technologies to study antibody/B-cell and T-cell receptor repertoires. Develops and promotes standards and recommendations for obtaining, analyzing, curating and comparing/sharing AIRR-seq datasets;using and validating tools for analyzing AIRR-seq data;relating AIRR-seq datasets to other “big data” sets, such as microarray, flow cytometric, and MiSeq and single-cell gene-expression data; legal and ethical issues involving use and sharing of AIRR-seq data sets derived from human sources.
Proper citation: AIRR Community (RRID:SCR_022598) Copy
https://quality-preclinical-data.eu/about-eqipd/eqipd-quality-system/
Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD.
Proper citation: Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) Copy
International data repository for science, engineering and design. Services include curation, sharing, long-term access and preservation of research datasets. These services are available to anyone around the world. In addition, 4TU.ResearchData also offers training and resources to researchers to support them in making research data findable, accessible, interoperable and reproducible (FAIR).
Proper citation: 4TU.ResearchData (RRID:SCR_023125) Copy
https://cytotrace.stanford.edu/
Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data.
Proper citation: CytoTRACE (RRID:SCR_022828) Copy
Interoperable online network of marine and climate data resources.AODN Portal provides access to all available Australian marine and climate science data and provides the primary access to IMOS data.
Proper citation: Australian Ocean Data Network (RRID:SCR_023134) Copy
Astrobiology Habitable Environments Database (AHED) is a new data system being developed as a long-term, open-access repository for astrobiology data. AHED is intended to store user-contributed results from NASA or externally-funded research in astrobiology, and to encourage sharing and synergy within the astrobiology community.
Proper citation: Astrobiology Habitable Environments Database (RRID:SCR_023133) Copy
http://researchdata.aston.ac.uk/
Aston University's repository for their research data. It is one of three services providing information about Aston University�s research. Aston Publications Explorer holds Aston's research publications and Aston Research Explorer has broader information about Aston's research work including research staff, awards and activities, projects and research groups.Metadata will be accessible to anyone free of charge. The metadata may be re-used in any medium without prior permission and re-sold commercially provided the repository is mentioned.Aston�s repository holds datasets and corresponding metadata that have been produced by Aston University staff and students. The datasets deposited in Aston Publications Explorer range from metadata records only through to full datasets. Content is the sole responsibility of the authors, and any questions over content should be directed to them.Aston Data Explorer, Aston Publications Explorer AND Aston Research Explorer allow users to re-use full-text and other full-data items under the terms of the Creative Commons Attribution Non-Commercial No Derivatives (CC BY NC ND) licence. This means that users must give appropriate credit to the authors and link to the licence. Users may not re-use the material for commercial purposes. Users cannot distribute material that has been remixed, transformed or built upon the original published output. Where a full-text or other full-data item has a licence that is more restrictive or permissive than the CC BY NC ND default licence, this licence should be adhered to.
Proper citation: Aston Data Explorer (RRID:SCR_023132) Copy
http://arch.library.northwestern.edu/
Arch is an open access repository for the research and scholarly output of Northwestern University. Log in with your NetID to deposit, describe, and organize your research for public access and long-term preservation. We'll use our expertise to help you curate, share, and preserve your work.
Proper citation: Arch (RRID:SCR_023130) Copy
https://www.vosesoftware.com/products/modelrisk/
Monte Carlo simulation software that makes quantitative risk analysis intuitive. Monte Carlo simulation Excel add-in that allows user to include uncertainty in their spreadsheet models.
Proper citation: ModelRisk (RRID:SCR_022836) Copy
A group which aims to create open standards for metabolomics data shsaring and analysis.
Proper citation: Coordination of Standards in Metabolomics (RRID:SCR_014662) Copy
Archive for storing and sharing digital data (and accompanying documentation) generated or collected through qualitative and multi method research in social sciences. QDR provides data management consulting services and actively curates all data projects, maintaining value and usefulness of data over time, and ensuring their availability and findability for re-use.
Proper citation: Qualitative Data Repository (RRID:SCR_022833) Copy
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