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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://idr.openmicroscopy.org/about/
Public repository of reference image datasets from published scientific studies. Platform for publishing, mining and integrating bioimaging data, following FAIR principles and Euro-BioImaging/ELIXIR imaging strategy using OMERO and Bio-Formats open source software built by Open Microscopy Environment. Deployed on OpenStack cloud running on EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super resolution microscopy, and digital pathology.
Proper citation: Image Data Resource (IDR) (RRID:SCR_017421) Copy
Medical image repository to store medical research data.
Proper citation: SICAS Medical Image Repository (RRID:SCR_017420) Copy
https://timothyspringer.org/files/tas/files/biacore3000-instrument.pdf
Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants.
Proper citation: GE: Biacore 3000 Real Time Biomolecular Interaction Analyzer (RRID:SCR_018044) Copy
Standardized method to export statistical data, associated with KOMP project. Standard way to keep data and results of analyzing that data together.
Proper citation: StatPackets (RRID:SCR_017613) Copy
https://www2.bri.nrc.ca/ccb/pub/sietraj_main.php
Software tool for binding free energies from Amber-generated MD trajectories. Alternative to MM-PBSA software provided by AMBER distribution. Virtual alanine mutations are also possible. Solvated interaction energies are calculated using parameters that have been fitted to reproduce binding free energies of data set of 99 protein-ligand complexes.
Proper citation: sietraj (RRID:SCR_018021) Copy
https://github.com/bcgsc/NanoSim
Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software.
Proper citation: NanoSim (RRID:SCR_018243) Copy
http://www.prisma-statement.org/
Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.
Proper citation: PRISMA (RRID:SCR_018721) Copy
https://github.com/mrc-ide/PhyDyn
Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST.
Proper citation: PhyDyn (RRID:SCR_018544) Copy
https://github.com/stekhoven/missForest
Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values.
Proper citation: missForest (RRID:SCR_018543) Copy
Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets.
Proper citation: PyRx (RRID:SCR_018548) Copy
Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives.
Proper citation: OpenCOR (RRID:SCR_019001) Copy
https://www.crd.york.ac.uk/PROSPERO
International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol.
Proper citation: PROSPERO (RRID:SCR_019061) Copy
http://www.softberry.com/berry.phtml?topic=fgenesh_plus_plus&group=help&subgroup=pipelines
Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.
Proper citation: Fgenesh plus plus (RRID:SCR_018928) 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
http://krasnow1.gmu.edu/CENlab/software.html
Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways.
Proper citation: NeuroRD (RRID:SCR_014769) Copy
https://www.comsol.com/comsol-multiphysics
General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating.
Proper citation: COMSOL Multiphysics (RRID:SCR_014767) Copy
http://www.lsm.tugraz.at/pcsim/
Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI.
Proper citation: PCSIM (RRID:SCR_014770) Copy
http://mvaspike.gforge.inria.fr/
Tool for modeling and simulating large, complex biological neural networks, particularly pulse-coupled, spiking neural networks. Its main features include modular or hierarchical modeling strategy of networks, phase-coded neurons, event-driven simulation, and integration of standard file formats.
Proper citation: Mvaspike (RRID:SCR_014760) Copy
http://www.jadesantiago.com/Electrophysiology/IonChannelLab/
Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista.
Proper citation: IonChannelLab (RRID:SCR_014762) Copy
Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.
Proper citation: libRoadRunner (RRID:SCR_014763) Copy
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