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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.
Database of commercially accessible screening compounds from international chemistry suppliers. iResearchLibrary is updated on a weeky basis and offers support for creating internal screening libraries containing commercially accessible compounds, developing exploratory and targeted libraries, selecting commercially accessible compounds for SAR, lead expansion, and hit follow-up projects, and using structures for pharmacophore searching, virtual screening and other computational work.
Proper citation: iResearch Library (RRID:SCR_014890) 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
Supplier and servicer of products for expression studies in Xenopus laevis oocytes. Products include overnight delivery of freshly prepared Xenopus laevis oocytes, Cell & Tissue Media necessary during preparation, maintenance, and recording of Xenopus oocytes and lab chemicals. Services for pharmacological studies include heterologous expression and in vitro electrophysiology.
Proper citation: EcoCyte Bioscience (RRID:SCR_014773) Copy
http://bix.ucsd.edu/repeatscout/
Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RepeatScout (RRID:SCR_014653) Copy
Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites.
Proper citation: Genezilla (RRID:SCR_014657) Copy
https://pythonhosted.org/eelbrain/
Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases.
Proper citation: Eelbrain (RRID:SCR_014661) Copy
https://github.com/marcel-goldschen-ohm/SingleMoleculeImageAnalysis
MATLAB software tool collection for data acquisition and image analysis from zero mode waveguides.
Proper citation: Zero Mode Waveguide Imaging and Analysis package tools (RRID:SCR_014660) Copy
https://www.ebi.ac.uk/metabolights/
A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments.
Proper citation: MetaboLights (RRID:SCR_014663) Copy
Commercial ogranization which provides molecular and drug discovery software and services to researchers. American software company that develops chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Provides products ranging from general molecular modeling programs to a full suite of chemical simulation and drug design software, including ligand- and structure-based methods.
Proper citation: Schrodinger (RRID:SCR_014879) Copy
http://store.neurosky.com/products/neuroexperimenter
Software which provides an interface for MindWave Mobile hardware, allowing users to view and listen to brainwave output of different "mind states". Users can: view any or all brainwaves, specify a combination of brainwaves via a formula, compare a base line session to a performance session, and create a log and run it through the application to view different graphical outputs. NeuroExperimenter only runs on Windows
Proper citation: NeuroExperimenter (RRID:SCR_014759) 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.eyesopen.com/oedocking
Complementary OEDocking tool for virtual screening, it performs a systematic and non-stochastic examination of all possible protein-ligand poses. The software also filters for shape complementarity and chemical feature alignment before selecting and optimizing protein-ligand poses.
Proper citation: FRED - Fast exhaustive docking (RRID:SCR_014885) Copy
https://cactus.nci.nih.gov/ncidb2.2/
Public web server that provides structures, data, tools, programs and other useful information to the public for computer-aided drug design. It is the official database of the Computer-Aided Drug Design (CADD) Group.
Proper citation: Open National Cancer Institute Database (RRID:SCR_014886) 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
Institute dedicated to research in immunology by utilizing the academic and research communities in the La Jolla area as well as technological advances in biomedical research, imaging and analysis. Specific topics include autoimmune disease, cancer, allergies, infectious diseases and inflammation.
Proper citation: La Jolla Institute for Immunology (RRID:SCR_014845) Copy
A public research university in Colchester, Essex, England. The institution has degree programs that span the humanities, social sciences, and health.
Proper citation: University of Essex; England; United Kingdom (RRID:SCR_014725) Copy
https://imdevsoftware.wordpress.com/tutorials/
A portal and resource for tutorials on a variety of data analysis techniques, the use of tools such as MetaMapR, workshops on data visualization, and R code manuals.
Proper citation: TeachingDemos (RRID:SCR_014689) Copy
Database of Coherent X-ray Imaging (CXI) experiments. This data is widely accessible to researchers worldwide.
Proper citation: Coherent X-Ray Imaging Data Bank (CXIDB) (RRID:SCR_014722) Copy
Open access repository for Johns Hopkins University researchers to share their research data. Data repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). Each dataset has citation and DOI, facilitating attribution, and connection to research publications.
Proper citation: Johns Hopkins Research Data Repository (RRID:SCR_014728) Copy
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