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https://cosmiic.org/

Open source neurostimulation and recording hardware instrument platform. Part of the SPARC project. COSMIIC is based on the Networked Neuroprosthesis developed at Case Western Reserve University.

Proper citation: COSMIIC HORNET (RRID:SCR_023679) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/glimmerhmm/

A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).

Proper citation: GlimmerHMM (RRID:SCR_002654) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/NIHbmic/nih_data_sharing_repositories.html

A listing of NIH supported data sharing repositories that make data accessible for reuse. Most accept submissions of appropriate data from NIH-funded investigators (and others), but some restrict data submission to only those researchers involved in a specific research network. Also included are resources that aggregate information about biomedical data and information sharing systems. The table can be sorted according by name and by NIH Institute or Center and may be searched using keywords so that you can find repositories more relevant to your data. Links are provided to information about submitting data to and accessing data from the listed repositories. Additional information about the repositories and points-of-contact for further information or inquiries can be found on the websites of the individual repositories.

Proper citation: NIH Data Sharing Repositories (RRID:SCR_003551) Copy   

•   Source: SciCrunch Registry

http://neurospy.org

neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware.

Proper citation: neurospy (RRID:SCR_007016) Copy   

•   Source: SciCrunch Registry

http://dockground.bioinformatics.ku.edu/

Data sets, tools and computational techniques for modeling of protein interactions, including docking benchmarks, docking decoys and docking templates. Adequate computational techniques for modeling of protein interactions are important because of the growing number of known protein 3D structures, particularly in the context of structural genomics. The first release of the DOCKGROUND resource (Douguet et al., Bioinformatics 2006; 22:2612-2618) implemented a comprehensive database of cocrystallized (bound) protein-protein complexes in a relational database of annotated structures. Additional releases added features to the set of bound structures, such as regularly updated downloadable datasets: automatically generated nonredundant set, built according to most common criteria, and a manually curated set that includes only biological nonobligate complexes along with a number of additional useful characteristics. Also included are unbound (experimental and simulated) protein-protein complexes. Complexes from the bound dataset are used to identify crystallized unbound analogs. If such analogs do not exist, the unbound structures are simulated by rotamer library optimization. Thus, the database contains comprehensive sets of complexes suitable for large scale benchmarking of docking algorithms. Advanced methodologies for simulating unbound conformations are being explored for the next release. The Dockground project is developed by the Vakser lab at the Center for Bioinformatics at the University of Kansas. Parts of Dockground were co-developed by Dominique Douguet from the Center of Structural Biochemistry (INSERM U554 - CNRS UMR5048), Montpellier, France.

Proper citation: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING (RRID:SCR_007412) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/icr

Facility provides service operations for sample analysis that requires ultrahigh resolution and high mass accuracy of Fourier Transform Ion Cyclotron Resonance. Used for research in biomolecular analysis, hydrogen-deuterium exchange and environmental and petrochemical analysis. Four FT-ICR mass spectrometers feature high magnetic fields including the world-record 21 tesla and are compatible with multiple ionization and fragmentation techniques.

Proper citation: National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility (RRID:SCR_017361) Copy   

•   Source: SciCrunch Registry

https://www.unmc.edu/vcr/cores/vcr-cores/flow-cytometry/index.html

Provides central location for flow cytometry instrumentation and education. Services include Flow Cytometry,Cell sorting, data analysis, training. Software packages to analyze data include ModFit LT, BD FACSDiva v6, Cell Quest Pro, and FlowJo vX, from facility workstations.

Proper citation: Nebraska University Medical Center Flow Cytometry Research Core Facility (RRID:SCR_017736) Copy   

•   Source: SciCrunch Registry

http://www.columbia.edu/cu/biology/resources/proteomics/

Core provides identification of proteins and metabolites with differential quantitative expression in cells, tissues or in protein affinity purifications. Particular emphasis is on quantitative analysis of posttranslational modifications such as phosphorylation.

Proper citation: Columbia University Quantitative Proteomics and Metabolomics Core Facility (RRID:SCR_017747) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/emr/

EMR Facility offers home-built, high-frequency and high-field continuous-wave instruments providing frequency coverage from 9 GHz to 1 THz, with additional frequencies available up to 2.5 THz using molecular gas laser. EMR covers variety of magnetic resonance techniques associated with electron like Electron Paramagnetic/Spin Resonance (EPR/ESR). EPR/ESR can be performed on any sample that has unpaired electron spins and used in applications in physics, materials science, chemistry and biology, including studies of impurity states, molecular clusters, antiferromagnetic, ferromagnetic and thin film compounds, natural or induced radicals, optically excited paramagnetic states, electron spin-based quantum information devices, transition-metal based catalysts; and for structural and dynamical studies of metallo-proteins, spin-labeled proteins and other complex bio-molecules and their synthetic models.

Proper citation: National High Magnetic Field Laboratory Electron Magnetic Resonance Core Facility (RRID:SCR_017359) Copy   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/dc-field

Facility located at MagLab headquarters near Florida State University in Tallahassee. Contains 14 resistive magnet cells connected to 56 megawatt DC power supply and 15,000 square feet of cooling equipment to remove heat generated by magnets. Includes several superconducting magnets operating at millikelvin temperatures. Among these instruments is 45-tesla hybrid magnet, which offers scientists strongest continuous magnetic field in world. Research is supported by magnet plant and cryogenic system operators. Technicians design, build and repair instruments for user research.

Proper citation: National High Magnetic Field Lab DC Field Core Facility (RRID:SCR_017358) Copy   

•   Source: SciCrunch Registry

http://mass-spec.stanford.edu

Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development.

Proper citation: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility (RRID:SCR_017801) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/microscopy-laboratory

Core offers comprehensive light and electron microscopy technologies. Our scientists use light microscopes and electron microscopes at resolutions ranging from centimeters to angstroms, providing clear and detailed images.We assist at every stage of your experiment, offering research-design consultation and instrument training, as well as guidance in study execution, analysis, and presentation for publication.

Proper citation: New York University School of Medicine Langone Health Microscopy Laboratory Core Facility (RRID:SCR_017934) Copy   

•   Source: SciCrunch Registry

https://brcf.medicine.umich.edu/cores/bioinformatics-core/

Core helps researchers identify and interpret patterns in RNA and DNA by placing sequencing data into biologically meaningful context. Services include experimental design, developing reproducible workflows, analyzing next-generation sequencing data, and supporting manuscript development/publication.

Proper citation: University of Michigan Medical School Bioinformatics Core (RRID:SCR_019168) Copy   

•   Source: SciCrunch Registry

https://www.biotech.cornell.edu/core-facilities-brc/facilities/epigenomics-facility

Provides service that maps protein DNA interactions genome wide, tracks experimental metadata, and implements quality controlled data processing and research based analysis pipelines. Provides epigenomic and bioinformatic research resources and services that include sample preparation services and data generation. Open source platforms enable and reinforce FAIR data practices. Core is able to receive and process cell and tissue samples for various diagnostic epigenetic assays.

Proper citation: Cornell University BRC Epigenomics Core Facility (RRID:SCR_021287) Copy   

•   Source: SciCrunch Registry

https://www.socr.umich.edu/

SOCR designs, validates and freely disseminates knowledge. The Resource develops AI/ML tools, mathematical models, and end-to-end data analytic protocols for biomedical and health studies. It provides portable online aids for probability, statistics and health science education, promotes technology enhanced instruction, supports efficient statistical computing, supports AI-services, and advances predictive big data analytics. The SOCR platform includes repository of interactive apps, datasets and case-studies, computational tools, visualization approaches, instructional resources, learning materials, and curricular components. SOCR faculty, staff, and students support data and information science collaborations and analytic partnerships involving biomedical, healthcare, and biostatistical investigations.

Proper citation: University of Michigan Statistics Online Computational Resource Core Facility (RRID:SCR_022917) Copy   

•   Source: SciCrunch Registry

https://www.cores.emory.edu/iemc/

Core helps investigators use the latest technologies on structural research in their projects. Provides expertise in experimental needs.

Proper citation: Emory University Robert P. Apkarian Integrated Electron Microscopy Core Facility (RRID:SCR_023537) Copy   

•   Source: SciCrunch Registry

https://www.pharmgkb.org/

NIH-funded resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relationships.

Proper citation: PharmKGB (RRID:SCR_025580) Copy   

•   Source: SciCrunch Registry

https://sparc.science/about/consortia/precision

Project titled Program to Reveal and Evaluate Cells-to-gene Information that Specify Intricacies, Origins, and Nature of Human Pain (PRECISION) Network to develop meaningful resource for knowledge transfer, and to integrate and share Human Pain Associated Genes and Cell Datasets. Building knowledge platform to visualize, query, and interact with these data will support researchers and help accelerate dissemination of vital data to the larger scientific community. These goals align with NIH Helping to End Addiction Long-term (HEAL) Initiative, which seeks to accelerate the discovery and successful translation of non-addictive pain therapeutics. PRECISION Human Pain Network will leverage prior interdisciplinary collaboration to create workflows, tools, and infrastructure to define data and metadata types, to improve data management and sharing, and to integrate datasets and visualization tools.

Proper citation: NIH PRECISION Human Pain Network (RRID:SCR_025458) Copy   

•   Source: SciCrunch Registry

https://github.com/jefftc/changlab

Software system for performing bioinformatics analyses. System includes knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. Backwards-chaining rule-based expert system comprised of data model that can capture richness of biological data, and inference engine that reasons on knowledge base to produce workflows. Knowledge base is populated with rules to analyze microarray and next generation sequencing data.

Proper citation: BETSY (RRID:SCR_026239) Copy   

•   Source: SciCrunch Registry

https://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

Offers access to instrumentation, training and services for structure determination of macromolecular molecules using single crystal X-ray diffraction and/or cryo-EM Single Particle Analysis (SPA). Instrumentation is available for initial crystallization trials, optimization of crystallization, single crystal X-ray diffraction and data collection at synchrotron radiation facilities, as well as electron microscopy grid preparation for cryo-EM (SPA), screening and data collection using a Thermo Scientific Tundra Cryo-TEM and assistance for data collection at national laboratories.

Proper citation: University of Oklahoma Biomolecular Structure Core Facility (RRID:SCR_028074) Copy   

•   Source: SciCrunch Registry