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http://msr.dom.wustl.edu/

Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry

Proper citation: NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) Copy   

•   Source: SciCrunch Registry

http://glycotech.ccrc.uga.edu/

Biomedical technology research center that develops technologies to increase understanding of the molecular basis of the involvement of carbohydrates in protein-carbohydrate interactions in disease and to develop more powerful technologies necessary to achieve this goal. Complex carbohydrates play an important role in many biomedically important processes, including inflammatory response, hormone action, malignancy, viral and bacterial infections and cell differentiation. The resource combines complimentary technologies: synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression and cell-based assays. As new technologies are developed, application to these processes will be pursued through collaborative and service projects.

Proper citation: Resource for Integrated Glycotechnology (RRID:SCR_009008) Copy   

•   Source: SciCrunch Registry

https://bioams.llnl.gov/

Biomedical technology research center that develops and refines accelerator mass spectrometry methods and instrumentation for the precise, quantitative and cost-effective measurement of the effects of drugs and toxicants on humans at safe doses. It facilitates the use of accelerator mass spectrometry in biomedical research and provides training and access for researchers.

Proper citation: National Resource for Biomedical Accelerator Mass Spectrometry (RRID:SCR_009006) Copy   

•   Source: SciCrunch Registry

http://cell.ccrc.uga.edu/world/glycomics/glycomics.php

Biomedical technology research center that develops and implements new technologies to investigate the glycome of cells, including glycoproteomics and glycoconjugate analysis, transcript analysis and bioinformatics. It develops the tools and technology to analyze in detail the glycoprotein and glycolipid expression of mouse embryonic stem cells and the cells into which they differentiate. The technology developed in the Center will allow an understanding of how glycosylation is controlled during differentiation and will allow the development of tools to promote the use of stem cells to treat human disease. In addition, the technology developed will be applicable to the study of other cell types, including cancer cells that are progressing to a more invasive phenotype. The technology developed will also allow others in the scientific community to participate in glycomics research through dissemination of the new methods developed and through the analytical services provided by the resource to other scientists requesting assistance in glycomic analyses.

Proper citation: Integrated Technology Resource for Biomedical Glycomics (RRID:SCR_009003) Copy   

•   Source: SciCrunch Registry

http://www-ssrl.slac.stanford.edu/content/science/ssrl-smb-program

Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis.

Proper citation: SSRL Structural Molecular Biology (RRID:SCR_009000) Copy   

•   Source: SciCrunch Registry

http://www.seg3d.org

A free volume processing segmenting tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering.

Proper citation: Seg3D (RRID:SCR_002552) Copy   

•   Source: SciCrunch Registry

http://smd.stanford.edu/cgi-bin/source/sourceSearch

SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool

Proper citation: SOURCE (RRID:SCR_005799) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/sbo/

A set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. The ontology consists of seven orthogonal vocabularies defining: the roles of reaction participants (eg. substrate), quantitative parameters (eg. Michaelis constant), a precise classification of mathematical expressions that describe the system (eg. mass action rate law), the modeling framework used (eg. logical framework), and a branch each to describe entity (eg. macromolecule) and interaction (eg. process) types, and a branch to define the different types of metadata that may be present within a model. SBO terms can be used to introduce a layer of semantic information into the standard description of a model, or to annotate the results of biochemical experiments in order to facilitate their efficient reuse. SBO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use. A programmatic access to the content of the Systems Biology Ontology is provided by Web Services.

Proper citation: SBO (RRID:SCR_006753) Copy   

•   Source: SciCrunch Registry

http://www.ibioseminars.org/

iBioSeminars offers: * Free, on-demand lectures: Many universities/colleges have limited access to high profile leaders in biological research. Our goal is to add 15-20 seminars per year, of similar quality to outstanding lectures that are currently in this library. Access, through web streaming or download, is completely free-of-charge. * Targeting a broad audience: iBioSeminars start with an extended introduction, making them accessible to non-specialists and students, and then progress to cover current research. Senior scientists and students can view and enjoy these lectures. * Education: iBioSeminars are being used by undergraduate and graduate teachers to augment their classroom material. We have now added an education component to this web site (including lecture notes, questions/answers and short video clips for teaching). * International communication: iBioSeminars have viewers in 115 countries and they are being internally promoted in several countries as an educational tool and scientific resource. * Goodwill: Lecturers generously donate their time to prepare these lectures. The project, largely funded by HHMI, is a grass roots efforts with time invested by several individuals at UCSF, HHMI and ASCB.

Proper citation: iBioSeminars (RRID:SCR_005848) Copy   

•   Source: SciCrunch Registry

https://neuroscienceblueprint.nih.gov/Resources-Tools/Blueprint-Resources-Tools-Library

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2023. National initiative to advance biomedical research through data sharing and online collaboration that provides data sharing infrastructure, software tools, strategies and advisory services. Groups may choose whether to share data internally or with external audiences. Hardware and data remain under control of individual user groups.

Proper citation: Biomedical Informatics Research Network (RRID:SCR_005163) Copy   

•   Source: SciCrunch Registry

http://www.physionet.org/

Collection of dissemination and exchange recorded biomedical signals and open-source software for analyzing them. Provides facilities for cooperative analysis of data and evaluation of proposed new algorithm. Providies free electronic access to PhysioBank data and PhysioToolkit software. Offers service and training via on-line tutorials to assist users at entry and more advanced levels. In cooperation with annual Computing in Cardiology conference, PhysioNet hosts series of challenges, in which researchers and students address unsolved problems of clinical or basic scientific interest using data and software provided by PhysioNet. All data included in PhysioBank, and all software included in PhysioToolkit, are carefully reviewed. Researchers are further invited to contribute data and software for review and possible inclusion in PhysioBank and PhysioToolkit. Please review guidelines before submitting material.

Proper citation: PhysioNet (RRID:SCR_007345) Copy   

•   Source: SciCrunch Registry

https://github.com/nbcrrolls/workflows/tree/master/Production/AmberGPUMDSimulation

A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like.

Proper citation: Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/gernerlab/cytomap/-/wikis/home

Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.

Proper citation: CytoMAP (RRID:SCR_021227) Copy   

•   Source: SciCrunch Registry

https://github.com/CEGRcode/stencil

Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise.

Proper citation: STENCIL (RRID:SCR_021878) Copy   

•   Source: SciCrunch Registry

http://www.mirtoolsgallery.org/miRToolsGallery/node/1055

Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: miRanda (RRID:SCR_017496) Copy   

•   Source: SciCrunch Registry

https://prokoplab.com/vistedd/

Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein.

Proper citation: Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) Copy   

•   Source: SciCrunch Registry

http://cisbp.ccbr.utoronto.ca

Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.

Proper citation: CIS-BP (RRID:SCR_017236) Copy   

•   Source: SciCrunch Registry

http://www.mrmatlas.org/

Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.

Proper citation: SRMAtlas (RRID:SCR_016996) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/131-shapeworks.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.

Proper citation: ShapeWorks (RRID:SCR_000424) Copy   

•   Source: SciCrunch Registry

https://github.com/plaisier-lab/sygnal

Software pipeline to integrate correlative, causal and mechanistic inference approaches into unified framework that systematically infers causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients. Used to decipher transcriptional regulatory networks from multi-omic and clinical patient data. Applicable for integrating genomic and transcriptomic measurements from human cohorts.

Proper citation: SYGNAL (RRID:SCR_023080) Copy   

•   Source: SciCrunch Registry