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http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://github.com/fmaguire/Bridger_Assembler

Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

Proper citation: Bridger (RRID:SCR_017039) Copy   

•   Source: SciCrunch Registry

https://modbase.compbio.ucsf.edu/foxs/

Web server for computing theoretical scattering profile of structure and fitting of experimental profile. Computes SAXS profile of given atomistic model and fits it to experimental profile. Used for structural modeling applications with small angle X-ray scattering data.

Proper citation: FoXS (RRID:SCR_017269) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/redcap-to-nda

Software for metadata-driven electronic data capture to export REDCap data dictionaries and data to the NIMH National Data Archive (NDA). Prepares data submissions as csv formatted spreadsheets for data dictionary spreadsheets and for data spreadsheets.

Proper citation: redcap-to-nda (RRID:SCR_016008) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

System designed for automated collection of images from a transmission electron microscope.

Proper citation: Leginon (RRID:SCR_016731) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/cfs

Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.

Proper citation: Cleveland Family Study (RRID:SCR_016585) Copy   

•   Source: SciCrunch Registry

http://proteogenomics.musc.edu/ma/musc_madb.php?page=home&act=manage

Database that is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community.

Proper citation: MUSC DNA Microarray Database (RRID:SCR_010977) Copy   

•   Source: SciCrunch Registry

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.

Proper citation: Skyline (RRID:SCR_014080) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/laplacebeltrami/

A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface.

Proper citation: Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) Copy   

•   Source: SciCrunch Registry

http://www.kojak-ms.org/

Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets.

Proper citation: Kojak (RRID:SCR_021028) Copy   

•   Source: SciCrunch Registry

http://superfly.ucsd.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions.

Proper citation: Homophila (RRID:SCR_007717) Copy   

•   Source: SciCrunch Registry

http://www.geneatlas.org/gene/main.jsp

This website allows visitors to search for genes of interest based on their spatial expression patterns in the Postnatal Day 7 mouse brain. Geneatlas provides two searching tools: A graphical interface for customized spatial queries; A textual interface for querying annotated structures. Geneatlas is the product of a collaboration between researchers at Baylor College of Medicine, Rice University, and University of Houston.

Proper citation: Gene Atlas (RRID:SCR_008089) Copy   

•   Source: SciCrunch Registry

http://mouseatlas.caltech.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on October, 01, 2019.
3D digital atlas of normal mouse development constructed from magnetic resonance image data. The download is a zipped file containing the six atlases Theiler Stages (ts) 13, 21,23, 24, 25 and 26 and MRI data for an unlabeled ts19 embryo. To view the atlases, download and install MBAT from: http://mbat.loni.ucla.edu Specimens were prepared in aqueous, isotonic solutions to avoid tissue shrinkage. Limited specimen handling minimized physical perturbation of the embryos to ensure accurate geometric representations of developing mouse anatomy. Currently, the atlas contains orthogonal sections through MRI volumes, three stages of embryos that have annotated anatomy, photographs of several stages of development, lineage trees for annotated embryos and a gallery of images and movies derived from the annotations. Anatomical annotations can be viewed by selecting a transverse section and selecting a pixel on the displayed slice.

Proper citation: 3D MRI Atlas of Mouse Development (RRID:SCR_008090) Copy   

•   Source: SciCrunch Registry

http://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) Copy   

•   Source: SciCrunch Registry

http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage

A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.

Proper citation: ArrayQuest (RRID:SCR_010935) Copy   

•   Source: SciCrunch Registry

https://www.eagle-i.net/

Web application to discover resources available at participating networked universities. This distributed platform for creating and sharing semantically rich data is built around semantic web technologies and follows linked open data principles.

Proper citation: Eagle I (RRID:SCR_013153) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/validate29/

Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels.

Proper citation: VALiDATe29 Squirrel Monkey Brain Atlas (RRID:SCR_015542) Copy   

•   Source: SciCrunch Registry

http://www.nbcr.net/

Biomedical technology research center that conducts, catalyzes and enables multiscale biomedical research, focusing on four key activities: 1) integrating computational, data and visualization resources in a transparent, advanced grid environment to enable better access to distributed data, computational resources, instruments and people; 2) developing and deploying advanced computational tools for modeling and simulation, data analysis, query and integration, three-dimensional image processing and interactive visualization; 3) delivering and supporting advanced grid/cyberinfrastructure for biomedical researchers; and 4) training a cadre of new researchers to have an interdisciplinary, working knowledge of computational technology relevant to biomedical scientists. NBCR enables biomedical scientists to address the challenge of integrating detailed structural measurements from diverse scales of biological organization that range from molecules to organ systems in order to gain quantitative understanding of biological function and phenotypes. Predictive multi-scale models and their driving biological research problems together address issues in modeling of sub-cellular biophysics, building molecular modeling tools to accelerate discovery, and defining tools for patient-specific multi-scale modeling. NBCR furthers these driving problems by developing tools and models based on rapid advances in mathematics and information technology, incorporating them into NBCR pipelines or problem solving environments, and addressing the inevitable changes in the underlying cyber-infrastructure technologies and continually adapting codes over time. Their technology focus integrates both the biological applications and the underlying support software into reproducible science workflows that can function across a number of physical infrastructures.

Proper citation: National Biomedical Computation Resource (RRID:SCR_002656) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/

Biomedical technology research center that develops computer-aided, advanced microscopy for the acquisition of structural and functional data in the dimensional range of 1 nm to 100 um, a range encompassing macromolecules, subcellular structures and cells. Novel specimen-staining methods, imaging instrumentsincluding intermediate high-voltage transmission electron microscopes (IVEMs) and high-speed, large-format laser-scanning light microscopesand computational capabilities are available for addressing mesoscale biological microscopy of proteins and macromolecular complexes in their cellular and tissue environments. These technologies are developed to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed. NCMIR fulfills its mission through technology development, collaboration, service, training, and dissemination. It aims to develop preparative methods and analytical approaches to 3D microscopy applicable to neurobiology and cell biology, incorporating equipment and implementing software that expand the analysis of 3D structure. The core research activities in the areas of specimen development, instrument development, and software infrastructures maximize the advantages of higher voltage electron microscopy and correlated light microscopies to make ambitious imaging studies across scales routine, and to facilitate the use of resources by biomedical researchers. NCMIR actively recruits outside users who will not only make use of these resources, but who also will drive technology development and receive training.

Proper citation: National Center for Microscopy and Imaging Research (RRID:SCR_002655) Copy   

•   Source: SciCrunch Registry

https://www.bio.aps.anl.gov/

Biomedical technology research center and training resource for the study of the structure of partially ordered biological molecules, complexes of biomolecules and cellular structures under conditions similar to those present in living cells and tissues. The goal of research at BioCAT is to determine the detailed structure and mechanism of action of biological systems at the molecular level. The techniques used are X-ray fiber diffraction, X-ray solution scattering and X-ray micro-emission and micro-absorption spectroscopy, with an emphasis on time-resolved studies and the development of novel techniques.

Proper citation: BioCAT (RRID:SCR_001440) Copy   

•   Source: SciCrunch Registry