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A commercial organization that suppplies software which creates separate HIPAA-compliant repositories of de-identified patient records and reports. This software allows clinicians, researchers, and administrative leadership to safely access, search, share, and analyze de-identified patient-level data. DE-ID can be acquired as stand-alone tool or integrated with data networks or clinical information systems.
Proper citation: DE-ID Data Corp (RRID:SCR_008668) Copy
http://www.opentox.org/dev/apis/api-1.1/structure
Tools for the integration of data from various sources (public and confidential), for the generation and validation of computer models for toxic effects, libraries for the development and seamless integration of new algorithms, and scientifically sound validation routines. The goal of OpenTox is to develop an interoperable predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications. OpenTox is relevent for users from a variety of research areas: Toxicological and chemical experts (e.g. risk assessors, drug designers, researchers) computer model developers and algorithm developers non specialists requiring access to Predictive Toxicology models and data OpenTox applications can combine multiple web services providing users access to distributed toxicological resources including data, computer models, validation and reporting. Applications are based on use cases that satisfy user needs in predictive toxicology. OpenTox was initiated as a collaborative project involving a combination of different enterprise, university and government research groups to design and build the initial OpenTox framework. Additionally numerous organizations with industry, regulatory or expert interests are active in providing guidance and direction. The goal is to expand OpenTox as a community project enabling additional expert and user participants to be involved in developments in as timely a manner as possible. To this end, our mission is to carry out developments in an open and transparent manner from the early days of the project, and to open up discussions and development to the global community at large, who may either participate in developments or provide user perspectives. Cooperation on data standards, data integration, ontologies, integration of algorithm predictions from different methods, and testing and validation all have significant collaboration opportunities and benefits for the community. OpenTox is working to meet the requirements of the REACH legislation using alternative testing methods to contribute to the reduction of animal experiments for toxicity testing. Relevant international authorities (e.g., ECB, ECVAM, US EPA, US FDA) and industry organizations participate actively in the advisory board of the OpenTox project and provide input for the continuing development of requirement definitions and standards for data, knowledge and model exchange. OpenTox actively supports the development and validation of in silico models and algorithms by improving the interoperability between individual systems (common standards for data and model exchange), increasing the reproducibility of in silico models (by providing a quality source of structures, toxicity data and algorithms) and by providing scientifically sound and easy-to-use validation routines. OpenTox is committed to the support and integration of alternative testing methods using in vitro assay approaches, systems biology, stem cell technology, and the mining and analysis of human epidemiological data. Hence the framework design must take into account extensibility to satisfy a broad range of scientific developments and use cases.
Proper citation: OpenTox Framework (RRID:SCR_008686) Copy
Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness.
Proper citation: NIMH Repository and Genomics Resources (RRID:SCR_006698) Copy
https://bionanogenomics.com/wp-content/uploads/2017/01/30047-Irys-User-Guide.pdf
System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies.
Proper citation: BioNano Irys system (RRID:SCR_016754) Copy
https://www.scanco.ch/microct100.html
Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.
Proper citation: SCANCO Medical microCT 100 system (RRID:SCR_017119) Copy
Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols.
Proper citation: BICCN Cell Registry (RRID:SCR_017267) Copy
http://www.informatics.jax.org/home/strain
MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes.
Proper citation: Strains, SNPs and Polymorphisms (RRID:SCR_017518) Copy
http://promoter.bx.psu.edu/hi-c/
Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: 3D Genome (RRID:SCR_017525) Copy
https://www.ncbi.nlm.nih.gov/pubmed/17539361
Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people.
Proper citation: Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) Copy
https://www.selectscience.net/products/gel-logic-212-pro/?prodID=83511#tab-2
Automated gel imaging system for imaging fluorescence or colorimetric data in sample formats such as gels (DNA/Coomassie/Silver stain) membranes, and 96 well plates. Features include autofocusing and directed autoexposure.
Proper citation: Carestream Gel Logic 212 PRO Imaging System (RRID:SCR_018029) Copy
Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted.
Proper citation: medRxiv (RRID:SCR_018222) Copy
Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.
Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy
http://bioinformatics.mdanderson.org/main/BreakFusion
Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data.
Proper citation: BreakFusion (RRID:SCR_001102) Copy
https://code.google.com/p/knime4bio/
A set of custom nodes for the KNIME (The Konstanz Information Miner) graphical workbench, for analysing next-generation sequencing (NGS) data without the requirement of programming skills.
Proper citation: Knime4Bio (RRID:SCR_005376) Copy
http://cran.r-project.org/web/packages/gap/
GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.
Proper citation: Genetic Analysis Package (RRID:SCR_003006) Copy
A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.
Proper citation: GraphPad (RRID:SCR_000306) Copy
https://pynwb.readthedocs.io/en/latest/
Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.
Proper citation: PyNWB (RRID:SCR_017452) Copy
https://github.com/BioDepot/nbdocker
Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.
Proper citation: nbdocker (RRID:SCR_017159) Copy
http://dsarm.niapublications.org/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 18, 2014.
A networking site for investigators using animal models to study aging, developed to provide a venue for sharing information about research models for aging studies. If you have tissue or data from animal models relevant to aging research that you are willing to share with other investigators, D-SARM allows you to identify the model and provides a secure, blinded email contact for investigators who would like to contact you about acquiring tissue or related resources. Investigators looking for resources from a particular model enter search terms describing the model of interest and then use the provided link to send emails to the contacts (names blinded) listed in the search results to initiate dialog about tissue or resources available for sharing. The database is housed on a secure server and admission to the network is moderated by the NIA Project Officer and limited to investigators at academic, government and non-profit research institutions. The goal is to provide a secure environment for sharing information about models used in aging research, promoting the sharing of resources, facilitating new research on aging in model systems, and increasing the return on the investment in research models.
Proper citation: Database for Sharing Aging Research Models (RRID:SCR_008691) Copy
http://connectivity.brain-map.org/transgenic
Data detailing transgene expression in Cre and other driver lines for adult and developing brain. Experiments include colorimetric in situ hybridization, fluorescent in situ hybridization and other histological methods. Expression maps of transgenic Cre and other driver lines in mice.
Proper citation: Allen Brain Atlas expression map of Cre and other drivers (RRID:SCR_017510) Copy
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