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http://www.de-idata.com

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.nimhgenetics.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://biccn.org/data

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.medrxiv.org

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   

•   Source: SciCrunch Registry

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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://graphpad.com/

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   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/chembl/

Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.

Proper citation: ChEMBL (RRID:SCR_014042) Copy   

•   Source: SciCrunch Registry

http://www.rand.org/labor/FLS/MHSS.html

A data set of the health and socioeconomic factors that affect the elderly in Matlab, a region of rural Bangladesh. The survey captures measurements and statistics such as adult survival, health status, health care utilization, resource flows between generations and the impact of community services and infrastructure on adult health care. Data was collected through surveys that touch on four topics: household and individual information; determinants of natural fertility; migration out of the community; and community and provider survey of healthcare and education infrastructure.

Proper citation: Matlab Health and Socio-Economic Survey (RRID:SCR_008942) Copy   

•   Source: SciCrunch Registry

https://www.postgresql.org/

Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.

Proper citation: PostgreSQL (RRID:SCR_021067) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/genes.shtml

Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.

Proper citation: Genes, Genome Features and Maps (RRID:SCR_017524) Copy   

•   Source: SciCrunch Registry

http://www.cuilab.cn/transmir

Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.

Proper citation: TransmiR (RRID:SCR_017499) Copy   

•   Source: SciCrunch Registry