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http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

•   Source: SciCrunch Registry

http://vox.pharmacology.ucla.edu/home.html

Two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 cubic mm gene expression patterns in the brain obtained through voxelation. Voxelation employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems.

Proper citation: Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain (RRID:SCR_008065) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org

Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.

Proper citation: eMouseAtlas (RRID:SCR_002981) Copy   

•   Source: SciCrunch Registry

https://confluence.crbs.ucsd.edu/display/NIF/DRG

Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.

Proper citation: Drug Related Gene Database (RRID:SCR_003330) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/simple-t1-motion-detection

Software to measure the amount of ghosting artifacts in T1-weighted DICOM images. This program reads DICOM images and calculates a measure of the noise structure in one part of the image.

Proper citation: simple-t1-motion-detection (RRID:SCR_016022) Copy   

•   Source: SciCrunch Registry

https://ratgenes.org/

Portal includes information about genetic studies of drug abuse in outbred rats. Data center created in 2014 to perform genome wide association studies on numerous behavioral traits that have well established relevance to drug abuse using outbred rats.

Proper citation: NIDA center for genetic studies of drug abuse in outbred rats (RRID:SCR_021788) Copy   

•   Source: SciCrunch Registry

http://lrpath.ncibi.org/

Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.

Proper citation: LRPath (RRID:SCR_018572) Copy   

•   Source: SciCrunch Registry

http://crispr-era.stanford.edu/index.jsp

Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design.

Proper citation: CRISPR-ERA (RRID:SCR_018710) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/auto-scoring

Visualization software that calculates derived scores for the electronic record system REDCap (Research Electronic Data Capture) to build and manage online surveys and databases. Used in the ABCD-STUDY (Adolescent Brain Cognitive Development - STUDY) report framework.

Proper citation: auto-scoring (RRID:SCR_016015) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/little-man-task

Software tool to manage data and derived results. It is used for import of derived measures into REDCap (Research Electronic Data Capture).

Proper citation: little-man-task (RRID:SCR_016018) Copy   

•   Source: SciCrunch Registry

http://marmosetbrain.org/

Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex.

Proper citation: Marmoset Brain Connectivity Atlas (RRID:SCR_015964) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/redcap-completion

Software to measure item level completion in a large REDCap project. It provides a web-interface to review data and it is used in the ABCD project to assess data collection sites for the reached level of completion.

Proper citation: redcap-completion (RRID:SCR_016019) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/timeline-followback

Software to capture subject information about substance use using local copies of external files provided by the abcd-report framework of ABCD. No connection to REDCap is attempted to get events and participant names but local files are read in to supply this information.

Proper citation: timeline-followback (RRID:SCR_016017) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/aux-file-upload

Software application to upload functional MR imaging runs produce auxilary data that can be collected centrally. Connects to a subject database research electronic data capture (REDCap).

Proper citation: aux-file-upload (RRID:SCR_016026) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/FIONA-QC-PHANTOM

Software for online quality control operations performed on Phantom MRI data. It checks the accuracy and reproducibility of data.

Proper citation: FIONA-QC-PHANTOM (RRID:SCR_016024) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/nih-ipad-app-end-point

Data collection software for centrally and securely storing data from the NIH iPad application. It allows users to capture results from multiple iPads at a central location.

Proper citation: nih-ipad-app-end-point (RRID:SCR_016029) 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://prosightlite.northwestern.edu/

Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.

Proper citation: ProSight Lite (RRID:SCR_016908) Copy   

•   Source: SciCrunch Registry

https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

•   Source: SciCrunch Registry

https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

•   Source: SciCrunch Registry