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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
https://github.com/hakyimlab/PrediXcan
Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.
Proper citation: PrediXcan (RRID:SCR_016739) Copy
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
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
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
Manually curated database of exosomal proteins, RNA and lipids. Web based compendium of exosomal cargo. Database catalogs information from both published and unpublished exosomal studies. Mode of exosomal purification and characterization, biophysical and molecular properties are listed.
Proper citation: ExoCarta (RRID:SCR_021960) Copy
https://github.com/ABCD-STUDY/delay-discounting
Software that performs a delay-discounting task measuring impulsivity. Used in ABCD study.
Proper citation: delay-discounting (RRID:SCR_016031) Copy
Software that generates container-based behavioral experiments for reproducible science. It offers a library of experiments, games, and surveys, support for multiple kinds of databases, and robust documentation for the provided tools.
Proper citation: The Experiment Factory (RRID:SCR_016107) Copy
Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children.
Proper citation: Patient-Reported Outcomes Measurement Information System (RRID:SCR_004718) Copy
http://courses.jax.org/2012/addiction.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This course emphasizes genetic applications and approaches to drug addiction research through methodological instruction based on literature, data sets and informatics resources drawn from studies of addiction related phenotypes. The course includes plenary sessions on major progress in addiction genetics, and discussion sessions in which students present their work for discussion on applications of genetic methods. Students will leave the course able to design and interpret genetic and genomic studies of addiction as they relate to their specific research question, and will be able to make use of current bioinformatics resources to identify research resources and make use of public data sources in their own research.
Proper citation: Short Course on the Genetics of Addiction (RRID:SCR_005560) Copy
Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.
Proper citation: zfishbook (RRID:SCR_006896) Copy
https://reprint-apms.org/?q=chooseworkflow
Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.
Proper citation: CRAPome (RRID:SCR_025008) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST
Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.
Proper citation: FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) Copy
https://github.com/calico/borzoi
Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.
Proper citation: Borzoi (RRID:SCR_026619) Copy
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