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https://github.com/ABCD-STUDY/tick-tock
Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface.
Proper citation: tick-tock (RRID:SCR_016023) Copy
https://github.com/ABCD-STUDY/Fast-Track-Image-Sharing
Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA).
Proper citation: Fast-Track-Image-Sharing (RRID:SCR_016021) Copy
https://github.com/ABCD-STUDY/eprime-data-clean
Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests.
Proper citation: eprime-data-clean (RRID:SCR_016020) Copy
https://github.com/ABCD-STUDY/geocoding
Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.
Proper citation: geocoding (RRID:SCR_016007) Copy
Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.
Proper citation: National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) Copy
https://github.com/ABCD-STUDY/numerical-fitting
Software for a numerical computation library that performs numerical calculations. Used in ABCD study.
Proper citation: numerical-fitting (RRID:SCR_016025) Copy
http://www.duke.edu/web/gpcr-assay/index.html
Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.
Proper citation: Addiction Research GPCR Assay Bank (RRID:SCR_002895) Copy
http://www.kaluefflab.com/znpindex.html
Database of neurobehavioral and physiological data of adult zebrafish models, complementing the available repositories for zebrafish genetic information, by providing a dynamic, open-access data repository of comprehensive, curated collection of results from zebrafish neurobehavioral experiments. As of May 2012, it contains over 4,500 experimental results, from over 75 unique physiological and behavioral tests and 330 different drug treatments. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models. Overall, this program will allow investigators to rapidly review data, to direct their research using these models. Data and protocol submissions are now being accepted.
Proper citation: Zebrafish Neurophenome Project Database (RRID:SCR_004482) Copy
Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.
Proper citation: exRNA Atlas (RRID:SCR_017221) Copy
Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.
Proper citation: EpiModel (RRID:SCR_018539) Copy
Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords.
Proper citation: RatsPub (RRID:SCR_018905) Copy
http://www.nitrc.org/projects/voxbo
Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.
Proper citation: VoxBo (RRID:SCR_002166) Copy
http://www.icpsr.umich.edu/icpsrweb/NAHDAP/
Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. Collection of data on drug addiction and HIV infection in United States. Most of datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available . Provides access to research data and technical assistance for data depositors. Provides e-workshops on data preparation and data systems.
Proper citation: National Addiction and HIV Data Archive Program (NAHDAP) (RRID:SCR_000636) Copy
Database of bibliographic details of over 9,000 references published between 1951 and the present day, and includes abstracts, journal articles, book chapters and books replacing the two former separate websites for Ian Stolerman's drug discrimination database and Dick Meisch's drug self-administration database. Lists of standardized keywords are used to index the citations. Most of the keywords are generic drug names but they also include methodological terms, species studied and drug classes. This index makes it possible to selectively retrieve references according to the drugs used as the training stimuli, drugs used as test stimuli, drugs used as pretreatments, species, etc. by entering your own terms or by using our comprehensive lists of search terms. Drug Discrimination Drug Discrimination is widely recognized as one of the major methods for studying the behavioral and neuropharmacological effects of drugs and plays an important role in drug discovery and investigations of drug abuse. In Drug Discrimination studies, effects of drugs serve as discriminative stimuli that indicate how reinforcers (e.g. food pellets) can be obtained. For example, animals can be trained to press one of two levers to obtain food after receiving injections of a drug, and to press the other lever to obtain food after injections of the vehicle. After the discrimination has been learned, the animal starts pressing the appropriate lever according to whether it has received the training drug or vehicle; accuracy is very good in most experiments (90 or more correct). Discriminative stimulus effects of drugs are readily distinguished from the effects of food alone by collecting data in brief test sessions where responses are not differentially reinforced. Thus, trained subjects can be used to determine whether test substances are identified as like or unlike the drug used for training. Drug Self-administration Drug Self-administration methodology is central to the experimental analysis of drug abuse and dependence (addiction). It constitutes a key technique in numerous investigations of drug intake and its neurobiological basis and has even been described by some as the gold standard among methods in the area. Self-administration occurs when, after a behavioral act or chain of acts, a feedback loop results in the introduction of a drug or drugs into a human or infra-human subject. The drug is usually conceptualized as serving the role of a positive reinforcer within a framework of operant conditioning. For example, animals can be given the opportunity to press a lever to obtain an infusion of a drug through a chronically-indwelling venous catheter. If the available dose of the drug serves as a positive reinforcer then the rate of lever-pressing will increase and a sustained pattern of responding at a high rate may develop. Reinforcing effects of drugs are distinguishable from other actions such as increases in general activity by means of one or more control procedures. Trained subjects can be used to investigate the behavioral and neuropharmacological basis of drug-taking and drug-seeking behaviors and the reinstatement of these behaviors in subjects with a previous history of drug intake (relapse models). Other applications include evaluating novel compounds for liability to produce abuse and dependence and for their value in the treatment of drug dependence and addiction. The bibliography is updated about four times per year.
Proper citation: Comprehensive Drug Self-administration and Discrimination Bibliographic Databases (RRID:SCR_000707) Copy
https://medicine.yale.edu/keck/nida/yped/
Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards.
Proper citation: YPED (RRID:SCR_001436) Copy
https://cloudreg.neurodata.io/
Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration.
Proper citation: CloudReg (RRID:SCR_022795) Copy
http://www.rhesusbase.org/drugDisc/CAM.jsp
OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families. Totally 496 human CAM genes were compiled and annotated. We have mapped these genes onto a novel cell adhesion molecule ontology (CAMO) that provides a hierarchical description of cell adhesion molecules and their functions. It is intended to provide a means to facilitate better and better understanding of the global and specific properties of CAMs through their genomic features, regulatory modes, expression patterns and disease associations become clearer. You may browse by CAM ontology, Chromosomes and Full Gene list.
Proper citation: OKCAM: Ontology-based Knowledgebase for Cell Adhesion Molecules (RRID:SCR_010696) Copy
https://github.com/QTIM-Lab/DeepNeuro
Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.
Proper citation: DeepNeuro (RRID:SCR_016911) Copy
https://github.com/smorabit/hdWGCNA
Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics.
Proper citation: hdWGCNA (RRID:SCR_027496) Copy
https://www.ohsu.edu/custom/library/digital-collections/projectionmap
Data set of thalamo-centric mesoscopic projection maps to the cortex and striatum. The maps are established through two-color, viral (rAAV)-based tracing images and high throughout imaging.
Proper citation: Mouse Thalamic Projectome Dataset (RRID:SCR_015702) Copy
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