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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).
Proper citation: iTools (RRID:SCR_009626) Copy
http://www.jneurosci.org/supplemental/18/12/4570/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest.
Proper citation: Hippocampal Slice Wave Animations (RRID:SCR_008372) Copy
https://github.com/ABCD-STUDY/redcap-importer
Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import.
Proper citation: redcap-importer (RRID:SCR_016032) Copy
https://github.com/ABCD-STUDY/ABCDreport
Software application as a simple system to review study progress. Used in ABCD study.
Proper citation: ABCDreport (RRID:SCR_016030) Copy
https://github.com/ABCD-STUDY/FIONASITE
Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive.
Proper citation: FIONASITE (RRID:SCR_016012) Copy
https://github.com/ABCD-STUDY/Minimally-Processed-Image-Sharing
Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository.
Proper citation: Minimally-Processed-Image-Sharing (RRID:SCR_016016) Copy
https://github.com/ABCD-STUDY/enroll
Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study.
Proper citation: enroll (RRID:SCR_016011) Copy
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/FIONA-protocol-compliance
Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance.
Proper citation: FIONA-protocol-compliance (RRID:SCR_016027) 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
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
http://umcd.humanconnectomeproject.org
Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately.
Proper citation: USC Multimodal Connectivity Database (RRID:SCR_012809) Copy
http://www.nida.nih.gov/mediaguide/index.html
The latest findings on the science of drug abuse and addiction and commonly abused drugs, and lists resources for more information. They are committed to bringing timely, factual information on addiction and treatment to the press and public. NIDA''s Public Information and Liaison Branch (PILB) is part of NIDA''s Office of Science Policy and Communications. Linking scientists, the scientific community, and the media, PILB supports the rapid dissemination of research information to inform policy and to improve practice. NIDA''s goal is to ensure that science - not ideology or anecdote - forms the foundation of public information on drug abuse and addiction. NIDAs online MEDIA GUIDE provides answers on how to find what you need to know about drug abuse and addiction, including information on the basics (The Science of Drug Abuse and Addiction and Commonly Abused Drugs), resources (Where to Find Nationwide Trends and Statistics, NIDA Resources, and Other Government Web Sites for Health and Science Information), NIDAs history and background, a glossary and relevant contact information. NIDA is pleased to offer this guide to the important findings that are emerging as a result of research on addiction and its treatment. NIDA, part of the National Institutes of Health under the U.S. Department of Health and Human Services, supports most of the world''s research on drug abuse and addiction, including basic and behavioral science research that addresses fundamental and essential questions relevant to drug abuse, ranging from its causes and consequences to its treatment and prevention. The purpose of this guide is to give journalists fast and user-friendly access to the latest scientific information but it is useful for anyone interested in how to access accurate information about drug abuse and addiction. In more than three decades as a researcher, I have seen the impact that science and health journalists have had in bringing scientific research to the public. It is through information that Americans gain hope and understanding. I have come to know many of you over the years and remain committed to releasing scientific information as quickly as possible for rapid dissemination to the public. Please keep this guide nearby as a useful tool and let us know how NIDA''s public liaison staff can help you reach your information and deadline needs. A PDF version is available for download.
Proper citation: National Institute on Drug Abuse Media Guide (RRID:SCR_006850) 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
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
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
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