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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
Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science.
Proper citation: BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) Copy
https://github.com/ABCD-STUDY/DEAP
Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.
Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy
Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.
Proper citation: NeMOarchive (RRID:SCR_016152) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
http://abacus.gene.ucl.ac.uk/software/indelible/
Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.
Proper citation: Indelible (RRID:SCR_016163) 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://www.microsoft.com/en-gb/
Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.
Proper citation: Microsoft Excel (RRID:SCR_016137) 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
Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
Proper citation: Gentle (RRID:SCR_016127) Copy
http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bio++ (RRID:SCR_016055) Copy
https://github.com/thegenemyers/DAZZ_DB
Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.
Proper citation: Dazzler (RRID:SCR_016069) Copy
Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.
Proper citation: GOTrack (RRID:SCR_016399) Copy
https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html
Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.
Proper citation: Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) Copy
Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users.
Proper citation: OmicsBean (RRID:SCR_016322) Copy
https://github.com/Sung-Huan/ANNOgesic
Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.
Proper citation: ANNOgesic (RRID:SCR_016326) Copy
Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.
Proper citation: CycIF.org (RRID:SCR_016267) Copy
https://github.com/alesssia/YAMP
Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability.
Proper citation: YAMP (RRID:SCR_016236) Copy
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