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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

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/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/bbuchfink/diamond

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

Proper citation: DIAMOND (RRID:SCR_016071) Copy   

•   Source: SciCrunch Registry

https://savannah.gnu.org/projects/datamash/

Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.

Proper citation: Datamash (RRID:SCR_016067) Copy   

•   Source: SciCrunch Registry

https://github.com/Ashod/garli

Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution.

Proper citation: GARLI (RRID:SCR_016117) Copy   

•   Source: SciCrunch Registry

https://web.archive.org/web/20180212152753/http://www.frantz.fi/software/gdpc.php

Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame.

Proper citation: gdpc (RRID:SCR_016119) Copy   

•   Source: SciCrunch Registry

https://biosyntax.org/

Software for syntax highlighting for computational biology.

Proper citation: bioSyntax (RRID:SCR_016207) Copy   

•   Source: SciCrunch Registry

http://phonbank.talkbank.org/

Database for study of early phonological development using Phon program. Child phonology component of TalkBank system.

Proper citation: PhonBank (RRID:SCR_016312) Copy   

•   Source: SciCrunch Registry

https://www.nichd.nih.gov/research/supported/NCS/researchers

Data and sample repository for National Children's Study. Provides access to data and samples collected from over 5,600 U.S. birth families to study environmental influences on child health and development. Data and biological and environmental samples are freely available, with approved request, for scientific research.

Proper citation: National Children's Study (NCS) Archive (RRID:SCR_016311) Copy   

•   Source: SciCrunch Registry

https://github.com/kingufl/cOMet

Software for error correction of optical mapping data.

Proper citation: cOMet (RRID:SCR_016276) Copy   

•   Source: SciCrunch Registry

https://www.biomax.com/neuroxm

Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data.

Proper citation: NeuroXM Brain Science Suite (RRID:SCR_016372) Copy   

•   Source: SciCrunch Registry

https://github.com/HicServices/RDMP/wiki

Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.

Proper citation: Research Data Management Platform (RRID:SCR_016268) Copy   

•   Source: SciCrunch Registry

http://starbase.sysu.edu.cn/index.php

Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.

Proper citation: Starbase V2.0 (RRID:SCR_016303) Copy   

•   Source: SciCrunch Registry

https://fractalis.lcsb.uni.lu/

Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis.

Proper citation: Fractalis (RRID:SCR_016362) Copy   

•   Source: SciCrunch Registry

https://github.com/lanagarmire/lilikoi

Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.

Proper citation: lilikoi (RRID:SCR_016361) Copy   

•   Source: SciCrunch Registry

https://www.pbcconsortium.org/

Portal to provide a repository for beta-cell data, to connect researchers from different backgrounds interested in contributing data, models and/or ideas for new insights into beta-cell biology. Used to understand beta-cell biology and diabetes through a cross-disciplinary approach for the assembly of spatiotemporal multi-scale whole cell models of human pancreatic beta-cells.

Proper citation: The Pancreatic Beta-Cell Consortium (RRID:SCR_016328) Copy   

•   Source: SciCrunch Registry