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http://bmsr.usc.edu/trainingdissemination/short-courses/

Short courses to train the broader biomedical research community in the modeling and simulation methodologies developed by Resource Scientists and others.

Proper citation: BMSR Short Courses (RRID:SCR_000100) Copy   

•   Source: SciCrunch Registry

https://github.com/CraigList056/iqas

Modeling document labels using Latent Dirichlet Allocation is component tool under Integrated Quality Assurance System of Camarines Sur Polytechnic Colleges which categorizes text of particular document and use it for auto-tagging.

Proper citation: IQAS (RRID:SCR_023146) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/WhatAndWhy/Sensation/Audition/Pages/NIH-Toolbox-Words-in-Noise-(WIN)-Test.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Assessment test that measures how much difficulty a person might have hearing in a noisy environment. A recorded voice instructs the participant to listen to and then repeat words. The task becomes increasingly difficult as the background noise gets louder. This test was developed to measure a person's ability to recognize single words presented amid varying levels of background noise. Recommended for participants ages 6-85 and takes approximately six minutes to administer.

Proper citation: NIH Toolbox Words-in Noise Test (RRID:SCR_000174) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-cleaner/

Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.

Proper citation: NGS-Cleaner (RRID:SCR_000574) Copy   

•   Source: SciCrunch Registry

https://github.com/LearningLocker/learninglocker

Open source software Learning Record Store implementing the xAPI (Tin Can API) e-learning standard.Type of data repository designed to store learning activity statements generated by xAPI (Tin Can) compliant learning activities.

Proper citation: Learning Locker (RRID:SCR_024401) Copy   

•   Source: SciCrunch Registry

http://psychology-tools.com/buss-perry-aggression-questionnaire

A 29 item aggression assessment where participants rank certain statements along a 5 point continuum from "extremely uncharacteristic of me"to "extremely characteristic of me". The scores are normalized on a scale of 0 to 1, with 1 being the highest level of aggression. The questionnaire returns scores for 4 dimensions of aggression: Physical Aggression, Verbal Aggression, Anger, Hostility.

Proper citation: Buss-Perry Aggression Questionnaire (RRID:SCR_000177) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/

An integrated set of tools for measuring cognitive, emotional, motor and sensory function. These tools are being validated for use in diverse cultures, ethnic and geographic groups, ages (3-85 years) and study types. The toolbox is expected to provide a more complete picture of neurological and behavioral health in large-scale longitudinal studies, epidemiological studies, and clinical trials; and to facilitate cross-study comparisons. Moreover, the toolbox will: * be minimally burdensome to subjects and investigators, * utilize state-of-the art psychometric approaches and technology, including computer-assisted evaluation, and * be dynamic and adaptable to changes in measurement and technology. * be available in English and Spanish Many clinical studies collect data on aspects of neurological and behavioral function. However, the neurological and behavioral tests currently available to researchers lack uniformity and often require specialized training to administer. These limitations make it difficult to compile data across the full range of normal neurological function, and to compare data across studies. The toolbox is royalty-free and is expected to be available online by summer 2012.

Proper citation: NIH Toolbox - Assessment of Neurological and Behavioral Function (RRID:SCR_002423) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/rft_fdr/

So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171).

Proper citation: RFT FDR (RRID:SCR_002533) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/olorin

An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)

Proper citation: OLORIN (RRID:SCR_002015) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/nirx2nirs/

A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge.

Proper citation: NIRx2nirs: A NIRx to .nirs data converter (RRID:SCR_002492) Copy   

•   Source: SciCrunch Registry

https://sites.pitt.edu/~weeks/docs/SimIBD.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: SIMIBD (RRID:SCR_002094) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

•   Source: SciCrunch Registry

http://haplopainter.sourceforge.net/

A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

Proper citation: HAPLOPAINTER (RRID:SCR_001710) Copy   

•   Source: SciCrunch Registry

http://www.rightfield.org.uk/

An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.

Proper citation: RightField (RRID:SCR_002649) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/genome-smasher/

Software repository for tools used to create diploid FASTA files with containing snps, indels, duplications, deletions, and translocations. They can be used to create artificial genomes for next-gen sequencing simulations.

Proper citation: GenomeSmasher (RRID:SCR_002406) Copy   

•   Source: SciCrunch Registry

http://www.softpedia.com/get/Science-CAD/DicomWorks.shtml

Software to help users work with DICOM files by organizing, managing and analyzing them. Key features: * a smart DICOM viewer with 4 panel display, annotations, arrows, multimodality synchronization, etc... * an export wizard to the most common picture or movie file formats * an export wizard to Microsoft PowerPoint * the most simple and compatible DICOM CD-ROM reader * the most simple and smart DICOM CD-ROM WRITER * an archiving solution with lossless compression of the data * a DICOM creation module to dicomize images from any image source (even video capture) * e-mail or FTP import end export functions (teleradiology) * 16 native localized versions

Proper citation: DicomWorks (RRID:SCR_001195) Copy   

•   Source: SciCrunch Registry

http://cerad.mc.duke.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Consortium that developed brief, standardized and reliable procedures for the evaluation and diagnosis of patients with Alzheimer's disease (AD) and other dementias of the elderly. These procedures included data forms, flipbooks, guidebooks, brochures, instruction manuals and demonstration tapes, which are now available for purchase. The CERAD assessment material can be used for research purposes as well as for patient care. CERAD has developed several basic standardized instruments, each consisting of brief forms designed to gather data on normal persons as well as on cognitively impaired or behaviorally disturbed individuals. Such data permit the identification of dementia based on clinical, neuropsychological, behavioral or neuropathological criteria. Staff at participating CERAD sites were trained and certified to administer the assessment instruments and to evaluate the subjects enrolled in the study. Cases and controls were evaluated at entry and annually thereafter including (when possible) autopsy examination of the brain to track the natural progression of AD and to obtain neuropathological confirmation of the clinical diagnosis. The CERAD database has become a major resource for research in Alzheimer's disease. It contains longitudinal data for periods as long as seven years on the natural progression of the disorder as well as information on clinical and neuropsychological changes and neuropathological manifestations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CERAD - Consortium to Establish a Registry for Alzheimer's Disease (RRID:SCR_003016) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html

Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.

Proper citation: PEDHUNTER (RRID:SCR_002031) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/LAMP/

Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.

Proper citation: LAMP (RRID:SCR_001740) Copy   

•   Source: SciCrunch Registry