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http://www.nitrc.org/projects/namicdtifiber/
Project hosting binary packaged distributions, scripts, example datasets, and corresponding results of analysis using their UNC/Utah NAMIC DTI Fiber Analysis Framework. This project can be seens as a master project encompassing several current NITRC projects into a coherent set. Their workflow utilizes tools already available on NITRC including: * DTIPrep * DTIAtlasBuilder * FiberViewerLight * DTIAtlasFiberAnalyzer * FADTTS
Proper citation: UNC/Utah NAMIC DTI Fiber Analysis Framework (RRID:SCR_009615) Copy
Center that facilitates the optimal use of nonhuman primate models in biomedical research by identifying, developing, characterizing and producing reagents for monitoring or modulating immune responses. They distribute non-human primate-specific antibodies for in vitro diagnostics, as well as develop and produce primate recombinant antibodies for in vivo cell depletion or modulating immune responses.
Proper citation: Nonhuman Primate Reagent Resource (RRID:SCR_012986) Copy
https://www.broadinstitute.org/ccle/
A collaborative project between the Broad Institute and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation, with the goal of conducting a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The CCLE also works to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.
Proper citation: Cancer Cell Line Encyclopedia (RRID:SCR_013836) Copy
An independent committee established to improve visibility of cell lines and promote awareness and authentication testing to combat false or misidentified cell lines. It contains a databases of cross-contaminated or otherwise misidentified cell lines, as well as resources to familiarize users of cell lines and the problem of misidentification. Their Terms of Reference defines false or misidentified cell lines and other commonly used terms, as well as sets out the committee goals and ground rules.
Proper citation: International Cell Line Authentication Committee (RRID:SCR_014414) Copy
http://becs.aalto.fi/en/research/bayes/drifter/
Model based Bayesian method for eliminating physiological noise from fMRI data. This algorithm uses image voxel analysis to isolate the cardiac and respiratory noise from the relevant data.
Proper citation: DRIFTER (RRID:SCR_014937) Copy
https://www.janelia.org/confocal-imagery-management-and-analysis-tools
A discovery platform used to analyze and annotate imagery for individual projects, while assembling shared data resources. It was originally applied to Drosophila neuronal anatomy and neuroblast lineage analysis and is currently being extended to support mouse whole-brain projection tracing. The Workstation is both a pipeline management system that extracts entities from 3D imagery and a suite of tools that enable scientists to annotate large imagery datasets. A Entity-Attribute-Value (EAV) graph permits any element to be annotated by users with custom ontologies. By allowing any entity to have multiple parents, the graph can be re-arranged by each user without copying the underlying image data.
Proper citation: Janelia Workstation (RRID:SCR_014302) Copy
http://www.brainvoyager.com/products/brainvoyagerqx.html
Commercial neuroimaging software package for multi-modal data analysis and management. It has been programmed in C++ with efficient statistical, numerical, and image processing routines. It supports parallelized basic math routines on all platforms and uses modern multi-core, multi-processor hardware for demanding computational routines.
Proper citation: BrainVoyager (RRID:SCR_013057) Copy
http://www.3dhistech.com/pannoramic_viewer
Software tool as a digital virtual microscope for viewing and moving scanned histological slides and for making annotations and measurements on them. Used in digital pathology. Helps to simplify the areas of the pathology workflow where imaging, slide digitization, storage, archivation, visualization and analysis are performed.
Proper citation: Pannoramic Viewer (RRID:SCR_014424) Copy
Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website.
Proper citation: Assisted Model Building with Energy Refinement (AMBER) (RRID:SCR_014230) Copy
https://sils.fnwi.uva.nl/bcb/Object-Image/object-image.html
Image analysis software package that allows non-destructive image marking, input for further image processing, and marking the results of automatic measurements. Object-Image integrates measurements, macros, graphical objects and image names in a closed unit called 'object file' so that it reduces file clutter.
Proper citation: Object-Image (RRID:SCR_015720) Copy
http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/home.htm
Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data.
Proper citation: Homer2 (RRID:SCR_009586) Copy
A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis.
Proper citation: HERMES (RRID:SCR_009584) Copy
https://github.com/MikkelSchubert/paleomix
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing.
Proper citation: PALEOMIX (RRID:SCR_015057) Copy
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.
Proper citation: TRACULA (RRID:SCR_013152) Copy
Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources.
Proper citation: Omics Discovery Index (RRID:SCR_010494) Copy
http://doa.nubic.northwestern.edu/pages/search.php
Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF).
Proper citation: DOAF (RRID:SCR_015666) Copy
http://subread.sourceforge.net/
Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.
Proper citation: Subread (RRID:SCR_009803) Copy
http://www.rhino3d.com/features
3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products.
Proper citation: Rhinoceros (RRID:SCR_014339) Copy
https://github.com/eead-csic-compbio/split_pairs
Software for processing NGS sequence reads in FASTQ and FASTA formats. split_pairs.pl is suited particularly for the task of sorting pair end reads and for modifying their headers with Perl-style regular expressions.
Proper citation: split_pairs.pl (RRID:SCR_015707) Copy
It is part of the Institute for Advanced Studies at The Australian National University (ANU). CBiS forms a bridge between two areas of major strength at ANU, mathematics and biological sciences. CBiS brings together researchers with backgrounds in mathematics, statistics and quantitative biology with the goal of developing a conceptual architecture for an information-based, integrative approach to complex biological systems. Software available for download or use is: * Pozitiv * GE Bi-Plot * Chip Stability * PyEvolve * Vestige Most software is freely available under the GPL or similar licenses. For details, see each individual package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CBiS (RRID:SCR_013408) Copy
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