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https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit
A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3
Proper citation: BRAINSFit (RRID:SCR_002340) Copy
Public research university in Tucson, Arizona that offers undergraduate and graduate degree programs in psychology, audiology, speech pathology, and medicine.
Proper citation: University of Arizona; Arizona; USA (RRID:SCR_002459) Copy
http://www.nitrc.org/projects/neuroscope/
An advanced viewer for electrophysiological and behavioral data: it can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities.
Proper citation: NeuroScope (RRID:SCR_002455) Copy
https://github.com/PhKoch/RepARK
Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.
Proper citation: RepARK (RRID:SCR_002333) Copy
Commercial supplier of antibodies, assay kits, conjugates and various toxins for biomedical research. ATS's product line is designed to assist scientists in the study of system functions, cell functionality, diseases and disorders.
Proper citation: Advanced Targeting Systems (RRID:SCR_002328) Copy
http://www.thermofisher.com/order/catalog/product/4385261
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017.
Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation.
Proper citation: Variant Reporter Software (RRID:SCR_002329) Copy
http://www.bic.mni.mcgill.ca/software/N3/
The perl script nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data, the method can be applied at an early stage in an automated data analysis, before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction.
Proper citation: MNI N3 (RRID:SCR_002484) Copy
A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker).
Proper citation: COGNISION (RRID:SCR_002362) Copy
Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data.
Proper citation: NIDB - Neuroinformatics Database (RRID:SCR_002488) Copy
Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.
Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) Copy
http://www.ncbi.nlm.nih.gov/genome
Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.
Proper citation: NCBI Genome (RRID:SCR_002474) Copy
https://github.com/seqan/seqan/tree/master/apps/mason2
Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads.
Proper citation: Mason (RRID:SCR_002476) Copy
A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.
Proper citation: iBEAT (RRID:SCR_002470) Copy
http://www07.grants.gov/applicants/find_grant_opportunities.jsp
A source to FIND and APPLY for federal grants. The U.S. Department of Health and Human Services is proud to be the managing partner for Grants.gov, an initiative that is having an unparalleled impact on the grant community. All discretionary grants offered by the 26 federal grant-making agencies can be found on Grants.gov. Grants.gov was established as a governmental resource named the E-Grants Initiative, part of the President's 2002 Fiscal Year Management Agenda to improve government services to the public. The concept has its origins in the Federal Financial Assistance Management Improvement Act of 1999, also known as Public Law 106-107. Public Law 106-107 has since sunset and is now known as the Grants Policy Committee (GPC). For more information on the Grants Policy Committee, click here. Today, Grants.gov is a central storehouse for information on over 1,000 grant programs and provides access to approximately $500 billion in annual awards. You may find information on *What is a Grant? *Who is Eligible for a Grant? *Program highlights and accomplishments *Grants.gov in the News (Articles, press releases, milestones and events) *Program Status (Detailed information about our relationship with partner federal agencies, financial contributions, grant opportunities, fiscal reports, planning strategies and statistics.)
Proper citation: Grants.gov (RRID:SCR_002661) Copy
http://scralyze.sourceforge.net
A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.
Proper citation: SCRalyze (RRID:SCR_002542) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer.
Proper citation: Cancer Genomics Hub (RRID:SCR_002657) Copy
A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI.
Proper citation: NiBabel (RRID:SCR_002498) Copy
http://www.nitrc.org/projects/pythagoras/
Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment.
Proper citation: Pythagorean Displacement and Motion Regressors (RRID:SCR_002525) Copy
Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PySurfer (RRID:SCR_002524) Copy
http://www.unc.edu/~yunmli/shotgun.html
Software for short read simulating in order to facilitate sequencing-based study designs.
Proper citation: ShotGun (RRID:SCR_002529) Copy
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