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http://bids.neuroimaging.io

Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data.

Proper citation: Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/FALCON

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

Proper citation: Falcon (RRID:SCR_016089) Copy   

•   Source: SciCrunch Registry

http://genome.imim.es/software/gfftools/GFF2APLOT.html

Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis.

Proper citation: Gff2aplot (RRID:SCR_016128) Copy   

•   Source: SciCrunch Registry

http://www.localite.de/en/products/tms-navigator/

An instrument. Navigation system for transcranial magnetic stimulation (TMS).

Proper citation: Localite TMS Navigator (RRID:SCR_016126) Copy   

•   Source: SciCrunch Registry

http://gentle.magnusmanske.de

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   

•   Source: SciCrunch Registry

https://www.singularity-hub.org

Database for singularity containers. It hosts container collections as well as articles about scientific advancements.

Proper citation: Singularity Hub (RRID:SCR_016248) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Exonerate (RRID:SCR_016088) Copy   

•   Source: SciCrunch Registry

https://github.com/minepy/mictools

Software which combines the TICe and MICe measures into a two-step procedure that allows to identify relationships of various degrees of complexity in large datasets. TICe is used to perform an efficient high throughput screening of all the possible pairwise relationships and a permutation based approach is used to assess their significance.

Proper citation: MICtools (RRID:SCR_016121) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMALIGN

Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress.

Proper citation: DOMALIGN (RRID:SCR_016085) Copy   

•   Source: SciCrunch Registry

https://github.com/nelpy

Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data.

Proper citation: nelpy (RRID:SCR_016209) Copy   

•   Source: SciCrunch Registry

http://uthscsa-imagetool.software.informer.com/

Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images.

Proper citation: UTHSCSA ImageTool (RRID:SCR_016208) Copy   

•   Source: SciCrunch Registry

http://interlex.org

The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. InterLex is being constructed to help improve the way that biomedical scientists communicate about their data, so that information systems like NIF and dkNET can find data more easily and provide more powerful means of integrating that data across distributed resources. One of the big roadblocks to data integration in the biomedical sciences is the inconsistent use of terminology in databases and other resources such as the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then it is hard to compare them. InterLex allows for the association of data values (i.e. the value of a field or text within a field) to terminologies enabling the crowdsourcing of data-terminology mappings. InterLex was built on the foundation of NeuroLex (see Larson and Martone 2013 Neurolex: An online framework for neuroscience knowledge. Frontiers in Neuroinformatics, 7:18) and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies. NIFSTD currently has about 60,000 concepts (includes both classes and synonyms) that span gross anatomy, cells, subcellular structures, diseases, functions and techniques. InterLex models terms using primitives of the Web Ontology Language (OWL) and can export directly to a variety of standard ontology formats. A primary goal of interlex is to provide a stable layer on top of the many other existing terminologies, lexicons, and ontologies (i.e. provide a way to federate ontologies for data applications) and to provide a set of inter-lexical and inter-data-lexical mappings. In the future, InterLex will support user specific namespaces so that users can customize the exact definitions or ontologies they source from, as well as the relationships on those terms. Importantly, however, InterLex enforces a simple rule which is that terms which represent the same concept under the same superclass will maintain the same identifier fragment (i.e. 'ilx_1234567'). However, each user will be able to 'fork' a term into their own namespace (e.g. http://uri.interlex.org/user/ilx_1234567). This enables the various perspectives on a term or concept to have equal space so that the full diversity of views on a term can be seen and expressed. Sign-up for updates to get notified about updates to InterLex and when new features are available.

Proper citation: InterLex (RRID:SCR_016178) Copy   

•   Source: SciCrunch Registry

https://www.hiv.lanl.gov/catnap

Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CATNAP (RRID:SCR_016170) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/l1000fwd/

Web application that provides interactive visualization of drug and small-molecule induced gene expression signatures. L1000FWD enables coloring of signatures by different attributes such as cell type, time point, concentration, as well as drug attributes such as MOA and clinical phase.

Proper citation: L1000 Fireworks Display (RRID:SCR_016175) Copy   

•   Source: SciCrunch Registry

https://beta.observablehq.com/

Web application for a code and text writing environment. It uses javascript and can be used to produce executable papers.

Proper citation: ObservableHQ (RRID:SCR_016173) Copy   

•   Source: SciCrunch Registry

https://github.com/Oshlack/necklace/wiki

Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations.

Proper citation: Necklace (RRID:SCR_016103) Copy   

•   Source: SciCrunch Registry

https://github.com/csn-le/wave_clus

Algorithm for spike detection and sorting that uses wavelets and super-paramagnetic clustering. It generates an unsupervised solution, but this can be modified according to the experimenters’ preference for semi-automatic sorting.

Proper citation: Wave_clus (RRID:SCR_016101) Copy   

•   Source: SciCrunch Registry

https://www.goldwave.com/goldwave.php

Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes.

Proper citation: GoldWave (RRID:SCR_016189) Copy   

•   Source: SciCrunch Registry

https://sci-f.github.io/

Organizational software that supports exposure of executables and metadata for discoverability. The software includes a known filesystem structure, a definition for a set of environment variables describing it, and functions for generation of the variables and interaction with the libraries, metadata, and executables located within.

Proper citation: Scientific Filesystem (RRID:SCR_016105) Copy   

•   Source: SciCrunch Registry

http://www3.gehealthcare.com/en/products/categories/ep_recording/cardio_lab_recording_systems

Prucka CardioLab system delivers the EP data and visualization we need for electrophysiological study and catheter ablation.

Proper citation: Prucka CardioLab System (RRID:SCR_016180) Copy   

•   Source: SciCrunch Registry