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https://github.com/WGS-TB/MentaLiST

Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.

Proper citation: MentaLiST (RRID:SCR_016469) Copy   

•   Source: SciCrunch Registry

https://cistem.org/

Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.

Proper citation: cisTEM (RRID:SCR_016502) Copy   

•   Source: SciCrunch Registry

https://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/

Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GCTF (RRID:SCR_016500) Copy   

•   Source: SciCrunch Registry

https://www.mirri.org/

Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application.

Proper citation: MIRRI (RRID:SCR_016461) Copy   

•   Source: SciCrunch Registry

http://gcm.wfcc.info/

Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.

Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy   

•   Source: SciCrunch Registry

https://imaps.genialis.com/iclip

Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions.

Proper citation: iMaps (RRID:SCR_016705) Copy   

•   Source: SciCrunch Registry

http://www.speciation.net/Database/Instruments/Carl-Zeiss-AG/LIBRA-120-;i672

Electron microscope by Carl Zeiss AG which combines flexibility and ease of use of new control electronics, Windows® based user interface and a vacuum system.

Proper citation: Zeiss: libra 120 transmission electron microscope (RRID:SCR_016703) Copy   

•   Source: SciCrunch Registry

https://corefacilities.iss.it/dw/lib/exe/fetch.php?media=aree:citometria:strumentazione:gallios-brochure.pdf

Instrument provides acquisition of up to 12 parameters with optical design for enhanced sensitivity for multicolor assays. With customized forward scatter, to achieve accurate size measurement, and optimized electronics for high resolution and fast, accurate processing for researchers needs.

Proper citation: Gallios: Flow Cytometer (RRID:SCR_016702) Copy   

•   Source: SciCrunch Registry

https://github.com/fbreitwieser/pavian

Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.

Proper citation: Pavian (RRID:SCR_016679) Copy   

•   Source: SciCrunch Registry

https://github.com/tomazc/iCount

Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.

Proper citation: iCount (RRID:SCR_016712) Copy   

•   Source: SciCrunch Registry

https://www.neuronexus.com/files/catalog/NeuroNexus-2023ProbeDesignCatalog.pdf

Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications.

Proper citation: Neuronexus: Neural Probe A1x16-3mm-100-703 (RRID:SCR_016678) Copy   

•   Source: SciCrunch Registry

https://github.com/CSB5/INC-Seq

Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities.

Proper citation: INC-Seq (RRID:SCR_016711) Copy   

•   Source: SciCrunch Registry

https://www.a-msystems.com/p-285-model-2100-isolated-pulse-stimulator.aspx

Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols.

Proper citation: A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator (RRID:SCR_016677) Copy   

•   Source: SciCrunch Registry

https://github.com/umerijaz/nanopore

Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing.

Proper citation: NanoAmpli-Seq (RRID:SCR_016710) Copy   

•   Source: SciCrunch Registry

http://jefferis.github.io/nat/

Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.

Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy   

•   Source: SciCrunch Registry

http://biophysics.fsu.edu/facilities/physical-biochemistry-facility/

Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students.

Proper citation: Florida State University Physical Biochemistry Core Facility (RRID:SCR_016714) Copy   

•   Source: SciCrunch Registry

https://www.colinst.com/oxymax-clams

Instrumentation for monitoring behavior and physiology in lab animals by Columbus Instruments. Used for simultaneous multi parameter assessment of 1 to 32 test animals with automated operation for experiments lasting up to three days.

Proper citation: Columbus Instruments: Oxymax-CLAMS (RRID:SCR_016718) Copy   

•   Source: SciCrunch Registry

https://molecular.pathology.ufl.edu/

Histology and light microscopy facility for paraffin and frozen blocks and all aspects of sample preparation, fixation, embedding, sectioning, staining, and imaging. Consultations, technical assistance and training are also provided. Standard operating procedures compliant with good laboratory and clinical processes are followed for all procedures. Services include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays..

Proper citation: University of FLorida College of Medicine Molecular Pathology Core Facility (RRID:SCR_016601) Copy   

•   Source: SciCrunch Registry

http://www.bdbiosciences.com/us/instruments/research/cell-sorters/bd-influx/m/744777/features/software

Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems.

Proper citation: BD FACS Sortware sorter software (RRID:SCR_016722) Copy   

•   Source: SciCrunch Registry

http://vectormap.si.edu/

Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap.

Proper citation: VectorMap (RRID:SCR_016721) Copy   

•   Source: SciCrunch Registry