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https://omictools.com/bisogenet-tool

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18, 2020. Software package to create, visualize and analyze biological networks. Can include coding relations to distinguish between genes and their products. BisoGenet client is designed to work as Cytoscape plugin for querying server along with graph topology analysis and visualization options for easing interpretation process.

Proper citation: BisoGenet (RRID:SCR_018502) Copy   

•   Source: SciCrunch Registry

http://www.limef.com/Downloads/752-752M%20manual.pdf

Vibrating microtome manufactured by Campden Instruments. 752 Vibroslice tissue cutter for manual tissue transport.

Proper citation: Campden Instruments: Vibroslice vibrating microtome (RRID:SCR_018460) Copy   

•   Source: SciCrunch Registry

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018581.pdfhttp://www.bio-medicine.org/biology-products/Fujifilm-FLA-5100-from-FUJIFILM--Life-Science-1727-1/

EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method.

Proper citation: Fujifilm: FLA-5100 Scanner (RRID:SCR_018581) Copy   

•   Source: SciCrunch Registry

https://www.illumina.com/documents/products/datasheets/datasheet_cbot.pdf

Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures.

Proper citation: Illumina: cBot Genetic Amplifier (RRID:SCR_018580) Copy   

•   Source: SciCrunch Registry

https://www.kentscientific.com/products/coda-high-throughput-system/

CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. Using the included software allows you to continuously view data in real-time.

Proper citation: Kent Scientific: Coda Blood Pressure System (RRID:SCR_018585) Copy   

•   Source: SciCrunch Registry

http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#install

Software package for sequence alignment. Pairwise aligner for aligning DNA sequences. Designed to handle sequences size of human chromosomes and from different species. Useful for sequences produced by NGS sequencing technologies.

Proper citation: LASTZ (RRID:SCR_018556) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/cs/library/brochures/5990-5596EN.pdf

Agilent 3100 OFFGEL Fractionator performs isoelectric focusing of proteins or peptides in immobilized pH gradient (IPG) gel strips.

Proper citation: Agilent: 3100 OFFGEL Fractionator (RRID:SCR_018433) Copy   

•   Source: SciCrunch Registry

https://mobile.labwrench.com/equipment/8044/applied-biosystems/voyager-de-pro

Benchtop MALDI TOF mass spectrometer that has linear and reflector analyzer. It is used to analyze organic and inorganic compounds, protein identification, synthetic peptide validation, and polymer analysis.

Proper citation: Thermo Fisher: Applied Biosystems: ABI Voyager DE Pro MALDI-Mass Spectrometer (RRID:SCR_018432) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/minimap2

Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.

Proper citation: Minimap2 (RRID:SCR_018550) Copy   

•   Source: SciCrunch Registry

http://nanotomy.org/

Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes.

Proper citation: Nanotomy (RRID:SCR_018565) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/timezone1/

Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.

Proper citation: TimeZone (RRID:SCR_018564) Copy   

•   Source: SciCrunch Registry

http://doriclenses.com/life-sciences/software/955-doric-neuroscience-studio.html

Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected.

Proper citation: Doric Neuroscience Studio (RRID:SCR_018569) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry

http://clavius.bc.edu/~clotelab/DiANNA/

Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification.

Proper citation: DiANNA (RRID:SCR_018529) Copy   

•   Source: SciCrunch Registry

http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx

Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.

Proper citation: DAMBE (RRID:SCR_018528) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/BepiPred/index.php

Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BepiPred-2.0 (RRID:SCR_018499) Copy   

•   Source: SciCrunch Registry

https://jetfighter.ecrlife.org

Web tool that automatically screens bioRxiv preprints for rainbow colormaps, which are not colorblind safe. Emails authors information on replacing these colormaps with colorblind safe alternatives. Screens preprints to improve data representation and colour-blind accessibility.

Proper citation: JetFighter (RRID:SCR_018498) Copy   

•   Source: SciCrunch Registry

https://ambermd.org/AmberTools.php

Software suite that works by themselves, and with Amber20 itself. Can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

Proper citation: AmberTools (RRID:SCR_018497) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/DiscoTope/

Web server to predict discontinuous B cell epitopes from protein three dimensional structures.

Proper citation: DiscoTope (RRID:SCR_018530) Copy   

•   Source: SciCrunch Registry

https://www.ddg-pharmfac.net/AllerTOP/

Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin.

Proper citation: AllerTop (RRID:SCR_018496) Copy   

•   Source: SciCrunch Registry