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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
  

https://emcore.ucsf.edu/cryoem-software

Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux.

Proper citation: MotionCor2 (RRID:SCR_016499) Copy   

•   Source: SciCrunch Registry
  

http://www.mediacy.com/imagepro

Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection.

Proper citation: Image Pro (RRID:SCR_016497) Copy   

•   Source: SciCrunch Registry
  

https://ihg.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl

Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.

Proper citation: Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) Copy   

•   Source: SciCrunch Registry
  

http://www.cyto.purdue.edu/cdroms/micro1/7_spon/vaytek/voxblast.htm

Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint.

Proper citation: VoxBlast (RRID:SCR_016491) Copy   

•   Source: SciCrunch Registry
  

https://cm.jefferson.edu/rna22/

Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.

Proper citation: RNA22 (RRID:SCR_016507) Copy   

•   Source: SciCrunch Registry
  

http://cajadb.neuro.ufrn.br

Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.

Proper citation: CajaDB (RRID:SCR_016506) Copy   

•   Source: SciCrunch Registry
  

https://www.genome.jp/tools/dinies/

Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.

Proper citation: DINIES (RRID:SCR_016505) Copy   

•   Source: SciCrunch Registry
  

http://www.compbio.dundee.ac.uk/jpred/

Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.

Proper citation: Jpred (RRID:SCR_016504) Copy   

•   Source: SciCrunch Registry
  

https://mirmap.ezlab.org/

Software application as an open source Pyton library to search and predict miRNA targets.

Proper citation: miRmap (RRID:SCR_016508) Copy   

•   Source: SciCrunch Registry
  

https://www.janelia.org/open-science/mimms-10-2016

Modular platform for performing two‐photon laser scanning microscopy (TPLSM) optimized for in vivo applications.

Proper citation: MIMMS microscope 1.0 (2016) (RRID:SCR_016511) Copy   

•   Source: SciCrunch Registry
  

http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf

Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution.

Proper citation: Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html

Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.

Proper citation: BLASTClust (RRID:SCR_016641) Copy   

•   Source: SciCrunch Registry
  

http://ecogenomics.github.io/CheckM/

Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes.

Proper citation: CheckM (RRID:SCR_016646) Copy   

•   Source: SciCrunch Registry