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https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html

Conversion software developed by Illumina that both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

Proper citation: bcl2fastq (RRID:SCR_015058) Copy   

•   Source: SciCrunch Registry

http://www.oif.org

Foundation for improving the quality of life for people affected by OI through treatment and cure research, education, awareness, and mutual support. OIF lists personal resources for individuals affected by osteogenesis imperfecta as well as professional and clinical resources for researchers.

Proper citation: Osteogenesis Imperfecta Foundation (RRID:SCR_015034) Copy   

•   Source: SciCrunch Registry

https://www.cdc.gov/labstandards/index.html

Standardization program which helps assure the quality of laboratory test data and results so patients, healthcare providers, researchers, and public health officials can be confident that laboratory test results they receive are accurate. CDC services include reference materials, proficiency testing, training, guideline creation, and consultations. Quality assurance and standardization programs can be can be customized by and for users and laboratories.

Proper citation: CDC Laboratory Quality Assurance and Standardization Programs (RRID:SCR_015000) Copy   

•   Source: SciCrunch Registry

https://www.keyence.co.jp/products/microscope/fluorescence-microscope/bz-9000/models/bz-9000/

Microscope system performs fluorescence, bright-field and phase-contrast imaging on various specimen holders. The system allows users to switch between four fluorescent channels, automatically adjusting the filter and exposure time while preserving the longevity of the specimen.

Proper citation: BZ 9000 Fluorescence Microscope (RRID:SCR_015486) Copy   

•   Source: SciCrunch Registry

http://spectrumlabs.com/

Commercial organization which supplies products for bioseparation and cell line management.

Proper citation: Spectrum Labs (RRID:SCR_015488) Copy   

•   Source: SciCrunch Registry

http://mbm.cs.uga.edu/mouse/transcriptome_architecture/

Image collection of transcriptome architecture of adult mouse brain revealed by sparse coding of genome-wide in situ hybridization images.

Proper citation: Transcriptome architecture of adult mouse brain (RRID:SCR_015483) Copy   

•   Source: SciCrunch Registry

https://www.bsc.es/marenostrum/marenostrum

Operating software for a supercomputer in Spain. The software is maintained and updated by the Centro Nacional de Supercomputación (Barcelona Supercomputing Center) and is used for research projects on climate change, gravitational waves, a vaccination against AIDS, new radiation treatments to fight cancer, and other subjects.

Proper citation: MareNostrum (RRID:SCR_015737) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/archs4/

ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome.

Proper citation: ARCHS4 (RRID:SCR_015683) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/cancer/software/genepattern/modules/docs/Cuffmerge/3

The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.

Proper citation: Cuffmerge (RRID:SCR_015688) Copy   

•   Source: SciCrunch Registry

http://www.mightexsystems.com/family_info.php?cPath=245_347_346&categories_id=346

Software used in tandem with the Polygon 400 from Mightex systems to define areas of illumination, control light intensity and duration, and calibrate the device.

Proper citation: Dynamic Spatial Illuminator Software (RRID:SCR_015725) Copy   

•   Source: SciCrunch Registry

https://ita.promega.com/products/fluorometers-luminometers-multimode-readers/multimode-readers/glomax_multi-detection-system/?catNum=E7061

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 6, 2017. Detection instrument that gathers absorbance, fluorescence, and luminescence data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Glo-Max Multi Detection System (RRID:SCR_015575) Copy   

•   Source: SciCrunch Registry

https://github.com/iontorrent/TS

A variant vcf file analysis tool.

Proper citation: Torrent Variant Caller Standalone (RRID:SCR_015694) Copy   

•   Source: SciCrunch Registry

http://www.iitcinc.com/rotarod.html

Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard.

Proper citation: IITC Life Sciences: Rotarod Test (RRID:SCR_015698) Copy   

•   Source: SciCrunch Registry

https://www.visiopharm.com/solutions/oncotopix

Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.

Proper citation: Oncotopix Discovery (RRID:SCR_015690) Copy   

•   Source: SciCrunch Registry

http://www.neurocaregroup.com/dc-stimulator-neuroconn.html

Device for administering transcranial electrical stimulation. It has applications in cranial electrotherapy that provides a weak direct current for non-invasive Interventional Neurophysiology.

Proper citation: Neurocare: Neuroconn DC-Stimulator Plus (RRID:SCR_015520) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAHMS-SystemML/brahms

Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models.

Proper citation: BRAHMS (RRID:SCR_015642) Copy   

•   Source: SciCrunch Registry

https://www.quantumbiologyinstitute.org/

Institute that provides resources and researches the concepts and mechanisms which underlie the complexities of biology. In particular, it incorporates concepts in physics and mathematics to resolve, unravel, and explain complex biological mechanisms and conditions.

Proper citation: Quantum Biology Institute (RRID:SCR_015855) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/

University-affiliated center that promotes research in diabetes and related metabolic and endocrine disorders at Stanford University.

Proper citation: Stanford Diabetes Research Center (RRID:SCR_015856) Copy   

•   Source: SciCrunch Registry

https://compumedicsneuroscan.com/product/synamps-rt-64-channel-eeg-erp-ep-amplifier/

Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300.

Proper citation: Neuroscan SynAmps RT 64-channel Amplifier (RRID:SCR_015818) Copy   

•   Source: SciCrunch Registry

https://www.sigmaaldrich.com/US/en/products/labware/cell-culture-and-cryogenics/millicell-cell-culture-inserts-and-plates

Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides.

Proper citation: Sigma: Millicell Cell Culture Inserts (RRID:SCR_015799) Copy   

•   Source: SciCrunch Registry