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http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development

A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

Proper citation: ARACHNE (RRID:SCR_000351) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/beckerjeremie/home/nucleofinder

A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.

Proper citation: NucleoFinder (RRID:SCR_000368) Copy   

•   Source: SciCrunch Registry

http://graphpad.com/

A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.

Proper citation: GraphPad (RRID:SCR_000306) Copy   

•   Source: SciCrunch Registry

http://www.arb-home.de/

Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.

Proper citation: ARB project (RRID:SCR_000515) Copy   

•   Source: SciCrunch Registry

http://www.rostlab.org/cms/

A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.

Proper citation: ROSTLAB (RRID:SCR_000792) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/molbiolib/

A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.

Proper citation: MolBioLib (RRID:SCR_005372) Copy   

•   Source: SciCrunch Registry

http://goldenhelix.com/

Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.

Proper citation: Golden Helix Incorporated (RRID:SCR_012191) Copy   

•   Source: SciCrunch Registry

http://genomejack.net/

A genome browser specialized in next-generation sequencing data.

Proper citation: GenomeJack (RRID:SCR_012026) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/

Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.

Proper citation: Leica Application Suite X (RRID:SCR_013673) Copy   

•   Source: SciCrunch Registry

http://www.cyto.purdue.edu/flowcyt/software/Winmdi.htm

Software to analyze flow cytometry listmode data files.

Proper citation: WinMDI Software (RRID:SCR_013745) Copy   

•   Source: SciCrunch Registry

http://www.preger.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods.

Proper citation: Primate Embryo Gene Expression Resource (RRID:SCR_002765) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_StemCells.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) Copy   

•   Source: SciCrunch Registry

https://www.mangold-international.com/en/products/software/behavior-research-with-mangold-interact

Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software.

Proper citation: Interact (RRID:SCR_019254) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/00-0210

Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

Proper citation: Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) Copy   

•   Source: SciCrunch Registry

https://www.nzytech.com/

Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins.

Proper citation: NZYTech (RRID:SCR_016772) Copy   

•   Source: SciCrunch Registry

https://bionanogenomics.com/wp-content/uploads/2017/01/30047-Irys-User-Guide.pdf

System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies.

Proper citation: BioNano: Irys system (RRID:SCR_016754) Copy   

•   Source: SciCrunch Registry

https://www.scanco.ch/microct100.html

Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.

Proper citation: Scanco: Medical microCT 100 system (RRID:SCR_017119) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/cs/library/usermanuals/Public/G2505-90019_ScannerC_User.pdf

Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays.

Proper citation: Agilent: G2565CA Microarray Scanner (RRID:SCR_017206) Copy   

•   Source: SciCrunch Registry

https://bpcinstruments.com/bpc_products/ampts3/?gad_source=5&gclid=CjwKCAiApaarBhB7EiwAYiMwqs8UHkyeggWkwFZPlUI3pLd9rJBWQ3bJ9ixnkNuq3dw4Fay4W6lwnxoC1RIQAvD_BwE

Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry.

Proper citation: BPC Instruments: Biomethane Potential Test (RRID:SCR_017319) Copy   

•   Source: SciCrunch Registry

https://brainreader.net

Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain.

Proper citation: Brainreader (RRID:SCR_017308) Copy   

•   Source: SciCrunch Registry