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http://xoonips.sourceforge.jp/

Neuroinformatics (NI) is a new discipline that challenges the understanding of the structure and mechanism of the brain by combining neuroscience and information technology. The global collaborations in this field have been actively started with the support of the International Neuroinformatics Coordinating Facility (INCF) launched in November 2005. The Laboratory for Neuroinformatics at RIKEN Brain Science Institute (BSI) is involved in developing various cutting-edge technologies related to NI such as XooNIps. XooNIps succeeded the concept and basic feature of the vision science platform; Visiome, constructed by the NRV (i.e., Neuroinformatics Research in Vision) Project and has been developed based on a content management system (CMS); XOOPS, as infrastructure for NI databases to share different types of data on the Internet. :XooNIps has three features: :The first is the flexibility of developing databases. CMS-based XooNIps makes it easy to change the design or to extend the functions of databases by combining the different modules available on XOOPS. Therefore, even those who are not expert in computer system can develop their database on XooNIps. :The second is the diversity and extensibility of the data which can be handled by XooNIps. In order to handle different types of actual data, it provides not only the various data forms per se, but also the extension method to handle a new data form, which enables to deal easily with even a non-standardized data form. :The third is the facility to distribute metadata. XooNIps implements OAI-PMH (i.e., Open Archive Initiative-Protocol for Metadata Harvesting) which is one of the standard protocols to distribute metadata. This enables to collect information on other databases which are developed on XooNIps or to coordinate databases by exchanging metadata with other databases which implement OAI-PMH than those on XooNIps. :Since April 2007, Neuroinformatics Japan Center (NIJC) at RIKEN BSI takes charge of extending and maintaining XooNIps, and is committed to manage the documentation hereafter. :NIJC, as a national node of INCF, is developing and operating various NI platforms in neuroscience based on XooNIps to establish and facilitate NI research in Japan. XooNIps is also being applied to databases or organizational repositories in several institutions and universities, and laboratory groupware in various fields. We hope XooNIps will be of universal use in and out of Japan. :database; binary executable; software development tool; metadata; data set; :

Proper citation: XooNIps - Neuroinformatics Base Platform System (RRID:SCR_013590) Copy   

•   Source: SciCrunch Registry

https://github.com/yhoogstrate/dr-disco

Software tool fo detecting genomic breakpoints of fusion transcripts in random hexamer RNA-seq data. Used for detection of exonic, intronic and intergenic fusion transcripts and their genomic breakpoints in poly(A)+ and rRNA-minus RNA sequencing data.

Proper citation: Dr. Disco (RRID:SCR_021739) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012c-c7e5-e09d-a061-4a6580000000

Core facility that provides the following services: Flow cytometry assay service, Data management system.

The BD FACSCalibur system combines unique dual-laser technology, an automated sample loader option, and powerful software to provide the high throughput necessary to meet productivity requirements of clinical laboratories. The modularity and innovative technology designed into the BD FACSCalibur system also offers investigators the performance and flexibility required for a variety of research applications. Please note that since the NERCE program will end in February 2014, our ability to support new requests for services is limited.

Proper citation: HMS NERCE FACSCalibur Flow Cytometer Resource (RRID:SCR_000879) Copy   

•   Source: SciCrunch Registry

http://mmrrc.ucdavis.edu/

Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators.

Proper citation: University of California at Davis Mutant Mouse Resource and Research Center (RRID:SCR_016448) Copy   

•   Source: SciCrunch Registry

http://www.mmrrc.missouri.edu/

Center that supplies mice and conducts research projects focused on the role of mice as animal models. Some of these projects include refinement of models to ensure study reproducibility, as well as development and improvement of economical methods for cryopreservation of mouse strains.

Proper citation: Mutant Mouse Resource and Research Center - University of Missouri (RRID:SCR_016447) Copy   

•   Source: SciCrunch Registry

https://golang.org/

Software tool as open source programming language to build simple, reliable, and efficient software. Developed by team at Google and many contributors from open source community.

Proper citation: golang (RRID:SCR_017096) Copy   

•   Source: SciCrunch Registry

http://web.mit.edu/spectroscopy/facilities/lbrc.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale.

Proper citation: Laser Biomedical Research Center (RRID:SCR_000106) Copy   

•   Source: SciCrunch Registry

https://github.com/olivierfriard/BORIS

Open source event logging software for video/audio coding and live observations.Multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.

Proper citation: Behavioral Observation Research Interactive Software (RRID:SCR_021509) Copy   

•   Source: SciCrunch Registry

http://www.perl.org

Software tool to accompany existing resources such as Python programming language resource and comprehensive Perl archive network (CPAN) resource. Perl is family of two high level, general purpose, interpreted, dynamic programming languages. Perl refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned sister language, Perl 6, before name was officially changed to Raku in October 2019.

Proper citation: Perl Programming Language (RRID:SCR_018313) Copy   

•   Source: SciCrunch Registry

https://www.rankinbiomed.com/product/refurbished-american-optical-860-sliding-micrtome/

THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns.

Proper citation: American Optical: 860 Sliding Microtome (RRID:SCR_018434) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhenjiangFan/DAG-deepVASE

Software tool for identifying nonlinear causal relations and estimating their effect size help to understand complex disease pathobiology.

Proper citation: DAG-deepVASE (RRID:SCR_023612) Copy   

•   Source: SciCrunch Registry

https://github.com/lapphe/raspberry_rat

Software Python platform for recording, converting, and uploading videos to cloud and for performing scheduled video recordings. Repository also includes wiki section with comprehensive guide to setting up Raspberry Pis for this purpose. Raspberry Pis are often cheaper than camcorder and can produce HD video. They are also equipped with infrared camera, making them ideal for recordings of animals that are active in low light conditions.

Proper citation: Rasberry rat (RRID:SCR_023467) Copy   

•   Source: SciCrunch Registry

https://github.com/chenxinfeng4/ArControl

Software tool as Arduino UNO/Mega based, visual programming and real-time behavioral platform for neuroscience. It can run Go/No-Go, 2AFPC and Optogenetic stimulation tasks. Stand alone and intuitive Gaphical User Interface application.Part of ArControl system.

Proper citation: ArControl (RRID:SCR_021605) Copy   

•   Source: SciCrunch Registry

https://github.com/vinguyenle/k-FLBPCM-method

Software tool as novel k-FLBPCM method for detecting morphologically similar crops and weeds based on combination of contour masks and Local Binary Pattern operators.

Proper citation: k-FLBPCM method (RRID:SCR_017973) Copy   

•   Source: SciCrunch Registry

https://github.com/PedroMTQ/mantis

Software homology based protein function annotation tool that integrates multiple reference data sources. Custom reference data sources can also be added.Accepts as input aminoacids sequence fasta. Customizable and is available on Linux.

Proper citation: Mantis (RRID:SCR_021001) Copy   

•   Source: SciCrunch Registry

https://pypi.org/

Software repository for Python programming language.Used to find and install software developed and shared by Python community.

Proper citation: PyPI (RRID:SCR_023145) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/FilterFFPE/

Software R package to find and filter artificial chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissues. These artificial chimeric reads can lead to large number of false positive structural variant calls. Artifact chimeric read filter to improve SV detection in FFPE samples.

Proper citation: FilterFFPE (RRID:SCR_021086) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/panelcn.mops.html

Software R package as CNV detection tool for targeted NGS panel data. Extension of cn.mops package. Used for detecting copy number variations in targeted next generation sequencing panel data. Suitable to use for clinical geneticists for routine clinical diagnostics.

Proper citation: panelcn.mops (RRID:SCR_023657) Copy   

•   Source: SciCrunch Registry

http://www.raraf.org/

Biomedical technology research center dedicated for radiobiological research with available ionizing radiations such as protons, alpha particles, and neutrons. RARAF is well-established and highly user-friendly. The focus of RARAF is the development of high-throughput single-cell/single-particle microbeams, which can deliver defined amounts of ionizing radiation into individual cells with a spatial resolution of a few microns or better. The ability of a microbeam to put double strand break damage at any specific known location in a given cell has allowed new approaches to the study of damage signaling.

Proper citation: Radiological Research Accelerator Facility (RRID:SCR_001425) Copy   

•   Source: SciCrunch Registry

https://www.sutter.com/manuals/P-2000_OpMan.pdf

Microprocessor controlled, CO2 laser based micropipette puller.Default configuration allows fabrication of micropipettes for intracellular recording, patch clamping, microinjection and microperfusion.Can store up to 100 separate programs, each consisting of up to 8 command lines. The five parameters set in each command line allow exquisite control of the micropipette taper geometry. Allows the use of wide range of glass diameters from 0.125 to 1.2 mm.

Proper citation: Sutter: P-2000 Laser Micropipette Puller (RRID:SCR_018640) Copy   

•   Source: SciCrunch Registry