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http://dbmi.mc.vanderbilt.edu/research/dnadatabank.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. BioVU is a research resource providing a View into biology at the level of DNA and other important macromolecules. BioVU has two major components. The first is a repository of DNA samples (extracted from discarded blood samples) that are coded solely by a Research Unique Identifier (RUI) derived from the Medical Record Number (MRN) using a one-way hash function. This is a computer algorithm that creates a transformation of each MRN such that the resulting RUI (which is in this instance is a 512 byte identifier) is unique, and has the property that it is not possible to infer or compute the MRN that generated it. As of early 2009, over 50,000 DNA samples were in the biobank, with new samples being added at the rate of approximately 700 per week. The second component of the resource is the creation of a database known as the Synthetic Derivative which is a collection of de-identified information extracted from VUMC''s electronic clinical information systems, indexed by the same one-way RUI used to track samples, and with content changed by deletion or permutation of all identifiers contained within each record. The Synthetic Derivative search interface is available to Vanderbilt researchers via the StarBRITE research portal created and maintained by the Vanderbilt Institute for Clinical and Translational Research. This user interface enables investigators meeting protocol approval criteria and other user agreement requirements to receive protocol-specific sets of data derived from DNA samples and from the Synthetic Derivative., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Vanderbilt BioVU (RRID:SCR_004632) Copy   

•   Source: SciCrunch Registry

http://www.knhi.zks.uni-leipzig.de/en/Research/SP03/

The goal of this project is the creation of an extensive biomaterials bank. Materials (blood, serum, plasma, DNA) from all patients who participate in studies in the network will be collected for this purpose. The objective is a consistently high quality standard for the processing, storage and management of all samples. The biomaterials bank is an investment in the future by the network. It enables the competence network and the research community in general to acquire new scientific knowledge about the development, progression and prognosis of the different forms of heart failure. Each time a patient is documented in a study in the competence network, blood (EDTA whole blood and serum) is drawn from the patient, sent by post to the central biomaterials bank and processed there in the central incoming sample laboratory according to specified standards. In the first two subsidization periods, a total of 100,000 samples from approximately 10,000 patients was documented and processed (aliquoting, DNA extraction). These samples are stored in climate-controlled rooms used especially for this purpose at the biomaterial bank of the Experimental and Clinical Research Center (ECRC) in Berlin-Buch at temperatures between -20 and -80 degrees C. As the central infrastructure project for all samples, the biomaterials bank is deeply involved in the networking. There are also intensive collaborations with other competence networks (e.g. the Competence Network for Congenital Heart Defects) and biobanks. The biomaterial bank of the Heart Failure Competence Network also participates in domestic and European pilot projects for networking biomaterial banks (BBMRI, ESFRI, etc.). The goal of these projects is to develop uniform methods for sample processing and use.

Proper citation: Central Biomaterial Bank - German Heart Failure Network (RRID:SCR_004667) Copy   

•   Source: SciCrunch Registry

http://www.mnbb.org/

The Michigan Neonatal Biobank (Biobank) is a storage and management facility for The Michigan Department of Community Health''s archive of dried blood spot cards. A 501(c)3 non-profit charitable organization, the Biobank is contracted to serve as the repository for storage and management of the samples in a temperature controlled facility at Wayne State University''s Biobanking Center of Excellence in Tech Town. The Biobank''s roots are planted in the State''s Newborn Screening Program which began in 1965 in the Department of Community Health. Newborn screening is a public health program required by Michigan law to find babies with rare but serious disorders that require early treatment. A few drops of blood taken from the baby''s heel are sent to the State Public Health Laboratory and are tested for 49 disorders. Each year more than 200 Michigan babies are found to have a disorder detected by Newborn Screening. Once screening in the State laboratory is complete, residual dried blood spot samples that are no longer needed for testing are each assigned a unique code which assures anonymity for the sample and its donor. The samples are then sent for storage in the Michigan Neonatal Biobank.

Proper citation: Michigan Neonatal Biobank (RRID:SCR_004541) Copy   

•   Source: SciCrunch Registry

http://www.store-a-tooth.com/

Provia Laboratories Inc. offers Store-A-Tooth, the industry-leading dental stem cell banking service for preserving the stem cells found in baby teeth and wisdom teeth. Store-A-Tooth is a service that provides you the opportunity to store the stem cells inside of teeth that come out. Eligible teeth include baby teeth, wisdom teeth, and other healthy teeth that need to be surgically extracted during the normal course of dental care. Store-A-Tooth has been available since 2006 from dentists across the U.S. At the core of our tooth transport device is the Save-A-Tooth device, which is FDA-approved and ADA accepted for the preservation of avulsed teeth. We use Save-A-Tooth for tooth collection and transport to ensure optimal viability of your sample for processing and cryopreservation. Our laboratory is FDA-registered, CLIA-certified, and AABB-accredited.

Proper citation: Store-a-Tooth Stem Cell Bank (RRID:SCR_004252) Copy   

•   Source: SciCrunch Registry

https://github.com/strawlab/freemovr_engine

Software tool as virtual reality engine built on ROS and OpenSceneGraph.Perspective correct Virtual Reality for freely moving animals engine. Used for multicomputer realtime tracking and display with goal of being useful for scientific studies of vision and behavior.Part of FreemoVR system.

Proper citation: FreemoVR (RRID:SCR_021601) Copy   

•   Source: SciCrunch Registry

https://github.com/FlySorterLLC

Software tool to automate various fly handling tasks.Control software for Drosophila handling robot MAPLE.

Proper citation: Modular Automated Platform for Large Scale Experiments (RRID:SCR_021600) Copy   

•   Source: SciCrunch Registry

https://github.com/amchagas/poke_device_arduino

Software tool as script to test if IR led, IR photodiode, arduino and 3D printed nose poke device work properly. Part of Nose Poke Device system.

Proper citation: poke device arduino (RRID:SCR_021608) Copy   

•   Source: SciCrunch Registry

https://github.com/delcasso/hope

Softwre tool as part of Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project for brain implant.

Proper citation: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology (RRID:SCR_021606) Copy   

•   Source: SciCrunch Registry

https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/

Integrated commercial system comprising hardware, software and nCounter chemistry that enables simultaneous, highly multiplex spatial profiling of proteins or RNA in FFPE tissues. DSP platform quantifies abundance of protein or RNA by counting unique indexing oligonucleotides assigned to each target of interest. Used to rapidly and quantitatively assess biological implications of heterogeneity within tissue samples.

Proper citation: NanoString: GeoMx Digital Spatial Profiler (RRID:SCR_021660) Copy   

•   Source: SciCrunch Registry

https://meyerinst.com/library/NanoZoomer_RS_Brochure_Catalog.pdf

High speed, high resolution digital scanner with network features. User friendly full slide scanner designed to process up to 210 slides automatically.

Proper citation: Hamamatsu: NanoZoomer 2.0-HT (RRID:SCR_021658) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/ontquery/

Software tool as framework querying ontology terms within SciCrunch and SciCrunch SciGraph endpoints.

Proper citation: ontquery (RRID:SCR_021659) Copy   

•   Source: SciCrunch Registry

https://www.nexcelom.com/nexcelom-products/automated-cell-counters/cellometer-auto-t4-automated-cell-counter/

System includes automated cell counter for trypan blue viability for cell lines and bright field imaging and pattern recognition software to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported.

Proper citation: McKinley: Cellometer Auto T4 (RRID:SCR_021656) Copy   

•   Source: SciCrunch Registry

https://pdf.medicalexpo.com/pdf/ge-healthcare-life-sciences/amersham-imager-600/80554-135352.html

Amersham Imager 600 is CCD camera system that produces digitial images of samples in gels or membranes in three different modes: chemiluminescence, colorimetric and fluorescent image capture. Provides imaging system to capture and analyze protein and DNA sample gels and membranes in high resolution.

Proper citation: GE: Amersham Imager 600 (RRID:SCR_021853) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/BorutaShap/

Software tool as wrapper feature selection method which combines both Boruta feature selection algorithm with shapley values.

Proper citation: BorutaShap (RRID:SCR_021696) Copy   

•   Source: SciCrunch Registry

https://lightgbm.readthedocs.io/en/latest/

Software tool as gradient boosting framework that uses tree based learning algorithms. Designed to be distributed and efficient with advantages:Faster training speed and higher efficiency;Lower memory usage;Better accuracy;Support of parallel, distributed, and GPU learning;Capable of handling large scale data.

Proper citation: LightGBM (RRID:SCR_021697) Copy   

•   Source: SciCrunch Registry

https://github.com/gfairchild/pyxDamerauLevenshtein

Software tool implements Damerau-Levenshtein (DL) edit distance algorithm for Python in Cython for high performance.

Proper citation: pyxDamerauLevenshtein (RRID:SCR_021858) Copy   

•   Source: SciCrunch Registry

https://www.physikinstrumente.com/en/products/motion-control-software/

Software to control positioning systems without their own macro facility.

Proper citation: PI Motion Control Software (RRID:SCR_021867) Copy   

•   Source: SciCrunch Registry

http://phenex.phenoscape.org/

Software application for annotating character matrix files with ontology terms. Character states can be annotated using Entity-Quality syntax, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from taxonomy ontology. Phenex saves ontology annotations alongside original free text character matrix data using new NeXML format standard for evolutionary data.

Proper citation: Phenex (RRID:SCR_021748) Copy   

•   Source: SciCrunch Registry

https://www.nanostring.com/products/ncounter-analysis-system/ncounter-systems-overview/

System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification.

Proper citation: NanoString: nCounter Analysis System (RRID:SCR_021712) Copy   

•   Source: SciCrunch Registry

https://yaml.org

YAML is a human friendly data serialization language for all programming languages. Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing.

Proper citation: YAML (RRID:SCR_021710) Copy   

•   Source: SciCrunch Registry