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Open source game engine and framework for 3D rendering and game development for Python and C++ programs. Graphics engine and programming environment to support everything from real time graphics applications to development of high end virtual reality theme park attractions or video games.
Proper citation: Panda3D (RRID:SCR_021216) Copy
Data repository for Friedrich Miescher Institute for Biomedical Research in areas of epigenetics, quantitative biology, and neurobiology.
Proper citation: Friedrich Miescher Institute data repository (RRID:SCR_021214) Copy
https://doi.org/10.7910/DVN/XD1A6B
Portal for cross sectional study where population based sample of adult cancer patients were recruited for mailed survey (with telephone follow-up of non-responders) to evaluate equivalence of PROMIS measures across socio-demographic and clinical sub-groups.
Proper citation: PROMIS 2 MY Health (RRID:SCR_021215) Copy
https://sourceforge.net/projects/iris-scanning/
Software LabView package for two-photon calcium imaging acquisition. Used for controlling two-photon microscope and preprocessing of calcium imaging data.
Proper citation: IRIS two photon acquisition package (RRID:SCR_021212) Copy
https://sourceforge.net/p/iris-scanning/calliope
Software package for image processing for MATLAB. Used for processing of calcium imaging data.
Proper citation: Calliope calcium imaging processing package (RRID:SCR_021213) Copy
https://github.com/slimsuite/depthsizer
Software tool for read-depth based genome size prediction. Wrapper for genome size estimate methods of Diploidocus.Uses long read depth of coverage and BUSCO single copy orthologue prediction to estimate genome size.
Proper citation: DepthSizer (RRID:SCR_021232) Copy
Portal enables browsing, searching, and analysis of human genetic information linked to lung diseases and related traits, while protecting integrity and confidentiality of underlying data.
Proper citation: Lung Disease Knowledge Portal (RRID:SCR_021352) Copy
https://evidencegraph.github.io/EVI/index.html
Evidence Graph Ontology extends core concepts from W3C Provenance Ontology PROV-O to describe evidence for correctness of findings in biomedical publications. Semantic data model in EVI is expressed using OWL2 Web Ontology Language.
Proper citation: Evidence Graph Ontology (RRID:SCR_021225) Copy
Open source software tool as 3D finite element grid generator with build in CAD engine and post processor. Provides meshing tool with parametric input and advanced visualization capabilities. Built around geometry, mesh, solver and post processing modules.Specification of any input to these modules is done either interactively using graphical user interface, in ASCII text files using Gmsh own scripting language (.geo files), or using C plus plus, C, Python or Julia Application Programming Interface.
Proper citation: GMSH (RRID:SCR_021226) Copy
https://github.com/diriano/ploidyNGS
Open source software tool for visually exploring ploidy with Next Generation Sequencing data.Used to visualize and explore ploidy levels in newly sequenced genome, exploiting short read data. Allows identification of ploidy level of newly sequenced genome in visual way. Implemented in Python and R.
Proper citation: ploidyNGS (RRID:SCR_021320) Copy
https://github.com/cihga39871/Atria
Open source software tool as adapter and quality trimmer for Next-Generation Sequence data.
Proper citation: Atria (RRID:SCR_021313) Copy
https://biospherix.com/a-chamber/
Animal Cage Enclosures for use in in vivo models that require control of experimental gases such as O2, CO2, NO, or CO. May be used together with gas controllers from BioSpherix. Chamber is outfitted with adjustable ventilation holes which permit ventilation of animal vapors and gases while simultaneously ensuring stable control of experimental conditions within. Available in three standard sizes.
Proper citation: BioSpherix: A-Chamber (RRID:SCR_021177) Copy
https://github.com/HeardLibrary/linked-data/tree/master/vanderbot
Software Python tool as Vanderbilt University curation tool.Used for exporting public profiles of university faculty from Vanderbilt University database into Wikidata.Used to create or update items in Wikidata using data from CSV spreadsheet data.
Proper citation: VanderBot (RRID:SCR_021298) Copy
https://github.com/tanghaibao/jcvi/wiki/ALLMAPS
Software tool for computing scaffold ordering that maximizes colinearity to collection of maps, including genetic, physical or comparative maps into final chromosome build.Robust scaffold ordering based on multiple maps.
Proper citation: ALLMAPS (RRID:SCR_021171) Copy
https://github.com/aidenlab/Juicebox
Visualization and analysis software for Hi-C data.
Proper citation: Juicebox (RRID:SCR_021172) Copy
https://biospherix.com/safety-hood/
Hood holds any animal lab chambers while continuously sweeping all experiment related off gases away.Used to capture and exhaust gases or vapors which escape from animal chamber and directs them to safe location.Helps to control animal odor in the lab. Available in standard and customized dimensions.
Proper citation: BioSpherix: Biological Safety Hood (RRID:SCR_021206) Copy
https://emea.support.illumina.com/sequencing/sequencing_software/experiment_manager/downloads.html
Software to create and edit sample sheet in order to perform next generation sequencing on Illumina paltforms. Used for MiniSeq, MiSeq, NextSeq 500/550, HiSeq, and NovaSeq 6000 Systems.
Proper citation: Illumina Experiment Manager (RRID:SCR_021202) Copy
https://www.noldus.com/catwalk-xt
Gait analysis system for quantitative assessment of footfalls and locomotion in rats and mice. System includes corridor that directs free movement in straight line, hardened glass walkway that enables CatWalk XT Illuminated Footprints technology,high speed color camera for spatial and temporal resolution, CatWalk XT software for recording and automated analysis of locomotor ability of rodents.
Proper citation: Noldus: CatWalk XT (RRID:SCR_021262) Copy
https://github.com/ngaggion/ChronoRoot
System which combines 3D printed open hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. Deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process.
Proper citation: ChronoRoot (RRID:SCR_021259) Copy
https://www.leicabiosystems.com/digital-pathology/scan/aperio-at2/
Digital whole slide scanner.400 slide capacity brightfield scanner. High throughput with small footprint. 2x3 slide option available.Aperio AT2 runs on Microsoft Windows 10 operating system.
Proper citation: Leica: Aperio AT2 scanner (RRID:SCR_021256) Copy
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