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https://www.norlab.com/library/brochure/11566

Multi channel peristaltic pump for applications with different viscous or abrasive fluids. Allows for channel cartridges, from one to sixteen, to be changed while pump is running.

Proper citation: Gilson: Minipuls Evolution peristaltic pump (RRID:SCR_018955) Copy   

•   Source: SciCrunch Registry

https://www.harvardapparatus.com/tabletop-anesthesia-systems.html#collapseTwo

Tabletop anesthesia system suitable for mice, rats and other small animals under 10 lb. Passive scavenging systems. Funnel fill isoflurane vaporizers.

Proper citation: Harvard Apparatus: Single Animal Tabletop Isoflurane Anesthesia System with Small Induction Box (RRID:SCR_018956) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vmas_2020/

Software tool to generate whole connected 3D brain ventricular shape model and encode ventricular surface deformation information that is inaccessible by ventricle volume measure. Contains automated segmentation approach and surface based multivariate morphometry statistics.

Proper citation: Ventricular Morphometry Analysis System (RRID:SCR_019007) Copy   

•   Source: SciCrunch Registry

https://opencor.ws/

Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives.

Proper citation: OpenCOR (RRID:SCR_019001) Copy   

•   Source: SciCrunch Registry

http://enterobase.warwick.ac.uk/

Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella.

Proper citation: EnteroBase (RRID:SCR_019019) Copy   

•   Source: SciCrunch Registry

http://dgenies.toulouse.inra.fr/

Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

Proper citation: D-GENIES (RRID:SCR_018967) Copy   

•   Source: SciCrunch Registry

http://amphibian.hiroshima-u.ac.jp/english/ARC_HP_English_ver./english_page.html

Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis.

Proper citation: Hiroshima University Amphibian Research Center (RRID:SCR_019015) Copy   

•   Source: SciCrunch Registry

https://www.crd.york.ac.uk/PROSPERO

International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol.

Proper citation: PROSPERO (RRID:SCR_019061) Copy   

•   Source: SciCrunch Registry

http://www.softberry.com/berry.phtml?topic=fgenesh_plus_plus&group=help&subgroup=pipelines

Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.

Proper citation: Fgenesh plus plus (RRID:SCR_018928) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger

Software tool as set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants by 10x Genomics.

Proper citation: Long Ranger (RRID:SCR_018925) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/software/elda/

Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.

Proper citation: ELDA (RRID:SCR_018933) Copy   

•   Source: SciCrunch Registry

https://github.com/Trinotate/Trinotate.github.io/wiki

Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Proper citation: Trinotate (RRID:SCR_018930) Copy   

•   Source: SciCrunch Registry

https://open.scayle.es/about

Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models.

Proper citation: Scayle (RRID:SCR_019064) Copy   

•   Source: SciCrunch Registry

https://www.unileon.es/

Spanish public university with campus in Leon and Ponferrada.

Proper citation: University of Leon, Spain (RRID:SCR_019071) Copy   

•   Source: SciCrunch Registry

http://webapps.embl-hamburg.de/rapido/

Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains.

Proper citation: RAPIDO (RRID:SCR_018935) Copy   

•   Source: SciCrunch Registry

http://xena.ucsc.edu/

Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables.

Proper citation: UCSC Xena (RRID:SCR_018938) Copy   

•   Source: SciCrunch Registry

https://docs.osparc.io

Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response.

Proper citation: o²S²PARC (RRID:SCR_018997) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/abcdrepronim/

Course provides training for reproducible analyses of Adolescent Brain Cognitive Development Study data. Designed to provide comprehensive background to ABCD study while delivering hands on instruction on reproducible ReproNim workflows and outcomes.

Proper citation: ABCD-ReproNim Course (RRID:SCR_018911) Copy   

•   Source: SciCrunch Registry

https://nanopore.usegalaxy.eu/

Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.

Proper citation: NanoGalaxy (RRID:SCR_018912) Copy   

•   Source: SciCrunch Registry

https://proteins.plus/

Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported.

Proper citation: Protein.Plus (RRID:SCR_019044) Copy   

•   Source: SciCrunch Registry