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Spanish public university with campus in Leon and Ponferrada.
Proper citation: University of Leon, Spain (RRID:SCR_019071) Copy
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
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
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
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
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
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
https://nrdg.github.io/fracridge
Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.
Proper citation: fracridge (RRID:SCR_019045) Copy
https://openwetware.org/wiki/RAVE
Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG).
Proper citation: RAVE (RRID:SCR_019040) Copy
http://cello.life.nctu.edu.tw/cello2go/
Web server for protein subcellular localization prediction with functional gene ontology annotation. Web based system for screening various properties of targeted protein and its subcellular localization.
Proper citation: Cello2Go (RRID:SCR_019042) Copy
https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/
Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.
Proper citation: PROCHECK (RRID:SCR_019043) Copy
https://bioconductor.org/packages/scTHI/
Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.
Proper citation: scTHI (RRID:SCR_018918) Copy
https://www.t2dsystems.eu/t2dsystems
Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D.
Proper citation: T2DSystems (RRID:SCR_018913) Copy
http://diabeticfootconsortium.org/
Group of academic institutions committed to studying diabetic foot conditions, such as foot ulcers and wound healing, to develop predictive biomarkers which can be later used to create better treatment plans and improve health and quality of life for people living with diabetes.
Proper citation: Diabetic Foot Consortium (RRID:SCR_018914) Copy
https://www.leicabiosystems.com/histology-equipment/tissue-processors/products/leica-asp300-s/
Processor that automatically washes tissue sample which needs to be usable in downstream processes. Designed for routine and research histopathology of up to 300 cassettes.
Proper citation: Leica: ASP300S Fully Enclosed Tissue Processor (RRID:SCR_018916) Copy
Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties.
Proper citation: Mcule (RRID:SCR_018921) Copy
https://github.com/najasplus/hetindel_shinyapp
Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels.
Proper citation: Hetindel (RRID:SCR_018922) Copy
http://www.nonlinear.com/progenesis/qi-for-proteomics/
Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics.
Proper citation: Progenesis QI (RRID:SCR_018923) Copy
Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.
Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy
http://markummitchell.github.io/engauge-digitizer/
Software tool accepts image files (like PNG, JPEG and TIFF) containing graphs, and recovers the data points from those graphs. Used to convert graphs to data points. Imports image file and then digitizes it by placing points along axes and curves.
Proper citation: Engauge Digitizer (RRID:SCR_019056) Copy
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