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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://harperlab.connect.hms.harvard.edu/CARGO_Cellular_Autophagy_Regulation_GOlgiphagy/
Web browser for analysis of proteomic data. ShinyApp interface generated in R and RStudio.
Proper citation: CARGO (RRID:SCR_024474) Copy
https://www.planetmicrobe.org/
Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data.
Proper citation: Planet Microbe (RRID:SCR_024478) Copy
https://webprotege.stanford.edu
Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat.
Proper citation: WebProtege (RRID:SCR_024627) Copy
https://divbrowse.ipk-gatersleben.de/
Web tool for interactive visualization and analysis of diversity of genomic variants. Used for interactive exploration and analysis of very large SNP matrices based on VCF files.
Proper citation: DivBrowse (RRID:SCR_022780) Copy
A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.
Proper citation: EvidenceFinder (RRID:SCR_013764) Copy
http://www.cbs.dtu.dk/services/SignalP/
Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
Proper citation: SignalP (RRID:SCR_015644) Copy
http://dynamine.ibsquare.be/submission/
An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned.
Proper citation: DynaMine (RRID:SCR_014559) Copy
http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi
Web search tool to gain overview of set of articles retrieved by PubMed query. Used to support user driven summarization, drill down and browsing of PubMed search results. Value-added PubMed search engine for analysis and text mining.
Proper citation: Anne O'Tate (RRID:SCR_023086) Copy
Web tool for assessing exposure and human health risks at contaminated sites. Fate and distribution of chemical pollutants in soil are calculated according to steady-state conservation of mass principles.Risks are calculated by comparing exposures with toxicological reference values and concentrations with toxicological or legal reference concentrations.
Proper citation: S-Risk (RRID:SCR_023085) Copy
Web application search tool intended to help users find MRI data shared publicly on the Web, particularly from projects organized under the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI). Users can perform queries visually to select a cohort of participants with brain imaging data based on their demographics and phenotypic information and then link out to imaging measures.
Proper citation: MetaSearch (RRID:SCR_014751) Copy
http://sbi.postech.ac.kr/oasis/introduction/
A tool for various statistical tasks involved in analyzing survival data which provides a uniform platform to facilitate efficient statistical analyses of survival data in the aging field. The statistical features of OASIS include the calculation of Kaplan-Meier estimates, mean/median lifespan, mortality rate, Mantel-Cox Log-Rank test, Fishers exact test, weighted Log-Rank test, Kolmogorov-Smirnov test and Neymans smooth test. Moreover, OASIS generates survival and mortality curves that can be easily exported and modified by using common graphic softwares.
Proper citation: Online Application for Survival Analysis (OASIS) (RRID:SCR_014450) Copy
https://omictools.com/3omics-tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites.
Proper citation: 3Omics (RRID:SCR_014678) Copy
https://www.pacemweb.nl/simulation/assessment-settings
Web tool for aggregate consumer exposure assessment. Model is based on realistic product usage information obtained from surveys. Information on usage, frequency and amount of personal care products and household cleaning products in various European countries is included.
Proper citation: PACEMweb (RRID:SCR_023083) Copy
http://ml-neuronbrowser.janelia.org/
Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions.
Proper citation: MouseLight Neuron Browser (RRID:SCR_016669) Copy
Research assistant using language models like GPT-3 to automate parts of researchers’ workflows. Main workflow is Literature Review. If you ask question, Elicit will show relevant papers and summaries of key information about those papers in easy-to-use table.
Proper citation: Elicit (RRID:SCR_023362) Copy
https://developers.google.cn/earth-engine/
Web application as public data catalog, compute infrastructure, geospatial APIs and interactive app server. Geospatial processing service.
Proper citation: Google Earth Engine (RRID:SCR_023224) Copy
http://jupyterlab.github.io/jupyterlab/
Software extensible environment for interactive and reproducible computing, based on Jupyter Notebook and Architecture. Next generation user interface for Project Jupyter offering all familiar building blocks of classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in flexible and powerful user interface. Can be extended using npm packages that use our public APIs.
Proper citation: JupyterLab (RRID:SCR_023339) Copy
Web application that simplifies evaluation of confidence in findings from network meta analysis.
Proper citation: Confidence in network meta analysis (RRID:SCR_023193) Copy
https://github.com/tobiasrausch/alfred
Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.
Proper citation: Alfred (RRID:SCR_023354) Copy
http://www.ugr.es/local/abfr/tiempojm/
Web application that records the time devoted to each of the actions that are performed while playing motor games or active games. This recording system has applications in physical activity research and physical education.
Proper citation: Time in Motor Games (Tiempo en Juegos Motores) (RRID:SCR_015819) Copy
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