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Found 213 result(s)

PlutoF

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An online data management workbench and computing service provider for biology and related disciplines.

SISSA Open Data

Scuola Internazionale Superiore di Studi Avanzati Open Data

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SISSA Open Data is the Sissa repository for the research data managment. It is an institutional repository that captures, stores, preserves, and redistributes the data of the SISSA scientific community in digital form. SISSA Open Data is managed by the SISSA Library as a service to the SISSA scientific community.

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

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The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.

SITES Data Portal

Swedish Infrastructure for Ecosystem Science

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The Swedish Infrastructure for Ecosystem Science (SITES) is a national infrastructure for terrestrial and limnological field research. SITES aims to promote high-quality research through long-term field measurements and field experiments, and by making data available. Quality-controlled monitoring data from SITES is freely available on the SITES Data Portal from all participating stations and thematic programs. New datasets are continuously being uploaded.

National Omics Data Encyclopedia

NODE

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NODE (The National Omics Data Encyclopedia) provides an integrated, compatible, comparable, and scalable multi-omics resource platform that supports flexible data management and effective data release. NODE uses a hierarchical data architecture to support storage of muti-omics data including sequencing data, MS based proteomics data, MS or NMR based metabolomics data, and fluorescence imaging data. Launched in early 2017, NODE has collected and published over 900 terabytes of omics data for researchers from China and all over the world in last three years, 22% of which contains multiple omics data. NODE provides functions around the whole life cycle of omics data, from data archive, data requests/responses to data sharing, data analysis, data review and publish.

GeneLab

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GeneLab is an interactive, open-access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments. Users can explore GeneLab datasets in the Data Repository, analyze data using the Analysis Platform, and create collaborative projects using the Collaborative Workspace. GeneLab promises to facilitate and improve information sharing, foster innovation, and increase the pace of scientific discovery from extremely rare and valuable space biology experiments. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight. GeneLab helps scientists understand how the fundamental building blocks of life itself – DNA, RNA, proteins, and metabolites – change from exposure to microgravity, radiation, and other aspects of the space environment. GeneLab does so by providing fully coordinated epigenomics, genomics, transcriptomics, proteomics, and metabolomics data alongside essential metadata describing each spaceflight and space-relevant experiment. By carefully curating and implementing best practices for data standards, users can combine individual GeneLab datasets to gain new, comprehensive insights about the effects of spaceflight on biology. In this way, GeneLab extends the scientific knowledge gained from each biological experiment conducted in space, allowing scientists from around the world to make novel discoveries and develop new hypotheses from these priceless data.

IIT Dataverse

Italian Institute of Technology Dataverse

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IIT Dataverse is the institutional research data repository of the Istituto Italiano di Tecnologia. IIT Dataverse has been operative since May 2021 and is currently open to IIT-affiliated researchers for research data deposition and sharing.

Signaling Pathways Project

SSP

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The goal of the Signaling Pathways Project knowledgebase is to allow bench researchers to routinely ask sophisticated questions of the universe of multi-omics data points generated by the cellular signaling community. SPP is dedicated to helping researchers to make sense of the often overwhelming volume of multi-omics information in the field of cellular signaling.

NF Data Portal

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The NF Data Portal is designed to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis. Anyone can join the NF Open Science Initiative (NF-OSI) to participate! We welcome contributions from anyone in the neurofibromatosis and schwannomatosis research community, such as original datasets generated by the community or analyses of data from the NF Data Portal.

ZFMK Biodiversity Data Center

ZFMK Natural History Collections - occurrence data

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The ZFMK Biodiversity Data Center is aimed at hosting, archiving, publishing and distributing data from biodiversity research and zoological collections. The Biodiversity Data Center handles and curates data on: - The specimens of the institutes collection, including provenance, distribution, habitat, and taxonomic data. - Observations, recordings and measurements from field research, monitoring and ecological inventories. - Morphological measurements, descriptions on specimens, as well as - Genetic barcode libraries, and - Genetic and molecular research data associated with specimens or environmental samples. For this purpose, suitable software and hardware systems are operated and the required infrastructure is further developed. Core components of the software architecture are: The DiversityWorkbench suite for managing all collection-related information. The Digital Asset Management system easyDB for multimedia assets. The description database Morph·D·Base for morphological data sets and character matrices.

Canadian Open Neuroscience Platform Portal

CONP

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The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cycle of a typical research project: starting with data acquisition, followed by processing using already existing/published tools, and ultimately publication of the obtained results including a link to the original dataset. From more information on CONP, please visit https://conp.ca

DataON Repository

previous name: KORD

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DataON is Korea's National Research Data Platform. It provides integrated search of metadata for KISTI's research data and domestic and international research data and links to raw data. DataON allows users (researchers, policy makers, etc.) to perform the following tasks: Easily search for various types of research data in all scientific fields. By registering research results, research data can be posted and cited. Build a community among researchers and enable collaborative research. It provides a data analysis environment that allows one-stop analysis of discovered research data.

ProteomicsDB

PrDB

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ProteomicsDB started as a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. The data types and contents grew over time to include RNA-Seq expression data, drug-target interactions and cell line viability data.

DataHub Figshare

University of Hong Kong Data Repository

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Provided by the University Libraries, DataHub is the comprehensive institutional repository for research data and scholarly outputs produced by the researchers and students in the University of Hong Kong and their collaborators.

BioSimulations

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BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.

Datanator

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Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.

ClinVar

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ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation. ClinVar processes submissions reporting variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data. The alleles described in submissions are mapped to reference sequences, and reported according to the HGVS standard. ClinVar then presents the data for interactive users as well as those wishing to use ClinVar in daily workflows and other local applications. ClinVar works in collaboration with interested organizations to meet the needs of the medical genetics community as efficiently and effectively as possible

WikiPathways

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WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

Complex Portal

CP

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The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database (https://www.ebi.ac.uk/intact/). Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry.

Cellosaurus

Cellosaurus - a knowledge resource on cell lines

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The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines, Naturally immortal cell lines (example: stem cell lines), Finite life cell lines when those are distributed and used widely, Vertebrate cell line with an emphasis on human, mouse and rat cell lines, Invertebrate (insects and ticks) cell lines. Its scope does not include: Primary cell lines (with the exception of the finite life cell lines described above), Plant cell lines. Cellosaurus was initiated to be used as a cell line controlled vocabulary in the context of the neXtProt knowledgebase, but it quickly become apparent that there was a need for a cell line knowledge resource that would serve the needs of individual researchers, cell line distributors and bioinformatic resources. This leads to an increase of the scope and depth of the content of the Cellosaurus. The Cellosaurus is a participant of the Resource Identification Initiative and contributes actively to the work of the International Cell Line Authentication Committee (ICLAC). It is a Global Core Biodata Resource, an ELIXIR Core Data Resource and an IRDiRC Recognized Resource.

FaceBase

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FaceBase is a collaborative NIDCR-funded project that houses comprehensive data in support of advancing research into craniofacial development and malformation. It serves as a community resource by curating large datasets of a variety of types from the craniofacial research community and sharing them via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this project is to facilitate cooperation and collaboration between the central coordinating center (ie, the Hub) and the craniofacial research community.

GNPS: Global Natural Products Social Molecular Networking

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GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. GNPS aids in identification and discovery throughout the entire life cycle of data; from initial data acquisition/analysis to post publication.

UCL Research Data Repository

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The UCL Research Data Repository is the institutional data repository of University College London. Based on Figshare, it accepts data deposits from UCL staff and doctoral students from all disciplines. Depositors are encouraged to use CC0 licences to make their data available to the widest possible range of users and the widest range of uses.

BBMRI-ERIC Directory

Directory of Biobanks

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BBMRI-ERIC is a European research infrastructure for biobanking. We bring together all the main players from the biobanking field – researchers, biobankers, industry, and patients – to boost biomedical research. To that end, we offer quality management services, support with ethical, legal and societal issues, and a number of online tools and software solutions. Ultimately, our goal is to make new treatments possible. The Directory is a tool to share aggregate information about the biobanks that are willing external collaboration. It is based on the MIABIS 2.0 standard, which describes the samples and data in the biobanks at an aggregated level.

BAliBASE

Benchmark Alignment dataBASE

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A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.