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Found 16 result(s)

FAIRDOMHub

The SEEK datafiles

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The FAIRDOMHub is built upon the SEEK software suite, which is an open source web platform for sharing scientific research assets, processes and outcomes. FAIRDOM (Web Site) will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

Kinetic models of biological systems

KiMoSys

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KiMoSys, a web application for quantitative KInetic MOdels of biological SYStems. Kinetic models, with the aim to understand and subsequently design the metabolism of organism of interest are constructed iteratively and require accurate experimental data for both the generation and verification of hypotheses. Therefore, there is a growing requirement for exchanging experimental data and models between the systems biology community, and to automate as much as possible the kinetic model building, editing, simulation and analysis steps.

SABIO-RK

System for the Analysis of Biochemical Pathways - Reaction Kinetics

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The SABIO-RK is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. All the data are manually curated and annotated by biological experts, supported by automated consistency checks.

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.

InnateDB

A Knowlede Resource for Innate Immunity Interactions & Pathways

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InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.

MORPHYLL

Database for acquisition of ecophysiologically relevant morphometric data of fossil leaves

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The database MORPHYLL contains quantitative and qualitative morphometric data of fossil angiosperm leaves from the Paleogene. The data are compiled from different fossil sites housed in various European Natural History Museums.

Sextant

Infrastructure de Données Géographiques (IDG) marines et littorales

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Sextant is a marine and coastal geographic data infrastructure. It is operated by Scientific Information Systems for the Sea (SISMER) of Ifremer (https://www.ifremer.fr/). Sextant aims to document, disseminate and promote a catalog of data related to the marine environment. For Ifremer's laboratories and partners, as well as for national and European actors working in the marine and coastal field, Sextant provides tools that promote and facilitate the archiving, consultation and availability of these geographical data. Data published by Sextant are available free or restricted. They can be used in accordance with the terms of the Creative Commons license selected by the author of data. Sextant infrastructure and the technologies used are in line with the implementation of the INSPIRE Directive and make it possible to follow the Open Data approach. Some data set published by Sextant has a DOI which enables it to be cited in a publication in a reliable and sustainable way. The long-term preservation of data filed in Sextant is ensured by Ifremer infrastructure.

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.

Nuclear Receptor Signaling Atlas

NURSA Hub

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>>> !!! the repository is offline !!! <<< More information see: https://dknet.org/about/NURSA_Archive All NURSA-biocurated transcriptomic datasets have been preserved for data mining in SPP through an enhanced and expanded version of Transcriptomine named Ominer. To access these datasets, dkNET provides users with the information of 527 transcriptomic datasets that contain data related to nuclear receptors and nuclear receptor coregulators in the NURSA Datasets table view and redirects users to the current SPP dataset page. Once users find the specific dataset of research interest, users can download the dataset by clicking DOI and then clicking the Download Dataset button at the Signaling Pathways Project webpage. See https://www.re3data.org/repository/r3d100013650

GnpIS

Genetic and Genomic Information System

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GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Research Institute for Agriculture, Food and Environment. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.

Collaborative Research Centre Transregio 32 Database

TR32DB

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In the framework of the Collaborative Research Centre/Transregio 32 ‘Patterns in Soil-Vegetation-Atmosphere Systems: Monitoring, Modelling, and Data Assimilation’ (CRC/TR32, www.tr32.de), funded by the German Research Foundation from 2007 to 2018, a RDM system was self-designed and implemented. The so-called CRC/TR32 project database (TR32DB, www.tr32db.de) is operating online since early 2008. The TR32DB handles all data including metadata, which are created by the involved project participants from several institutions (e.g. Universities of Cologne, Bonn, Aachen, and the Research Centre Jülich) and research fields (e.g. soil and plant sciences, hydrology, geography, geophysics, meteorology, remote sensing). The data is resulting from several field measurement campaigns, meteorological monitoring, remote sensing, laboratory studies and modelling approaches. Furthermore, outcomes of the scientists such as publications, conference contributions, PhD reports and corresponding images are collected in the TR32DB.

CIAT Dataverse

CIAT Research Online

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The International Center for Tropical Agriculture (CIAT), a member of the CGIAR Consortium, believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture. Research data produced by CIAT and its Partners is distributed freely whenever possible. Kindly note that these datasets require proper citation and citation information is included with the metadata for each dataset.

ISIMIP Repository

Inter-Sectoral Impact Model Intercomparison Project Repository

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The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) is a community-driven climate impact modeling initiative that aims to contribute to a quantitative and cross-sectoral synthesis of the various impacts of climate change, including associated uncertainties. It is designed as a continuous model intercomparison and improvement process for climate impact models and is supported by the international climate impact research community. ISIMIP is organized into simulation rounds, for which a simulation protocol specifies a set of common experiments. The protocol further describes a set of climate and direct human forcing data to be used as input data for all ISIMIP simulations. Based on this information, modelling groups from different sectors (e.g. agriculture, biomes, water) perform simulations using various climate impact models. After the simulations are performed, the data is collected by the ISIMIP data team, quality controlled and eventually published on the ISIMIP Repository. From there, it can be freely accessed for further research and analyses. The data is widely used within academia, but also by companies and civil society. ISIMIP was initiated by the Potsdam Institute for Climate Impact Research (PIK) and the International Institute for Applied Systems Analysis (IIASA).

Open Research Data Online

ORDO

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The figshare service for The Open University was launched in 2016 and allows researchers to store, share and publish research data. It helps the research data to be accessible by storing metadata alongside datasets. Additionally, every uploaded item receives a Digital Object Identifier (DOI), which allows the data to be citable and sustainable. If there are any ethical or copyright concerns about publishing a certain dataset, it is possible to publish the metadata associated with the dataset to help discoverability while sharing the data itself via a private channel through manual approval.

MorpheusML model repository

Morpheus model repository

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The public MorpheusML model repository collects, curates, documents and tests computational models for multi-scale and multicellular biological systems. Model must be encoded in the model description language MorpheusML. Subsections of the repository distinguish published models from contributed non-published and example models. New models are simulated in Morpheus or Artistoo independently from the authors and results are compared to published results. Successful reproduction is documented on the model's webpage. Models in this repository are included into the CI and test pipelines for each release of the model simulator Morpheus to check and guarantee reproducibility of results across future simulator updates. The model’s webpage provides a History-link to all past model versions and edits that are automatically tracked via Git. Each model is registered with a unique and persistent ID of the format M..... The model description page (incl. the biological context and key results of that model), the model’s XML file, the associated paper, and all further files (often simulation result videos) connected with that model can be retrieved via a persistent URL of the format https://identifiers.org/morpheus/M..... - for technical details on the citable ModelID please see https://registry.identifiers.org/registry/morpheus - for the model definition standard MorpheusML please see https://doi.org/10.25504/FAIRsharing.78b6a6 - for the model simulator Morpheus please see https://morpheus.gitlab.io - for the model simulator Artistoo please see https://artistoo.net/converter.html

MatrixDB

Extracellular Matrix interactions DataBase

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MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides. MatrixDB takes into account the multimetric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB includes interaction data extracted from the literature by manual curation in our lab, and offers access to relevant data involving extracellular proteins provided by our IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009