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Found 100 result(s)
Content type(s)
The JCB DataViewer is an image hosting and presentation platform for original image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal from the Rockefeller University Press.
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.
BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature.
The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.
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.
CORUM is a manually curated dataset of mammalian protein complexes. Annotation of protein complexes includes protein complex composition and other valuable information such as method of purification, cellular function of complexes or involvement in diseases.
CorrDB has data of cattle, relating to meat production, milk production, growth, health, and others. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies.
SWATHAtlas is a repository of mass spectrometry data of the human proteome. The repository provides open access to libraries of SWATH-MS (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) datasets. SWATH-MS is a method which combines both data-independent acquisition (DIA) and targeted data analysis techniques for the collection and storage of fragmentation spectra of peptides. Compared to techniques of selected reaction monitoring (SRM), SWATH-MS allows for a more extensive throughput of proteins in a sample to be targeted. The spectra collected in SWATHAtlas can be interpreted with the help of software such as OpenSWATH or Peakview.
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
The Virtual Liver Network (VLN) represents a major research investment by the German Government focusing on work at the “bleeding edge” of Systems Biology and Systems Medicine. This Flagship Programme is tackling one of the major challenges in the life sciences: that is, how to integrate the wealth of data we have acquired post-genome, not just in a mathematical model, but more importantly in a series of models that are linked across scales to represent organ function. As the project is prototyping how to achieve true multi-scale modelling within a single organ and linking this to human physiology, it will be developing tools and protocols that can be applied to other systems, helping to drive forward the application of modelling and simulation to modern medical practice. It is the only programme of its type to our knowledge that bridges investigations from the sub-cellular through to ethically cleared patient and volunteer studies in an integrated workflow. As such, this programme is contributing significantly to the development of a new paradigm in biology and medicine.
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.
Content type(s)
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.
Content type(s)
The CEBS database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial and governmental laboratories. CEBS is designed to display data in the context of biology and study design, and to permit data integration across studies for novel meta analysis.
The mission of the platform is to enable access for academic projects towards experiments in high-throughput without loss of IP and on a cost basis, which does not restrict access towards HTS usage. The FMP hosts the central open access technology platform of EU-OPENSCREEN, the ChemBioNet and theHelmholtz-Initiative für Wirkstoffforschung, the Screening Unit. The Unit serves for systematic screening of large compound or genome-wide RNAi libraries with state-of-the-art equipment like automated microscopes and microfluidic systems. The Screening Unit is part of the Chemical Biology Platform of the FMP also supported by the MDC.
GLOBE (Global Collaboration Engine) is an online collaborative environment that enables land change researchers to share, compare and integrate local and regional studies with global data to assess the global relevance of their work.
The Leipzig Health Atlas (LHA) is an alliance of medical ontologists, medical systems biologists and clinical trials groups to design and implement a multi-functional and quality-assured atlas. It provides models, data and metadata on specific use cases from medical research projects from the partner institutions.
BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.
The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses.
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.
>>>!!!<<< As stated 2017-05-16 The BIRN project was finished a few years ago. The web portal is no longer live.>>>!!!<<< BIRN is a national initiative to advance biomedical research through data sharing and online collaboration. It supports multi-site, and/or multi-institutional, teams by enabling researchers to share significant quantities of data across geographic distance and/or incompatible computing systems. BIRN offers a library of data-sharing software tools specific to biomedical research, best practice references, expert advice and other resources.
The CAD-60 and CAD-120 data sets comprise of RGB-D video sequences of humans performing activities which are recording using the Microsoft Kinect sensor. Being able to detect human activities is important for making personal assistant robots useful in performing assistive tasks. Our CAD dataset comprises twelve different activities (composed of several sub-activities) performed by four people in different environments, such as a kitchen, a living room, and office, etc. Tested on robots reactively responding to the detected activities.
RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.
PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mutant cells.