A5084954396- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Evolution and Genetic Dynamics
- Artificial Intelligence in Healthcare
- Research Data Management Practices
- Viral Infectious Diseases and Gene Expression in Insects
- Mathematical Biology Tumor Growth
- COVID-19 diagnosis using AI
- Data-Driven Disease Surveillance
European Bioinformatics Institute
2013-2021
Wellcome Trust
2013-2020
Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), repository for mathematical models, was established 2005. The current allows submission of models encoded diverse formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. submitted are curated verify the computational...
BioModels (http://www.ebi.ac.uk/biomodels/) is a repository of mathematical models biological processes. A large set curated to verify both correspondence the process that model seeks represent, and reproducibility simulation results as described in corresponding peer-reviewed publication. Many submitted database are annotated, cross-referencing its components external resources such records, terms from controlled vocabularies ontologies. comprises two main branches: one composed derived...
Abstract Background Systems biology projects and omics technologies have led to a growing number of biochemical pathway models reconstructions. However, the majority these are still created de novo , based on literature mining manual processing data. Results To increase efficiency model creation, Path2Models project has automatically generated mathematical from representations using suite freely available software. Data sources include KEGG, BioCarta, MetaCyc SABIO-RK. Depending source data,...
Background: With the ever increasing use of computational models in biosciences, need to share and reproduce results published studies efficiently easily is becoming more important. To this end, various standards have been proposed that can be used describe models, simulations, data or other essential information a consistent fashion. These constitute separate components required given scientific result. Results: We Open Modeling EXchange format (OMEX). Together with standard formats from...
Reproducibility of scientific results is a key element science and credibility. The lack reproducibility across many fields has emerged as an important concern. In this piece, we assess mathematical model propose scorecard for improving in field.
Abstract The amount of omics data in the public domain is increasing every year. Modern science has become a data-intensive discipline. Innovative solutions for management, sharing, and discovering novel datasets are therefore increasingly required. In 2016, we released first version Omics Discovery Index (OmicsDI) as light-weight system to aggregate across multiple resources. OmicsDI aggregates genomics, transcriptomics, proteomics, metabolomics multiomics datasets, well computational...
BioModels serves as a central repository of mathematical models representing biological processes. It offers platform to make easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting broader range formats derived from diverse approaches and tools, new infrastructure for has been developed that is available at http://www.ebi.ac.uk/biomodels. This system allows submitting sharing wide with improved support other than SBML. also...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events 21st century. rapid global outbreak has had significant impacts on human society and is already responsible for millions deaths. Understanding tackling impact virus required a worldwide mobilisation coordination scientific research. COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released part European Platform, April 20th 2020 to facilitate open data...
BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 described in literature and 140,000 automatically generated from pathway resources. Most model are cross‐linked with external resources facilitate interoperability. A large proportion manually curated ensure reproducibility simulation results. This tutorial presents BioModels' content, features,...
The lack of a common exchange format for mathematical models in pharmacometrics has been long-standing problem. Such the potential to increase productivity and analysis quality, simplify handling complex workflows, ensure reproducibility research, facilitate reuse existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by Drug Disease Model Resources (DDMoRe) consortium, is intended become an standard providing means encode models, trial designs,...
One of the major bottlenecks in building systems biology models is identification and estimation model parameters for calibration. Searching from published literature an essential, yet laborious task.We have developed a new service, BioModels Parameters, to facilitate search retrieval parameter values Systems Biology Markup Language stored BioModels. Modellers can now directly entity (e.g. protein or drug) retrieve rate equations describing it; associated degradation rate, production Kcat,...
Abstract The amount of omics data in the public domain is increasing every year [1, 2]. Public availability datasets growing all disciplines, because it considered to be a good scientific practice (e.g. enable reproducibility), and/or mandated by funding agencies, journals, etc. Science now intensive discipline and therefore, new innovative ways for management, sharing, discovering novel are increasingly required [3, 4]. However, as volumes grow, quantifying its impact becomes more...
Abstract The reproducibility crisis has emerged as an important concern across many fields of science including life science, since published results failed to reproduce. Systems biology modelling, which involves mathematical representation biological processes study complex system behaviour, was expected be least affected by this crisis. While lack experimental and computational analysis could a repercussion several compounded factors, it not fully understood why systems models with...
Background: With the ever increasing use of computational models in biosciences, need to share and reproduce results published studies efficiently easily is becoming more important. To this end, various standards have been proposed that can be used describe models, simulations, data or other essential information a consistent fashion. These constitute separate components required given scientific result. Results: We Open Modeling EXchange format (OMEX). Together with standard formats from...