A5046119695- Scientific Computing and Data Management
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Bioinformatics, and Biomedical Research
- Cardiac electrophysiology and arrhythmias
- Biofuel production and bioconversion
- Analog and Mixed-Signal Circuit Design
- Simulation Techniques and Applications
- Slime Mold and Myxomycetes Research
- Microfluidic and Capillary Electrophoresis Applications
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Biomedical and Chemical Research
- Enzyme Catalysis and Immobilization
- Neuroscience and Neural Engineering
- Distributed and Parallel Computing Systems
- Receptor Mechanisms and Signaling
- Cell Image Analysis Techniques
- Graph Theory and Algorithms
- Biomedical Text Mining and Ontologies
- Model-Driven Software Engineering Techniques
- Metabolomics and Mass Spectrometry Studies
University of Rostock
2013-2023
Czech Academy of Sciences, Institute of Computer Science
2016
Stellenbosch University
2013
Institute for Advanced Study
2013
Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.We organized the 2015 Whole-Cell Modeling Summer School teach WC evaluate need new standards software by recoding recently published model in Systems Biology Markup Language.Our analysis revealed several challenges representing using current standards.We, therefore, propose standards, software,...
Computational modeling of cardiac cellular electrophysiology has a long history, and many models are now available for different species, cell types, experimental preparations. This success brings with it challenge: how do we assess compare the underlying hypotheses emergent behaviors so that can choose model as suitable basis new study or to characterize particular behaves in scenarios? We have created an online resource characterization comparison electrophysiological wide range scenarios....
Abstract Motivation: Repositories support the reuse of models and ensure transparency about results in publications linked to those models. With thousands available repositories, such as BioModels database or Physiome Model Repository, a framework track differences between their versions is essential compare combine Difference detection not only allows users study history but also helps errors inconsistencies. Existing repositories lack algorithms model’s development over time. Results:...
Abstract Motivation: Only models that are accessible to researchers can be reused. As computational evolve over time, a number of different but related versions model exist. Consequently, tools required manage not only well-curated also their associated versions. Results: In this work, we discuss conceptual requirements for version control. Focusing on XML formats such as Systems Biology Markup Language and CellML, present methods the identification explanation differences justification...
Metabolic heterogeneity is a hallmark of cancer and can distinguish normal phenotype from phenotype. In the systems biology domain, context-specific models facilitate extracting physiologically relevant information high-quality data. Here, to utilize metabolic patterns discover biomarkers all cancers, we benchmarked thousands using well-established algorithms for integration omics data into generic human model Recon3D. By analyzing active reactions capable carrying flux their magnitude...
Open model repositories provide ready-to-reuse computational models of biological systems. Models within those evolve over time, leading to different versions. Taken together, the underlying changes reflect a model's provenance and thus can give valuable insights into studied biology. Currently, however, cannot be semantically interpreted. To improve this situation, we developed an ontology terms describing in models. The used by scientists software characterise updates at level single...
<ns4:p>COMBINE archives are standardised containers for data files related to a simulation study in computational biology. This manuscript describes fully featured archive of previously published study, including (i) the original publication, (ii) model, (iii) analyses, and (iv) metadata describing their origin. With archived at hand, it is possible reproduce results work. The can be used both, educational research purposes. Anyone may reuse, extend update make valuable resource scientific...
Sharing in silico experiments is essential for the advance of research computational biology. Consequently, COMBINE archive was designed as a digital container format. It eases management files related to modelling result, fosters collaboration, and ultimately enables exchange reproducible simulation studies. However, manual handling archives tedious error prone. We therefore developed CombineArchiveWeb application support scientists promoting publishing their by means creating, exploring,...
The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, an online application creating, editing, simulating and validating documents. Tools implement all current specifications and, thus, support complex modifications co-simulation models in SBML CellML formats. Ultimately, lower bar on working with documents help users create valid...
Abstract Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing interoperability reusability such as well integration data needed model parameterization validation. Encoded machine-readable links knowledge resource terms, semantic annotations describe or meaning what represent. These help find repurpose models, accelerate composition, enable across repositories...
Abstract Genome-scale metabolic models (GEMs) are extensively used to simulate cell metabolism and predict phenotypes. GEMs can also be tailored generate context-specific GEMs, using omics data integration approaches. To date, many approaches have been developed, however, each with specific pros cons; none of these algorithms systematically outperforms the others. The key successful implementation such lies in optimal selection parameters, thresholding is a crucial component this process....
The COMBINE archive is a digital container format for files related to virtual experiment in computational biology. It eases the management of numerous simulation study, fosters collaboration, and ultimately enables exchange reproducible research results. CombineArchive Toolkit software creating, exploring, modifying, sharing archives. Open model repositories such as BioModels Database are valuable resource models associated descriptions. However, so far no tool exists export archives given...
Repositories, such as the BioModels Database and Physiome Model Repository support reuse of models ensure transparency about results in publications linked to those models. With thousands available, a framework track differences between their versions is essential compare combine Difference detection allows users study history but also helps errors inconsistencies. However, current repositories lack suitable methods model’s development over time. Consequently, researchers have problems grasp...
Computational modelling of cardiac cellular electrophysiology has a long history, with many models now available for different species, cell types, and experimental preparations. This success brings it challenge: how do we assess compare the underlying hypotheses emergent behaviours, in order to choose model as suitable basis new study, or characterize particular behaves scenarios? We have created an online resource characterization comparison electrophysiological under wide range scenarios....
Sharing in silico experiments is essential for the advance of research computational biology. Consequently, COMBINE archive was designed as a digital container format. It eases management files related to modelling result, fosters collaboration, and ultimately enables exchange reproducible simulation studies. However, manual handling archives tedious error prone. We therefore developed CombineArchiveWeb application support scientists promoting publishing their by means creating, exploring,...
A useful model is one that being (re)used. The development of a successful does not finish with its publication. During reuse, models are modified, i.e. expanded, corrected, and refined. Even small changes in the encoding can, however, significantly affect interpretation. Our motivation for present study to identify make them transparent traceable.We analysed 13734 from BioModels Database Physiome Model Repository. For each model, we studied frequencies types updates between first latest...
Motivation: Open model repositories provide ready-to-reuse computational models of biological systems. Models within those evolve over time, leading to many alternative and subsequent versions. Taken together, the underlying changes reflect a model’s provenance thus can give valuable insights into studied biology. Currently, however, cannot be semantically interpreted. To improve this situation, we developed an ontology terms describing in biology models. The used by scientists software...
Sharing in silico experiments is essential for the advance of research computational biology. Consequently, COMBINE archive was designed as a digital container format. It eases management numerous files, fosters collaboration, and ultimately enables exchange reproducible results. However, manual handling archives tedious error prone. We therefore developed CombineArchive Toolkit. supports scientists promoting publishing their work by means creating, exploring, modifying, sharing archives.
The COMBINE archive is a digital container format for files related to virtual experiment in computational biology. It eases the management of numerous simulation study, fosters collaboration, and ultimately enables exchange reproducible research results. CombineArchive Toolkit software creating, exploring, modifying, sharing archives. Open model repositories such as BioModels Database are valuable resource models associated descriptions. However, so far no tool exists export archives given...
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...