A5002460040- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Genetics, Bioinformatics, and Biomedical Research
- Water Systems and Optimization
- Biomedical Text Mining and Ontologies
- Advanced Neural Network Applications
- Advanced Memory and Neural Computing
- Semantic Web and Ontologies
- Genetics, Aging, and Longevity in Model Organisms
- Neural Networks and Applications
- Digital Filter Design and Implementation
- Ferroelectric and Negative Capacitance Devices
- Biochemical Acid Research Studies
- Numerical Methods and Algorithms
- Adaptive optics and wavefront sensing
- Diverse Scientific and Economic Studies
- Micro and Nano Robotics
- Social Robot Interaction and HRI
- RNA and protein synthesis mechanisms
- Topological and Geometric Data Analysis
- Social Sciences and Humanities
- Air Traffic Management and Optimization
Silicon Austria Labs (Austria)
2021-2024
Territoires
2022-2023
Centre d'Études Scientifiques et Techniques d'Aquitaine
2022-2023
Southwestern Medical Center
2023
Princeton University
2023
Instituto de Astrofísica de Canarias
2023
Centro Científico Tecnológico - Bahía Blanca
2019-2021
Babraham Institute
2013-2020
Georgia Institute of Technology
2020
European Bioinformatics Institute
2007-2019
Abstract Background Quantitative models of biochemical and cellular systems are used to answer a variety questions in the biological sciences. The number published quantitative is growing steadily thanks increasing interest use as well development improved software availability better, cheaper computer hardware. To maximise benefits this body models, field needs centralised model repositories that will encourage, facilitate promote dissemination reuse. Ideally, stored these should be...
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...
Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, well-suited for studies large While numerous groups have developed specific computational tools provide original methods analyse qualitative models, a standard format exchange models has been missing. We present Systems Biology Markup Language (SBML)...
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...
Abstract Summary: The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models biological processes in text files. In order to perform model simulations, graphical visualizations other software manipulations, an in-memory representation SBML is required. We developed JSBML this purpose. contrast prior implementations APIs, has been designed from ground up Java™ programming language, can therefore be used on all platforms...
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,...
In this contribution, we describe a multi-omics systems biology study of the metabolic changes that occur during aging in Caenorhabditis elegans. Sampling several time points from young adulthood until early old age, our covers full duration and include transcriptomics targeted MS-based metabolomics. order to focus on due age used two strains are metabolically close wild-type, yet conditionally nonreproductive. Using these data combination with whole-genome model metabolism C. elegans...
Neural Networks have significantly evolved, particularly in their application to computer vision. This paper presents a comprehensive comparison of different versions YOLOv8, such as YOLOv8n, YOLOv8s, YOLOv8m, YOLOv8l, and YOLOv8x for the detection pests bean plants, leveraging capabilities Convolutional Networks. To train neural network using identical conditions were applied, amount environment light, number labeled images, epochs, batch size. The results indicate that, complexity YOLO...
Phosphatidylinositol phosphate (PIP) lipids, located on the inner leaflet of membrane facing cytoplasm, are key regulators a wide range cellular events at plasma membrane, in some cases by interacting with partner proteins that regulate actin assembly. Supported lipid bilayers (SLBs) have been recognized as powerful model to dissect mechanisms underlying clustering and interactions PIP lipids their proteins. However, despite advances methods generate SLBs, it remains challenge robustly...
Abstract Background Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format another. However, they independently, resulting redundancy of efforts and lack synergy. Results Here we present the System Biology Format Converter (SBFC), which provide generic framework potentially any into The currently includes several converters translating following formats: SBML, BioPAX, SBGN-ML, Matlab,...
Computing accurate nucleic acid melting temperatures has become a crucial step for the efficiency and optimisation of numerous molecular biology techniques such as in situ hybridization, PCR, antigene targeting, microarrays. MELTING is free open source software which computes enthalpy, entropy temperature acids. 4.2 was able to handle several types hybridization DNA/DNA, RNA/RNA, DNA/RNA provided corrections due presence sodium. The program can use either an approximative approach or more...
Abstract Summary: JSBML, the official pure Java programming library for Systems Biology Markup Language (SBML) format, has evolved with advent of different modeling formalisms in systems biology and their ability to be exchanged represented via extensions SBML. JSBML matured into a major, active open-source project contributions from growing, international team developers who not only maintain compatibility SBML, but also drive steady improvements interface promote ease-of-use end users....
Metabolism is one of the attributes life and supplies energy building blocks to organisms. Therefore, understanding metabolism crucial for complex biological phenomena. Despite having been in focus research centuries, our picture still incomplete. Metabolomics, systematic analysis all small molecules a system, aims close this gap. In order facilitate such investigations blueprint metabolic network required. Recently, several reconstructions model organism Caenorhabditis elegans have...
Abstract Background With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, mathematical description dynamical systems has become an essential aspect research in biology. Models are often encoded formats such as SBML, whose structure is very complex difficult to evaluate due many special cases. Results This article describes efficient algorithm solve SBML models that interpreted terms ordinary differential equations. We begin our...
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats computational systems biology related fields. This report summarizes topics activities fourth edition annual COMBINE meeting, held Paris during September 16-20 2013, attended by a total 96 people. pioneered first day devoted modeling approaches biology, which attracted broad audience scientists thanks panel renowned speakers. During subsequent days,...
The increasing demand of intelligent devices on re-source constrained platforms requires neuromorphic accelerators that can compute several and complex operations while being low power energy efficient. Symmetric Simplicial have compact hardware implementations, making them promising solution to the trade-off between efficiency computational power. This paper presents DIGINEURON V2, latest System Chip (SoC) fabricated within internal research project works as a testbed for Neuromorphic Deep...
Abstract Background The need to build a tool facilitate the quick creation and editing of models encoded in Systems Biology Markup language (SBML) has been growing with number users increased complexity language. SBMLeditor tries answer this by providing very simple, low level editor SBML files. Users can create remove all necessary bits pieces controlled way, that maintains validity final file. Results is written JAVA using JCompneur, library interfaces easily display an XML document as...
Abstract Motivation: The biological pathway exchange language (BioPAX) and the systems biology markup (SBML) belong to most popular modeling data languages in biology. focus of SBML is quantitative dynamic simulation models, whereas BioPAX specification concentrates mainly on visualization qualitative analysis maps. describes reactions relations. In contrast, core exclusively processes such as reactions. With models extension (qual), it has recently also become possible describe relations...