ISBE-Light provides M4 service (Make Me My Mode) where non modelers can request (assistance with) the making of a computational model of their biological system.
These models are deposited here.
Web page: http://www.isbe.nlFunding details:
- People (11)
- Projects (14)
- Institutions (9)
- Investigations (0+1)
- Studies (0+2)
- Assays (0+3)
- Data files (1+6)
- Models (1+11)
- Presentations (4+2)
- Events (1+4)
- Documents (0+6)
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, NAD COMPARTMENTATIONhttps://orcid.org/0000-0003-3540-0402
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project
Projects: SulfoSys, FAIRDOM user meeting, Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript
Roles: Project Coordinator
Executive director of ISBE.NL
Institutions: Universitat Rovira i Virgili
I am research scholar in the Department of Chemical Engineering at the University of Rovira i Virgili, Spain, member of the ENVIRONMENTAL ANALYSIS AND MANAGEMENT (AGA) group and also part of TECNATOX a specialized research center in the area of Technology Transfer in Toxicology, Food and Environmental Health.
MY RESEARCH INTERESTS:
Knowledge Engineering and System modelling in environmental domain.
Uncertainty Modelling (Stochastic, Fuzzy and hybrid system)
Integrated Modelling and decision
Expertise: yeast, fungi, Metabolomics, Proteomics, Stoichiometric modelling, carbon metabolism, Systems Biology, dynamics and control of biological networks, coupling metabolome and environome, rapid sampling experiments, Biochemistry
Tools: parameter estimation, ODE, HPLC, GC and LC/MS analysis of metabolites, Mass spectrometry (LC-MS/MS), continuous cultivation, Enzyme assay, Material balance based modeling, stimulus response experiments, Chromatography, Fermentation, Matlab, Metabolomics, Biochemistry and protein analysis
I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to
Institutions: geneXplain GmbHhttps://orcid.org/0000-0001-6775-2467
Alexander Kel received his Ph.D. in Bioinformatics, Molecular Biology and Genetics in 1990. He studied biology and mathematics at Novosibirsk State University and obtained his M.S. in biology with special focus on mathematical biology in 1985. He worked for 15 years at the Institute of Cytology and Genetics, Russia (ICG) holding positions as a programmer, scientist, senior scientist and Vice-Head of the Laboratory of Theoretical Molecular Genetics. In 1995, he won the Academician Belaev Award.
Pesticides, plastics, cosmetics, electrical transformers and many other products contain Endocrine disruptors (EDCs). EDCs interfere with natural hormone functions and may cause the disease.
Creator: Alexey Kolodkin
Contributor: Alexey Kolodkin
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: JWS Online
Organism: Homo sapiens
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The 10th Young Scientists School “Systems biology and Bioinformatics” SBB-2018 will be held on 27–31th of August 2018 in Novosibirsk, Russia
Bioinformatics is a rapidly developing field of knowledge. Each of the past Young Scientists Schools concerned topics urgent at those times. To preserve this tradition, the SBB-2016 will be dedicated to bioinformatics and systems biology in such areas as:
Genomics and evolutionary bioinformatics
Structural biology and molecular dynamics