The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.
SEEK ID: https://fairdomhub.org/projects/49
Public web page: http://www.h-its.org/event/kinetics-on-the-move/
FAIRDOM PALs: No PALs for this Project
Project created: 19th May 2016
- People (40)
- Institutions (8)
- Investigations (1+2)
- Studies (1+2)
- Assays (1+3)
- Data files (3+7)
- Models (1+3)
- SOPs (1)
- Publications (7)
- Presentations (4+3)
- Organisms (3)
- Events (1+2)
Projects: Kinetics on the move - Workshop 2016
Research associate at HITS, software developer
Projects: de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, FAIRDOM, EnzymeML, GMDS Project Group FAIR Data Infrastructuresorcid.org/0000-0002-9077-5664
Reproducibility of results is fundamental to all sciences. In computational biology, standard formats like Systems Biology Markup Language (SBML), CellML, or NeuroML enable the exchange of simulation models, and foster interoperability between software tools importing and exporting these formats.
My main research interest is in developing methods and tools that (1) improve the reuse of computational models in biology, (2) ensure reproducibility of modeling results and (3) that lead to easier
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 Regulationorcid.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
Software developer for FAIRDOM
Projects: Kinetics on the move - Workshop 2016, Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), FAIRDOM user meeting, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Trainingorcid.org/0000-0003-1725-179X
We are investigating liver metabolism and function with the help of computational models and methods.
Read more about the LiSyM junior group at: www.livermetabolism.com
Junior Group Leader
Dr. Matthias König
Institute for Theoretical Biology
Invalidenstraße 43, 10117 Berlin, Germany
phone +49 30 2093-8450
The liver is the central metabolic organ of our body playing a crucial role in the clearance of drugs, xenobiotics and numerous metabolites
Projects: SysMO-LAB, de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, FAIRDOM, EnzymeML
Within the de.NBI project my functions in the de.NBI-SysBio node comprise content curation, requirements elicitation, and community engagement for the users of biochemical reaction kinetics database SABIO-RK as well as of the data management platform SEEK.
This is BIOMD0000000005.
Contributor: Ron Henkel
Model type: Ordinary differential equations (ODE)
Model format: SBML
A Standard Operating Procedure (SOP) is a document consisting of step-by-step information on how to execute a task. An existing SOP may need to just be modified and updated.
Creator: Olga Krebs
Contributor: Deleted contributor
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 2 hidden items
Author: Matthias König
Date Published: 2016
Citation: F1000Res 5 : 1736
Author: Crouch Thomas H.,Klee Claude B.
Date Published: 1st Aug 1980
Citation: Biochemistry 19(16) : 3692
Authors: Antoine Buetti-Dinh, Dethlefsen Olga,Friedman Ran,Dopson Mark
Date Published: 26th May 2016
Journal: Not specified
Citation: Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes
Author: Hirose Y.,Kaida H.,Kawahara A.,Matono S.,Tanaka T.,Kurata S.,Kage M.,Ishibashi M.,Abe T.
Date Published: 25th May 2016
Journal: Nucl Med Commun
PubMed ID: 27218430
Citation: Nucl Med Commun. 2016 May 23.
Authors: Melanie Stefan, Edelstein S. J.,Le Novere N.
Date Published: 31st Jul 2008
Journal: Proc Natl Acad Sci U S A
PubMed ID: 18669651
Citation: Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10768-73. doi: 10.1073/pnas.0804672105. Epub 2008 Jul 31.
Author: Tyson J. J.
Date Published: 15th Aug 1991
Journal: Proc Natl Acad Sci U S A
PubMed ID: 1831270
Citation: Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7328-32.
Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/3702
Synonyms: thale-cress, mouse-ear cress
Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/33059
Synonyms: Thiobacillus caldus
The 16th conference on Computational Methods in Systems Biology (CMSB 2018) will take place on the 12th to 14th September 2018 in Brno, Czech Republic. Its aim is to bring together researchers from across biological, mathematical, computational, and physical sciences who are interested in the study, modelling, simulation, advanced analysis, and design of biological systems.
CMSB 2018 will be hosted at Faculty of Informatics, Masaryk University, Brno. Brno is the city where the modern genetics has