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The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans).
de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the German community with this sharing space for their projects in the FAIRDOMHub, and provides other SEEK ecosystem related software development and services.
Web page: http://www.denbi.de
Funding details:BMBF: The Federal Ministry of Education and Research / Germany
Related items
- People (52)
- Projects (5)
- Institutions (13)
- Investigations (2+4)
- Studies (3+2)
- Assays (2+3)
- Data files (19+8)
- Models (2+6)
- SOPs (1)
- Publications (13)
- Presentations (16+15)
- Events (5+2)
I am a computer scientist by training with a specialisation on database and information systems. Since December 2018 I am professor of Medical Informatics at the University Medicine in Greifswald, Germany, at the Institute of Community Medicine. My lab focuses on research data management in biomedicine, data integration across health care providers, and provenance of clinical research data items within clinical information systems. Furthermore, I am actively involved in COMBINE standardisation
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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 Infrastructures
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Expertise: Biochemistry, Databases, Data Management, curation
Projects: Kinetics on the move - Workshop 2016
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Expertise: computational structural biology
Tools: Molecular Dynamics, Data Management, Databases, Data Science, web development, Ruby on Rails, Python
Research associate at HITS, software developer
Projects: SYSTERACT, Kinetics on the move - Workshop 2016, BESTER, iRhythmics, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis
Institutions: University of Rostock

Roles: Postdoc
Expertise: genome-scale modeling, metabolic systems biology, Kinetic modelling, metabolic networks
Tools: Matlab, Data integration, Cytoscape, Copasi, COBRA toolbox, R
Projects: Kinetics on the move - Workshop 2016, CausalDB, COMBINE Multicellular Modelling, Colosys, NTNU Health Druglogics
Institutions: Kinetics on the move Workshop at HITS, Norwegian University of Science and Technology

Expertise: Bioinformatics, Systems Biology, SBGN standard
Projects: SysMetEx, Kinetics on the move - Workshop 2016
Institutions: Università della Svizzera Italiana
Expertise: ODE modelling of biological interaction network, Bioinformatics
Tools: Python, c++, Java, bash, standard bioinformatic tools
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
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology

Expertise: semantics, data modelling, curation, ontology, Transcriptomics, Data Management, Bioinformatics, Molecular Biology, Genetics
Tools: RightField, Protege, seek, BioMart, Chip-chip, Databases, Cell and tissue culture
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
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Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, Kinetics on the move - Workshop 2016
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Expertise: Databases, Software Engineering, Data Management
Tools: Ruby on Rails, MySQL, HTML, Ruby, Java, Javascript
Software developer for FAIRDOM
The aim of the project is bioprospecting, isolation and characterization of novel secondary metabolites, produced by extremophilic microorganisms. The project is dedicated to a poorly investigated problem of antagonistic interactions between extremophilic microorganisms in their communities, namely, to the investigation of the ability of extremophiles to produce secondary metabolites with biocidic, cytotoxic and cytostatic activities. Working out this problem will fulfill an important applied
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Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Organisms: Not specified
The Systems Biology Service Center of de.NBI (de.NBI-SysBio) provides bioinformatics support and a standards-based data management for systems biology projects, with focus on the provenance of experimental results and on the reproducibility of modeling experiments, as well as high-quality curated biochemical data to modelers and experimentalists.
The node concentrates on two tools for the data management in life sciences research: SEEK, a catalogue for storage, registration and exchange of data
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Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Organisms: Not specified
Public showcase and collection of training material
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.denbi.de
Organisms: Not specified
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.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.h-its.org/event/kinetics-on-the-move/
ZucAt - Sucrose (from german Zucker) translocation in Arabidopsis thaliana. Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the
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Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Organisms: Arabidopsis thaliana
Snapshots: No snapshots
Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped
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Snapshots: Snapshot 8, Snapshot 9
Person responsible: Maja Rey
Snapshots: Snapshot 1
Investigation: 1 hidden item
Assays: No Assays
Person responsible: Ron Henkel
Snapshots: No snapshots
Investigation: Hands-on: Model Management in SEEK
we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll
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Person responsible: Maksim Zakhartsev
Snapshots: No snapshots
The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both
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Contributor: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Snapshots: No snapshots
Investigation: Metabolic analysis of effects of sucrose transl...
Study: Analysis of central carbon and energy metabolis...
Organisms: Arabidopsis thaliana
Models: ZucAt: multi-compartment metabolic model of gro...
SOPs: No SOPs
Data files: ZucAt: FBA constraints for dark conditions, ZucAt: FBA constraints for light conditions, ZucAt: FBA solution of the model under dark gro..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: The compound database, ZucAt: The gene database, ZucAt: The stoichiometric matrix of the model, ZucAt: The transformers database, ZucAt: the model documentation
Investigation: Hands-on: Model Management in SEEK
Study: Hands-On: Tyson1991 - Cell Cycle 6 var
Organisms: No organisms
Models: BIOMD0000000005 from BioModels Database
SOPs: No SOPs
Data files: SEDML for BIOMD0000000005
Creators: Maja Rey, Ulrike Wittig
Contributor: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Maja Rey, Ulrike Wittig
Contributor: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Ulrike Wittig, Maja Rey
Contributor: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Ulrike Wittig
Contributor: Ulrike Wittig
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Ulrike Wittig
Contributor: Ulrike Wittig
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Ulrike Wittig
Contributor: Ulrike Wittig
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.1 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for
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Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in the model under light growth conditions. In this solution, (i) the photorespiration was set to 0; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set of 0.1 of flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is under-produced in plastid and therefore is additionally imported to cytoplasm. Flux through FQR represents cyclic electron flow through
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Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.5 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is over-produced in plastid and a surplus is exported to cytoplasm. Flux through FQR
...
Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and ATP transport between plastid and cytoplasm has been set to 0. The last constraint allows finding the ratio between fluxes through FQR (ferredoxin-plastoquinone reductase) and FRN (ferredoxin-NADP oxidoreductase) under which the ATP balance in plastid becomes self-sufficient
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Creator: Maksim Zakhartsev
Contributor: Maksim Zakhartsev
This is BIOMD0000000005.
Creators: Ron Henkel, Dagmar Waltemath
Contributor: Ron Henkel
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: Hands-on: Model Management in SEEK
Studies: Hands-On: Tyson1991 - Cell Cycle 6 var
Modelling analyses: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var
The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that
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Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Contributor: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl...
Studies: Analysis of central carbon and energy metabolis...
Modelling analyses: Flux Balance Analysis of multi-compartment meta...
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
Abstract (Expand)
Author: Pritchard L.,Kell D. B.
Date Published: No date defined
Journal: Eur J Biochem
PubMed ID: 12180966
Citation: Eur J Biochem. 2002 Aug;269(16):3894-904.
Abstract (Expand)
Authors: Ulrike Wittig, Maja Rey, Renate Kania, Wolfgang Müller, Weidemann A.
Date Published: No date defined
Journal: Nucleic Acids Res
PubMed ID: 29092055
Citation: Nucleic Acids Res. 2018 Jan 4;46(D1):D656-D660. doi: 10.1093/nar/gkx1065.
Abstract:
Author: Schmoldt A.,Benthe H. F.,Haberland G.
Date Published: 1st Sep 1975
Journal: Biochem Pharmacol
PubMed ID: 10
Citation: Biochem Pharmacol. 1975 Sep 1;24(17):1639-41.
Abstract (Expand)
Authors: Katy Wolstencroft, Stuart Owen, Wolfgang Müller, Finn Bacall, Jacky Snoep, Quyen Nguyen, Olga Krebs, Carole Goble, Horridge Matthew,du Preez Franco
Date Published: 2012
Journal: Knowledge Engineering and Knowledge Management
DOI: 10.1007/978-3-642-33876-2_42
Citation: Lecture Notes in Computer Science 7603 : 438
Abstract:
Authors: Wolfgang Müller, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig, Bittkowski Meik
Date Published: 1st Mar 2017
Journal: Datenbank Spektrum
DOI: 10.1007/s13222-016-0243-4
Citation: Datenbank Spektrum 17(1) : 21
Abstract (Expand)
Authors: Maksim Zakhartsev, Irina Medvedeva, Yuriy Orlov, Ilya Akberdin, Olga Krebs, Waltraud Schulze
Date Published: 1st Dec 2016
Journal: BMC Plant Biol
DOI: 10.1186/s12870-016-0868-3
Citation: BMC Plant Biol 16(1) : e00669
Abstract (Expand)
Author: Matthias König
Date Published: 2016
Journal: F1000Res
DOI: 10.12688/f1000research.9211.1
Citation: F1000Res 5 : 1736
Abstract:
Author: Crouch Thomas H.,Klee Claude B.
Date Published: 1st Aug 1980
Journal: Biochemistry
DOI: 10.1021/bi00557a009
Citation: Biochemistry 19(16) : 3692
Abstract:
Authors: Antoine Buetti-Dinh, Dethlefsen Olga,Friedman Ran,Dopson Mark
Date Published: 26th May 2016
Journal: Not specified
DOI: 10.1099/mic.0.000314
Citation: Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes
Abstract (Expand)
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.
During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/SEEK is
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Start Date: 24th Apr 2018
End Date: 26th Apr 2018
Event Website: http://denbi-modsim.de/workshop_2018
Country: DE
City: 39106 Magdeburg
Start Date: 6th Aug 2017
End Date: 6th Aug 2017
Event Website: http://co.mbine.org/events/tutorial2017
Country: US
City: Blacksburg, Virginia
Participants will learn how to structure and share complex data in a Findable, Accessible, Interoperable and Reusable (FAIR) manner. Hands-on sessions, lectures and software demonstrations will provide attendees with the necessary skills to apply components of the FAIRDOM infrastructure in their daily work for interrelating and exchanging data, models and corresponding information.
FAIRDOM is a research infrastructure offering data management support. The SEEK software is designed as registry and
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Country: DE
City: Bremen
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
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Country: CZ
City: Brno
Target audience: Wet-lab scientists and people dealing with experimental and/or clinical data for research
Topics include:
- Best practice data structuring (spreadsheets) for experimental and (clinical) samples data
- Comprehensive and unambiguous data description and annotation
- Standard formats and terminologies for data and metadata
- Guidelines for reporting data (Minimum information standards)
- Annotation tools (e.g. RightField: http://www.rightfield.org.uk)
- Using SEEK &
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Start Date: 22nd Nov 2017
End Date: 23rd Nov 2017
Event Website: Not specified
Country: DE
City: Hünfeld