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 (83)
- Projects (8)
- Institutions (22)
- Investigations (3+20)
- Studies (5+25)
- Assays (6+24)
- Data files (22+43)
- Models (5+17)
- SOPs (1+5)
- Publications (14)
- Presentations (28+18)
- Events (8+2)
- Documents (0+16)
- Samples (1+11)
Projects: ZucAt, Modelling COVID-19 epidemics
Institutions: Institute of Cytology and Genetics, Novosibirsk State University
Expertise: Systems Biology, molecular genetic systems, gene networks, gene expression, Modeling
Tools: Java, Vaadin, Kinetic Modeling
I am staff scientist in the lab of molecular-genetic systems at the Department of Systems Biology, Institute of Cytology and Genetics SB RAS and Postdoc Research Fellow at San Diego State University. My research focus is dynamical modeling of gene network functioining.
Projects: MIX-UP
Institutions: RWTH Aachen University - Department ABBt, iAMB

Projects: MIX-UP
Institutions: University College Dublin
Projects: Kinetics on the move - Workshop 2016
Institutions: Kinetics on the move Workshop at HITS
Projects: ExtremoPharm
Institutions: Winogradsky Institute of Microbiology, Federal Research Center “Biotechnology", Russian Academy of Sciences
I am a Deputy Director of Vinogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia and the head of the laboratory in this Institute. I ams working in the field of diversity, ecology and metabolism of thermophilic prokaryotes. Together with colleagues we've described many new taxa of thermophilic prokaryotes including those of high level (families, orders, levels). I m especially interested in isolation and description of thermophilic prokaryotes with unusual types of ...
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: Working Group Nicole Radde
Institutions: University of Stuttgart
Projects: Working Group Nicole Radde
Institutions: University of Stuttgart
Projects: Working Group Nicole Radde
Institutions: University of Stuttgart
Projects: MPIEvolBio-SciComp
Institutions: Max Planck Institute for Evolutionary Biology

I'm heading the Scientific Computing Unit at Max Planck Institute for Evolutionary Biology in Plön, Germany. My interest is the application of high performance and high throughput computing in data processing, data analysis, and numerical simulations of dynamical processes. I have a background in Theoretical Physics with a Ph.D. from Rostock University (2008), where I studied analytical models and numerical simulations of extremely dense and hot matter.
After a postdoc at the Lawrence Livermore ...
Projects: Working Group Nicole Radde
Institutions: University of Stuttgart
Projects: FAIRDOM, Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, MS_DILI, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, ModeleXchange initiative
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Data management and standardization expert for systems biology and systems medicine, responsible for the data management user requirements and user contacts within the German LiSyM network (Liver Systems Medicine: http://lisym.org/) and associated to the FAIRDOM team. Involved in different standardization initiatives and committees, i.e. COMBINE (http://co.mbine.org), ISO/TC 276 Biotechnology (https://www.iso.org/committee/4514241.html), European COST action CHARME (http://www.cost-charme.eu) and ...
The group around Nicole Radde specializes in the modeling, analysis, and simulation of biochemical systems. This especially includes parameter optimization and identification.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: https://www.ist.uni-stuttgart.de/research/group-of-nicole-radde/
Start date: 11th Feb 2020
Organisms: Mus musculus
The main idea of MIX-UP (MIXed plastics biodegradation and UPcycling using microbial communities) is to showcase a novel approach for plastic recycling and therefore addresses one of the greatest challenges of our time: the establishment of a circular (bio)-economy for plastics. The continuing demand for plastic products, the lack of appropriate recycling and the ubiquitous pollution of the environment with plastic waste pose a global challenge. An ambitious vision and considerable efforts are ...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: https://www.mix-up.eu/
Organisms: Not specified
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Organisms: Not specified
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 ...
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 ...
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 ...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Organisms: Arabidopsis thaliana
Country: Germany
City: Aachen
Web page: https://www.avt.rwth-aachen.de/cms/AVT/Forschung/~inzz/Fluidverfahrenstechnik/
Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex cellular pathways and ...
Submitter: Olga Krebs
Studies: Experimental study for hands on session
Assays: How to use templates to structure experimental data, How to use templates to structure experimental data 222
Snapshots: Snapshot 1, Snapshot 2
Submitter: Ron Henkel
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 ...
Submitter: Maksim Zakhartsev
Studies: Analysis of central carbon and energy metabolisms of growing Arabidopsis...
Assays: Flux Balance Analysis of multi-compartment metabolic model of growing Ar...
Snapshots: Snapshot 8, Snapshot 9
Experimental study for hands on session
Submitter: Olga Krebs
Investigation: Using SEEK and I-S-A structure to integrate ex...
Assays: How to use templates to structure experimental data, How to use templates to structure experimental data 222
Snapshots: No snapshots
Submitter: Vincent Wagner
Investigation: 1 hidden item
Assays: SiCaSMA: An alternative stochastic description viaconcatenation of Marko...
Snapshots: No snapshots
Motivated by an increasing population and the desire to grow plants more efficiently, attention has turned to the use of Light Emitting Diodes (LEDs) to illuminate plants which are grown indoors. Indoor growing facilities enable closely controlled and mon- itored environmental conditions. More and more of these facilities exchange High Pressure Sodium (HPS) lamps for LED lighting since they provide more efficient lighting and the possibility to control light intensity and quality in order to ...
Submitter: Felix Steimle
Investigation: 1 hidden item
Assays: Biofeedback Control for Optimizing Light Intensity on Plants Based on Ca...
Snapshots: No snapshots
Submitter: Ron Henkel
Investigation: Hands-on: Model Management in SEEK
Snapshots: No snapshots
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 ...
Submitter: Maksim Zakhartsev
Investigation: Metabolic analysis of effects of sucrose transl...
Assays: Flux Balance Analysis of multi-compartment metabolic model of growing Ar...
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 ...
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Investigation: Metabolic analysis of effects of sucrose transl...
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
Snapshots: No snapshots
Submitter: Ron Henkel
Biological problem addressed: Cell Cycle
Investigation: Hands-on: Model Management in SEEK
Organisms: No organisms
Models: BIOMD0000000005 from BioModels Database
SOPs: No SOPs
Data files: SEDML for BIOMD0000000005
Snapshots: No snapshots
Here we will use JERM templates with embedded ontologies to describe and annotate example data
Submitter: Olga Krebs
Assay type: Interactomics
Technology type: Technology Type
Investigation: Using SEEK and I-S-A structure to integrate ex...
Organisms: No organisms
SOPs: Extraction and quantitative analysis of protein...
Data files: Master template, Transcriptomics Template (ArrayExpress Format)
Snapshots: No snapshots
Here we will use JERM templates with embedded ontologies to describe and annotate example data 222
Submitter: Olga Krebs
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Using SEEK and I-S-A structure to integrate ex...
Organisms: Bacillus subtilis : test 1 (insertion xyl / wild-type) (chemostat)
SOPs: Extraction and quantitative analysis of protein...
Data files: 0804_shake-flask-sigB-starvation
Snapshots: No snapshots
Motivated by an increasing population and the desire to grow plants more efficiently, attention has turned to the use of Light Emitting Diodes (LEDs) to illuminate plants which are grown indoors. Indoor growing facilities enable closely controlled and mon- itored environmental conditions. More and more of these facilities exchange High Pressure Sodium (HPS) lamps for LED lighting since they provide more efficient lighting and the possibility to control light intensity and quality in order to ...
Submitter: Felix Steimle
Assay type: Experimental Assay Type
Technology type: Chlorophyll Fluorescence Analysis
Investigation: 1 hidden item
Organisms: No organisms
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Submitter: Vincent Wagner
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Organisms: No organisms
Models: SiCaSMA: An alternative stochastic description ...
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Creator: Birger Wolter
Submitter: Birger Wolter
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Master template for hands on session
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: Using SEEK and I-S-A structure to integrate ex...
Creator: Ulrike Wittig
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Maja Rey, Ulrike Wittig
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Maja Rey, Ulrike Wittig
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Ulrike Wittig, Maja Rey
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Ulrike Wittig
Submitter: Ulrike Wittig
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Ulrike Wittig
Submitter: Ulrike Wittig
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Ulrike Wittig
Submitter: 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 ...
Creator: Maksim Zakhartsev
Submitter: 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 ...
Creator: Maksim Zakhartsev
Submitter: 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
Submitter: 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 ...
Creator: Maksim Zakhartsev
Submitter: 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 cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set to 0. Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for carbon fixation, therefore plastid imports ATP from cytoplasm.
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The solution of Flux Balance Analysis (FBA) represent metabolic flux distribution in the model under dark growth conditions (i.e. constraints)
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Flux Balance Analysis (FBA) constraints for light conditions
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Flux Balance Analysis (FBA) constraints for dark conditions
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The database in ASCII format includes information on compounds and metabolites (trivial name, elemental composition, charge, external database referece, etc) used in the model
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The database in ASCII format includes information on gene (gene models in ATG format, gene definition, catalyzed reactions in the model, external database refeneces, locus information, etc) used in the model
Creators: Maksim Zakhartsev, Irina Medvedeva
Submitter: Maksim Zakhartsev
The database in ASCII format includes information on transformers [reactions, transport steps, polymerizations] (model's identifier, trivial name, EC number, stoichiometric equation, external database referece, activators, belonging to a pathway, etc) used in the model
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
The Folder contains:
- The MCMC and simulation results, as well as the synthetic data of the Chemical Reaction Network model (DoubleDecayIndep)
- The MCMC and simulation results, as well as the synthetic data of the Lotka-Volterra model (LotkaVolterraJoint)
Together with an executable ipynb script (Exe.ipynb) and the MCMC plotting and execution functions (MCMCFunctions.py).
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: 1 hidden item
Studies: 1 hidden item
Assays: 1 hidden item
Creator: Vincent Wagner
Submitter: Vincent Wagner
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: 1 hidden item
This is BIOMD0000000005.
Creators: Ron Henkel, Dagmar Waltemath
Submitter: Ron Henkel
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: Hands-on: Model Management in SEEK
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 ...
Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Submitter: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Metabolic analysis of effects of sucrose transl... and 1 hidden item
Studies: Analysis of central carbon and energy metabolis... and 1 hidden item
Assays: Flux Balance Analysis of multi-compartment meta... and 1 hidden item
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
Submitter: Deleted submitter
Abstract (Expand)
Authors: Gina Welsing, Birger Wolter, Henric M.T. Hintzen, Till Tiso, Lars M. Blank
Date Published: 2021
Publication Type: Book
DOI: 10.1016/bs.mie.2020.12.025
Citation: Methods in Enzymology,Elsevier
Abstract (Expand)
Authors: U. Wittig, M. Rey, A. Weidemann, R. Kania, W. Muller
Date Published: 4th Jan 2018
Publication Type: Journal
PubMed ID: 29092055
Citation: Nucleic Acids Res. 2018 Jan 4;46(D1):D656-D660. doi: 10.1093/nar/gkx1065.
Abstract
Authors: Wolfgang Müller, Meik Bittkowski, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig
Date Published: 1st Mar 2017
Publication Type: Journal
DOI: 10.1007/s13222-016-0243-4
Citation: Datenbank Spektrum 17(1):21-28
Abstract (Expand)
Authors: Maksim Zakhartsev, Irina Medvedeva, Yury Orlov, Ilya Akberdin, Olga Krebs, Waltraud X. Schulze
Date Published: 1st Dec 2016
Publication Type: Journal
DOI: 10.1186/s12870-016-0868-3
Citation: BMC Plant Biol 16(1),262
Abstract
Authors: Antoine Buetti-Dinh, Olga Dethlefsen, Ran Friedman, Mark Dopson
Date Published: 26th May 2016
Publication Type: 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)
Authors: Y. Hirose, H. Kaida, A. Kawahara, S. Matono, T. Tanaka, S. Kurata, M. Kage, M. Ishibashi, T. Abe
Date Published: 25th May 2016
Publication Type: Not specified
PubMed ID: 27218430
Citation: Nucl Med Commun. 2016 May 23.
Abstract (Expand)
Author: Matthias König
Date Published: 2016
Publication Type: Not specified
DOI: 10.12688/f1000research.9211.1
Citation: F1000Res 5 : 1736
Abstract (Expand)
Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Mueller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble
Date Published: 2012
Publication Type: Journal
DOI: 10.1007/978-3-642-33876-2_42
Citation: Knowledge Engineering and Knowledge Management 7603:438-441,Springer Berlin Heidelberg
Abstract (Expand)
Authors: Maria Piques, Waltraud X Schulze, Melanie Höhne, Björn Usadel, Yves Gibon, Johann Rohwer, Mark Stitt
Date Published: 13th Oct 2009
Publication Type: Not specified
DOI: 10.1038/msb.2009.68
Citation: Mol Syst Biol 5
Abstract (Expand)
Authors: M. I. Stefan, S. J. Edelstein, N. Le Novere
Date Published: 31st Jul 2008
Publication Type: Not specified
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.
Abstract (Expand)
Authors: L. Pritchard, D. B. Kell
Date Published: 16th Aug 2002
Publication Type: Journal
PubMed ID: 12180966
Citation: Eur J Biochem. 2002 Aug;269(16):3894-904. doi: 10.1046/j.1432-1033.2002.03055.x.
Abstract (Expand)
Author: J. J. Tyson
Date Published: 15th Aug 1991
Publication Type: Not specified
PubMed ID: 1831270
Citation: Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7328-32.
Abstract
Authors: Thomas H. Crouch, Claude B. Klee
Date Published: 1st Aug 1980
Publication Type: Not specified
DOI: 10.1021/bi00557a009
Citation: Biochemistry 19(16) : 3692
Abstract
Authors: A. Schmoldt, H. F. Benthe, G. Haberland
Date Published: 1st Sep 1975
Publication Type: Journal
PubMed ID: 10
Citation: Biochem Pharmacol. 1975 Sep 1;24(17):1639-41.
The openbis tutorial covering all tasks and instructions.
Creators: Carsten Fortmann-Grote, Caterina Barillari (ETH Zuerich SIS)
Submitter: Carsten Fortmann-Grote
This presentation accompagnies the openbis hands-on tutorial.
Creator: Caterina Barillari (ETH Zuerich SIS)
Submitter: Carsten Fortmann-Grote
Creator: Caterina Barillari (ETH Zuerich SIS)
Submitter: Carsten Fortmann-Grote
The workshop gave an in-depth introduction to data management with SEEK and openBIS, two leading open-source data management solutions. Plenary talks including use cases by "power users" of SEEK and openBIS were complemented by hands-on sessions led by professional data management trainers.
Program Day 1 of the workshop is devoted to the data sharing and dissemination platform SEEK. Day 2 will cover the integrated data management solution openBIS, featuring an Electronic Lab Notebook, Laboratory ...
Start Date: 17th May 2021
End Date: 18th May 2021
Event Website: https://workshops.evolbio.mpg.de/event/42/
Country: Germany
City: Ploen
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 kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is ...
Start Date: 18th Mar 2019
End Date: 20th Mar 2019
Event Website: http://copasi.org/denbi-modsim/workshop_2019/
Country: Germany
City: 69120 Heidelberg
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 ...
Country: Czech Republic
City: Brno
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 ...
Country: Germany
City: Bremen
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 ...
Start Date: 24th Apr 2018
End Date: 26th Apr 2018
Event Website: http://denbi-modsim.de/workshop_2018
Country: Germany
City: 39106 Magdeburg
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 & FAIRDOMhub ...
Start Date: 22nd Nov 2017
End Date: 23rd Nov 2017
Event Website: Not specified
Country: Germany
City: Hünfeld
Start Date: 6th Aug 2017
End Date: 6th Aug 2017
Event Website: http://co.mbine.org/events/tutorial2017
Country: United States
City: Blacksburg, Virginia
Here we collect all the presentations, hands on instructions and documentation for Kinetics on the move Workshop on Data for Computational Modeling
Start Date: 30th May 2016
End Date: 31st May 2016
Event Website: http://www.h-its.org/de/research/sdbv/veranstaltungen/kinetics-on-the-move-practical-workshop-on-data-for-computational-modelling/
Country: Not specified
City: Heidelberg