Kinetics on the move - Workshop 2016

Overview

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)

SEEK ID: https://fairdomhub.org/projects/49

Public web page: http://www.h-its.org/event/kinetics-on-the-move/

Organisms: Bacillus subtilis, Acidithiobacillus caldus, Arabidopsis thaliana

FAIRDOM PALs: No PALs for this Project

Project created: 19th May 2016

Related items

Dewidar Bedair

Projects: Kinetics on the move - Workshop 2016

Institutions: Kinetics on the move Workshop at HITS

Antoine Buetti-Dinh palproject_administratorasset_housekeeperasset_gatekeeper

Projects: SysMetEx, Kinetics on the move - Workshop 2016

Institutions: Università della Svizzera Italiana

Anton Chechushkov

Projects: Kinetics on the move - Workshop 2016

Institutions: Kinetics on the move Workshop at HITS

https://orcid.org/0000-0002-0238-4533
Piotr Gawron

Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map

Institutions: Kinetics on the move Workshop at HITS, Luxembourg Centre for Systems Biomedicine (LCSB)

Martin Golebiewski project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

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)

https://orcid.org/0000-0002-8683-7084
Ekaterina Grafskaia

Projects: Kinetics on the move - Workshop 2016

Institutions: Novosibirsk State University

https://orcid.org/0000-0001-8957-6142
Antonio Guerreiro

Projects: Kinetics on the move - Workshop 2016

Institutions: Kinetics on the move Workshop at HITS

Ron Henkel

Projects: de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Rostock

Dragos Horvath

Projects: Kinetics on the move - Workshop 2016

Institutions: Kinetics on the move Workshop at HITS

Renate Kania

Projects: SysMO-LAB, de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Michael Kohl

Projects: Kinetics on the move - Workshop 2016

Institutions: Kinetics on the move Workshop at HITS

Olga Krebs adminproject_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

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 COMPARTMENTATION, HOTSOLUTE, Stress granules, FAIRDOM Community Workers, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, COVID-19 Disease Map, AquaHealth (ERA-BlueBio), LiSyM Core Infrastructure and Management (LiSyM-PD), Early Metabolic Injury (LiSyM-EMI - Pillar I), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, CC-TOP

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology, University of Rostock

https://orcid.org/0000-0003-3540-0402
Ursula Kummer

Projects: SysMO-LAB, Kinetics on the move - Workshop 2016, de.NBI-SysBio

Institutions: University of Heidelberg

Matthias König project_administratorasset_housekeeperasset_gatekeeper

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 Training

Institutions: Charité University Medicine Berlin, Humboldt-Universität zu Berlin, Humboldt University Berlin

https://orcid.org/0000-0003-1725-179X
Alan Lai

Projects: Kinetics on the move - Workshop 2016

Institutions: Kinetics on the move Workshop at HITS

https://orcid.org/0000-0003-0916-9227
Xin Lai

Projects: Kinetics on the move - Workshop 2016

Institutions: University of Erlangen-Nuernberg

https://orcid.org/0000-0003-4913-5822
Hadas Leonov

Projects: Kinetics on the move - Workshop 2016

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Wolfgang Mader

Projects: Kinetics on the move - Workshop 2016

Institutions: Kinetics on the move Workshop at HITS

Wolfgang Müller project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-4980-3512
Quyen Nguyen

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)

de.NBI Systems Biology Service Center (de.NBI-SysBio)

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 ...

Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, CEPLAS – Cluster of Excellence on Plant Sciences

Web page: http://www.denbi.de

Using SEEK and I-S-A structure to integrate experimentation and mathematical modelling
Kinetics on the move - Workshop 2016

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

Hands-on: Model Management in SEEK
Kinetics on the move - Workshop 2016
No description specified

Submitter: Ron Henkel

Studies: Hands-On: Tyson1991 - Cell Cycle 6 var

Assays: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

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Experimental study for hands on session
Kinetics on the move - Workshop 2016

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

Hands-On: Tyson1991 - Cell Cycle 6 var
Kinetics on the move - Workshop 2016
No description specified

Submitter: Ron Henkel

Investigation: Hands-on: Model Management in SEEK

Assays: BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var

1 hidden item
How to use templates to structure experimental data
Kinetics on the move - Workshop 2016

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...

Study: Experimental study for hands on session

How to use templates to structure experimental data 222
Kinetics on the move - Workshop 2016

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...

Study: Experimental study for hands on session

BIOMD0000000005 - Tyson1991 - Cell Cycle 6 var
Kinetics on the move - Workshop 2016
No description specified

Submitter: Ron Henkel

Biological problem addressed: Cell Cycle

Investigation: Hands-on: Model Management in SEEK

Study: Hands-On: Tyson1991 - Cell Cycle 6 var

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Master template
Kinetics on the move - Workshop 2016

Master template for hands on session

Creator: Olga Krebs

Submitter: Olga Krebs

Download
Workshop agenda
Kinetics on the move - Workshop 2016
No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Download
SABIO-RK documentation user interface
Kinetics on the move - Workshop 2016
No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Download
SABIO-RK documentation web services
Kinetics on the move - Workshop 2016
No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Download
6 hidden items
BIOMD0000000005 from BioModels Database
Kinetics on the move - Workshop 2016

This is BIOMD0000000005.

Creators: Ron Henkel, Dagmar Waltemath

Submitter: Ron Henkel

Download
3 hidden items
Extraction and quantitative analysis of proteins from FFPE tissue
Kinetics on the move - Workshop 2016

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

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SABIO-RK, von Daten in der Publikation zur Suchlösung für Spezialisten
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), Kinetics on the move - Workshop 2016

Abstract

Not specified

Authors: Wolfgang Müller, Meik Bittkowski, Martin Golebiewski, Renate Kania, Maja Rey, Andreas Weidemann, Ulrike Wittig

Date Published: 1st Mar 2017

Publication Type: Journal

Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes
Kinetics on the move - Workshop 2016

Abstract

Not specified

Authors: Antoine Buetti-Dinh, Olga Dethlefsen, Ran Friedman, Mark Dopson

Date Published: 26th May 2016

Publication Type: Not specified

Molecular biological correlation of fluorine-18 fluorodeoxyglucose uptake in esophageal squamous cell carcinoma
Kinetics on the move - Workshop 2016

Abstract (Expand)

OBJECTIVE: The aim of this study was to assess the relationship between fluorine-18 fluorodeoxyglucose (F-FDG) uptake and molecular biological markers in esophageal squamous cell carcinoma (ESCC) … patients. METHODS: Our patient population included 51 patients who underwent F-FDG PET/computed tomography before surgery. Excised tumor tissue was analyzed immunohistochemically using monoclonal antibodies for glucose transporter-1 (GLUT-1), GLUT-3, CD34 [microvessel density (MVD) marker], CD68 (macrophage marker), and CD163 (tumor-associated macrophage marker). The relationships among pathological factors [pathological T stage (p-T stage), pathological lymph node status (p-N status), pathological stage (p-stage), and pathological tumor length], the maximum standardized uptake value (SUVmax), and these molecular biological markers were evaluated using Spearman's rank test and the Kruskal-Wallis test. RESULTS: GLUT-1, GLUT-3, CD34, and CD163 significantly correlated with SUVmax (r=0.547, P<0.001 for GLUT-1; r=0.569, P<0.001 for GLUT-3; r=0.463, P=0.001 for CD34, r=0.455, P=0.001 for CD163), whereas SUVmax, GLUT-1, GLUT-3, CD34, and CD163 significantly correlated with p-T stage (r=0.552, P<0.001 for SUVmax, r=0.307, P=0.03 for GLUT-1, r=0.349, P=0.013 for GLUT-3, r=0.313, P=0.027 for CD34, r=0.526 for CD163, P<0.001), but not with p-N status. CD68 levels showed no significant correlation with SUVmax, p-T stage, p-stage, or p-N status. CONCLUSION: SUVmax, GLUT-1 expression, GLUT-3 expression, MVD, and TAMs show a relationship with the tumor stage and extent of ESCC. GLUT-1, GLUT-3, MVD, and TAMs are associated with the mechanism of F-FDG uptake in ESCC.

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

cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK
Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Kinetics on the move - Workshop 2016

Abstract (Expand)

Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks. One of the main resources of such information is SABIO-RK, a curated database for kinetic … data of biochemical reactions and their related information. Despite the importance for computational modelling there has been no simple solution to visualize the kinetic data from SABIO-RK. In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape. The kinetic information is accessible via a combination of graph structure and annotations of nodes, with provided information consisting of: (I) reaction details, enzyme and organism; (II) kinetic law, formula, parameters; (III) experimental conditions; (IV) publication; (V) additional annotations. cy3sabiork creates an intuitive visualization of kinetic entries in form of a species-reaction-kinetics graph, which reflects the reaction-centered approach of SABIO-RK. Kinetic entries can be imported in SBML format from either the SABIO-RK web interface or via web service queries. The app allows for easy comparison of kinetic data, visual inspection of the elements involved in the kinetic record and simple access to the annotation information of the kinetic record. I applied cy3sabiork in the computational modelling of galactose metabolism in the human liver.

Author: Matthias König

Date Published: 2016

Publication Type: Not specified

An allosteric model of calmodulin explains differential activation of PP2B and CaMKII
Kinetics on the move - Workshop 2016

Abstract (Expand)

Calmodulin plays a vital role in mediating bidirectional synaptic plasticity by activating either calcium/calmodulin-dependent protein kinase II (CaMKII) or protein phosphatase 2B (PP2B) at different … calcium concentrations. We propose an allosteric model for calmodulin activation, in which binding to calcium facilitates the transition between a low-affinity [tense (T)] and a high-affinity [relaxed (R)] state. The four calcium-binding sites are assumed to be nonidentical. The model is consistent with previously reported experimental data for calcium binding to calmodulin. It also accounts for known properties of calmodulin that have been difficult to model so far, including the activity of nonsaturated forms of calmodulin (we predict the existence of open conformations in the absence of calcium), an increase in calcium affinity once calmodulin is bound to a target, and the differential activation of CaMKII and PP2B depending on calcium concentration.

Authors: M. I. Stefan, S. J. Edelstein, N. Le Novere

Date Published: 31st Jul 2008

Publication Type: Not specified

Modeling the cell division cycle: cdc2 and cyclin interactions
Kinetics on the move - Workshop 2016

Abstract (Expand)

The proteins cdc2 and cyclin form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. A mathematical model for the interactions of cdc2 and cyclin is constructed. … Simulation and analysis of the model show that the control system can operate in three modes: as a steady state with high maturation promoting factor activity, as a spontaneous oscillator, or as an excitable switch. We associate the steady state with metaphase arrest in unfertilized eggs, the spontaneous oscillations with rapid division cycles in early embryos, and the excitable switch with growth-controlled division cycles typical of nonembryonic cells.

Author: J. J. Tyson

Date Published: 15th Aug 1991

Publication Type: Not specified

Positive cooperative binding of calcium to bovine brain calmodulin
Kinetics on the move - Workshop 2016

Abstract

Not specified

Authors: Thomas H. Crouch, Claude B. Klee

Date Published: 1st Aug 1980

Publication Type: Not specified

CMSB 2018 conference poster
Kinetics on the move - Workshop 2016
No description specified

Creator: Hadas Leonov

Submitter: Hadas Leonov

Download
SABIO-RK: Finding, curating, and publishing data
Kinetics on the move - Workshop 2016
No description specified

Creator: Ulrike Wittig

Submitter: Ulrike Wittig

Download
Data and model Management in Systems Biology
de.NBI-SysBio, Kinetics on the move - Workshop 2016

Presentation at the 10th anniversary of SABIO-RK, Heidelberg 2016

Creator: Dagmar Waltemath

Submitter: Dagmar Waltemath

External Link
Modelling calcium sensing in neurons: signals, switches and surprises
Kinetics on the move - Workshop 2016
No description specified

Creator: Melanie Stefan

Submitter: Melanie Stefan

Download
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16th International Conference on Computational Methods in Systems Biology -- CMSB 2018

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 ...

Start Date: 12th Sep 2018

End Date: 14th Sep 2018

Event Website: https://cmsb2018.fi.muni.cz/

Country:  Czech Republic

City: Brno

Kinetics on the move : Lectures, Hands On Sessions, Documents from Workshop

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

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