Systems Biology studies the properties and phenotypes that emerge from the interaction of biomolecules where such properties are not obvious from those of the individual molecules. 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 eventually of whole cells and organisms are generated as tools for research. ICYSB will provide a hands-on experience in integrating experimentation and mathematical modelling with an emphasis on kinetic modelling of cellular pathways. The course focuses on yeast because the development of the emerging field of Systems Biology requires suitable model systems for data generation.
Programme: Independent Projects
Public web page: http://www.icysb.se/
Organisms: Saccharomyces cerevisiae
FAIRDOM PALs: No PALs for this Project
- People (37)
- Institutions (29)
- Investigations (1+1)
- Studies (0+3)
- Assays (4+3)
- Strains (1+6)
- Data files (3+4)
- Models (7+6)
- SOPs (6+5)
- Publications (2)
- Presentations (7+7)
- Events (1+1)
- Samples (13+40)
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Training material, FAIRDOM user meeting, ErasysApp Funders, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, EmPowerPutida
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: 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, Training material, SBEpo - Systems Biology of Erythropoietin
I am group leader of the SDBV (Scientific Databases and Visualisation) group at the HITS gGmbH, the Heidelberg Institute for Theoretical Studies.
I am interested in finding data. Starting with my master's thesis I have always worked on how to store data in a way that you can find it, and how to make sense out of data that has been stored.
Within FAIRDOM I find interesting to help people to store their data in a way that they make sense even after years.
Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Software Engineer and Architect working within the FAIRDOM team.
Leading the development of SEEK and RightField.
I hold a Medical Doctor Diploma (Lviv, Ukraine) with the specialization in General Medicine. After the graduation from the Post Graduate Program in Bioinformatics at the Seneca College/York University (Toronto, Canada), I successfully participated in the number of scientific projects conducted at the University of Toronto (Canada) and the Toronto East General Hospital (Canada).
I obtained the PhD in Bioinformatics at the Swiss Institute of Bioinformatics (Geneva, Switzerland). As a PhD student,
Software developer for FAIRDOM
Institutions: VU University Amsterdam
I am a beginning PhD student at the VU in Amsterdam and study the heterogeneity of yeast cells at near zero growth conditions. I have a versatile background in Biophysics and Systems Biology.
Simple HOG model explaining Hog1 activation data for various osmotic stresses
Contributor: Jörg Schaber
Biological problem addressed: Stress response/Adaptation
Investigation: 1 hidden item
Study: 1 hidden item
Demonstrating Assay Generation
Contributor: Natalie Stanford
Biological problem addressed: Metabolism
Investigation: Temporary Investigation - No real data should b...
Study: 1 hidden item
Contributor: Ariane Scheuren
Provider Name: Lalvin
Provider's strain ID: EC1118
Organism: Saccharomyces cerevisiae
Genotypes: deletion YFG
Phenotypes: improved fermentation rate
Comment: Saccharomyces bayanus is a yeast of the genus Saccharomyces, used in wine making and cider fermentation and to make distilled beverages.
- heatshock producing trehalose and trehalose producing chaperone
- heatshock opening channel and letting glycerol out, chaperone closing channel (inhibiting reaction)
- Hog1 and Slt2 activated by pressure difference, calculated as "external pressure - (trehalose + glycerol)"
Model started from a high osmolarity state after adaptation (glycerol is high, no active Hog1)
Contributor: Eszter Lakatos
Model type: Ordinary differential equations
Model format: Copasi
Organism: Not specified
This document idecribes guidelines for the minimum information to report about the use of n-dimensional
gel electrophoresis in a proteomics experiment, in a manner compliant with the aims
as laid out in the ‘MIAPE Principles’ document (latest version available from
Creators: ICYSB Participant, HUPO Proteomics Standards Initiative
Contributor: ICYSB Participant
Author: Schaber J.,Lapytsko A.,Flockerzi D.
Date Published: No date defined
Journal: J R Soc Interface
PubMed ID: 24307567
Citation: J R Soc Interface. 2013 Dec 4;11(91):20130971. doi: 10.1098/rsif.2013.0971. Print 2014 Feb 6.
Author: Schaber J.,Baltanas R.,Bush A.,Klipp E.,Colman-Lerner A.
Date Published: 15th Nov 2012
Journal: Mol Syst Biol
PubMed ID: 23149687
Citation: Mol Syst Biol. 2012;8:622. doi: 10.1038/msb.2012.53.
Most of the prokaryotes live in complex laminated structures – bacterial mats or biofilms. Spatial distribution of species’ representatives plays a significant role in local microbial cooperation and competition. Migration processes in populations are important evolution factor as well. Interacting with the other evolution factors, they are capable to affect allele frequencies’ dynamics throughout the populations of community. Therefore, the impact of spatial distribution of cells and substances
Creator: Alexandra Klimenko
Contributor: Alexandra Klimenko
During the course, 3 slots are planed to give to participants the possibility to present their own work. Here all the presentations are available.
Start Date: 3rd Jun 2015
End Date: 10th Jun 2015
Event Website: Not specified