- Home
- Programmes Index
- SysMO
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO is to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research capacities and know-how in this field will set the trend in international competition.
Web page: http://sysmo.net/
Funding details:SysMO is financed by the partner countries Austria, Germany, The Netherlands, Norway, United Kingdom and Spain. They have issued a joint call in August/September 2005 and provide funding for transnational projects. SysMO is coordinated by Germany.
A list of the funding partners can be found at http://www.sysmo.eu/Partners
Related items
- People (10)
- Projects (12)
- Institutions (52)
- Investigations (8+12)
- Studies (9+13)
- Assays (29+9)
- Data files (42+37)
- Models (11+4)
- SOPs (5+6)
- Publications (16)
- Presentations (4+1)
- Events (1+1)
- Documents (0+4)
Projects: SysMO DB
Institutions: HITS gGmbH
Projects: SysMO DB
Institutions: HITS gGmbH
Expertise: Microarray, Microbiology, Bacillus subtilis, Systems Biology, PCR
Projects: SysMO DB
Institutions: HITS gGmbH
Projects: SysMO DB, FAIRDOM training
Institutions: HITS gGmbH
Roles: Project Coordinator
Expertise: Genetics, Molecular Biology, Bioinformatics, Data Management, Transcriptomics
Tools: Databases, data modeling, ontology
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
Institutions: HITS gGmbH
Expertise: Software Engineering, Information Retrieval
Tools: Data Management, Databases, Java, Spring, Groovy on Rails
I am leader of the SDBV group at the EML Research gGmbH.
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
* facilitates and maximises the potential for data exchange between SysMO research groups;
* maximises the ‘shelf life’ and
...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Saccharomyces cerevisiae, Lactic Acid Bacteria
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus
Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=54
Organisms: Clostridium acetobutylicum
Comparative Systems Biology: Lactic Acid Bacteria
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=57
Global metabolic switching in Streptomyces coelicolor
Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.
Programme: SysMO
Public web page: https://www.wsbc.warwick.ac.uk/groups/sysmopublic/
Organisms: Streptomyces coelicolor
Describet here is the ivnestigation
Snapshots: No snapshots
Scales: Not specified
Investigating moths
Snapshots: Snapshot 1, Snapshot 2, Snapshot 3
Studies: The moth study
Assays: Bupalus
Scales: Not specified
An investigation in the CCM of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.
Snapshots: Snapshot 1
Studies: Carbon loss at high T, Model gluconeogenesis, Pathway optimisation
Assays: Experimental assays of the temperature dependent degradation of GAP and ..., FBPA/ase, FBPAase model, GAPDH, GAPDH modeling, Gluconeogenic model, Model reconstituted system, Modelling pathway optimisation, Modelling temperature dependent degradation of GAP and DHAP, PGK, PGK and FBPAase titrations, PGK modeling, Reconstituted system reference state, TPI, TPI modeling
Scales: Not specified
Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.
This investigation shows public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Organism: Saccharomyces Cerevisiae
Snapshots: Snapshot 1
Studies: A time course analysis of transcription response in yeast treated with ..., Can yeast glycolysis be understood in terms of in vitro kinetics of the ...
Assays: Changes in flux on the metabolome, Changes in flux on the proteome, Changes in flux on the transcriptome, Glycolysis in Saccharomyces cerevisiae, Time course analysis of transcription
Scales: Not specified
It also is described, but as a study
Person responsible: Guest
Snapshots: No snapshots
Investigation: An Investigation Today
Assays: This is the first assay of the study of the investigation of today
Scales: Organism
Studying moths
Person responsible: Guest
Snapshots: No snapshots
Investigation: The moth investigation
Assays: Bupalus
Scales: Not specified
Person responsible: Jacky Snoep
Snapshots: No snapshots
Scales: Not specified
Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: Experimental assays of the temperature dependent degradation of GAP and ..., FBPA/ase, FBPAase model, GAPDH, GAPDH modeling, Gluconeogenic model, Modelling temperature dependent degradation of GAP and DHAP, PGK, PGK modeling, TPI, TPI modeling
Scales: Not specified
By varying the input or output flux via PGK and FBPAase manipulation respectively the pathway efficiency can be optimised.
Person responsible: Jacky Snoep
Snapshots: No snapshots
Scales: Not specified
It also has a description
Investigation: An Investigation Today
Study: This is the study of the investigation of today
Organisms: No organisms
SOPs: 2 hidden items
Data files: No Data files
Scales: Not specified
Assay to measure gene expression of Saccharomyces cerevisiae (yeast) under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index.
(http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: 1 hidden item
Data files: a_transcriptome from BII-S-1
Scales: Not specified
Assay to measure metabolites of yeast saccharomyces cerevisiae under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Metabolite Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: a_metabolome_BII-S-1
Scales: Not specified
Assay to measure protein expression in yeast saccharomyces cerevisiae under different nutrient limitations
Limiting Nutrients:
ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur
This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)
Submitter: Katy Wolstencroft
Assay type: Protein Expression Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: a_proteome from BII-S-1
Scales: Not specified
Assay for transcriptional profiling time course in yeast treated with rapamycin
This is public data from the BioInvestigation Index (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-2)
Submitter: Katy Wolstencroft
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Growth control of the eukaryote cell: a systems...
Study: A time course analysis of transcription respon...
Organisms: Saccharomyces cerevisiae
SOPs: Nutrient_limited_stationary
Data files: a_microarray from BII-S-2
Scales: Not specified
Combined plot fo the model simulations and the experimental data for the PGK and FBPAase titrations.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Pathway optimisation
Assays: Modelling pathway optimisation, PGK and FBPAase titrations
Scales: Not specified
Model simulation showing the effect of varying PGK or FBPAase concentration on the efficiency for 3PG to F6P conversion.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Pathway optimisation
Assays: Modelling pathway optimisation
Scales: Not specified
An exponential decay model was fitted to the experimental data set of GAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for GAP degradation at 70C was estimated to be 0.056 1/min, equivalent to a half life time of 12.4 min.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Modelling analyses: Modelling temperature dependent degradation of ...
Scales: Not specified
An exponential decay model was fitted to the experimental data set of DHAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for DHAP degradation at 70C was estimated to be 0.0225 1/min, equivalent to a half life time of 30.8 min.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Modelling analyses: Modelling temperature dependent degradation of ...
Scales: Not specified
Mathematical model for FBPAase kinetics
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Modelling analyses: FBPAase model
Scales: Not specified
Mathematical model for GAPDH kinetics, saturation for GAP, BPG, NADP, NADPH, Pi.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Modelling analyses: GAPDH modeling
Scales: Not specified
Cloning and heterologous expression of gluconeogenic enzymes in E. coli
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Scales: Not specified
Preparation of cell free extracts of the recombinant E. coli strains expressing the respective S. solfataricus enzymes.
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Scales: Not specified
The recombinant enzymes were purified from the cell free extracts of E. coli expressing the respective enzymes.
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Scales: Not specified
A stationary-phase culture (10ml) was used to inoculate the fermenter vessel.
Taken from ArrayExpress:
http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-MEXP-115
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Growth control of the eukaryote cell: a systems...
Scales: Not specified
The procedure describes the preparation of fluorescent DNA probes from human mRNA or total
RNA.
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Scales: Not specified
Abstract (Expand)
Authors: H. Loeffler-Wirth, M. Vogel, T. Kirsten, F. Glock, T. Poulain, A. Korner, M. Loeffler, W. Kiess, H. Binder
Date Published: 14th Sep 2018
Publication Type: Not specified
PubMed ID: 30212520
Citation: PLoS One. 2018 Sep 13;13(9):e0203628. doi: 10.1371/journal.pone.0203628. eCollection 2018.
Scales: Not specified
Abstract (Expand)
Authors: E. K. Allen, Firstname Lastname, J. O. Hendley, S. D. Turner, B. Winther, M. M. Sale
Date Published: 25th Jun 2014
Publication Type: Not specified
PubMed ID: 25028608
Citation:
Scales: Not specified
Abstract
Authors: Saminda Abeyruwan, Uma D Vempati, Hande Küçük-McGinty, Ubbo Visser, Amar Koleti, Ahsan Mir, Kunie Sakurai, Caty Chung, Joshua A Bittker, Paul A Clemons, Steve Brudz, Anosha Siripala, Arturo J Morales, Martin Romacker, David Twomey, Svetlana Bureeva, Vance Lemmon, Stephan C Schürer
Date Published: 2014
Publication Type: Not specified
DOI: 10.1186/2041-1480-5-S1-S5
Citation: J Biomed Sem 5(Suppl 1) : S5
Scales: Not specified
Abstract (Expand)
Authors: T. Kouril, D. Esser, J. Kort, H. V. Westerhoff, B. Siebers, J. L. Snoep
Date Published: 22nd Aug 2013
Publication Type: Not specified
PubMed ID: 23865479
Citation: FEBS J. 2013 Sep;280(18):4666-80. doi: 10.1111/febs.12438. Epub 2013 Aug 22.
Scales: Not specified
Abstract (Expand)
Authors: Andreas Petzold, Kathrin Reichwald, Marco Groth, Stefan Taudien, Nils Hartmann, Steffen Priebe, Dmitry Shagin, Christoph Englert, Matthias Platzer
Date Published: 16th Mar 2013
Publication Type: Not specified
PubMed ID: 23496936
Citation:
Scales: Not specified
An example of add a presentation hosted from SlideShare.
Creator: Stuart Owen
Submitter: Stuart Owen
Scales: Not specified
Hand on for Computer Practical04 Data management in praxis : Day 1 _ ISA in SEEK
Creator: Olga Krebs
Submitter: Olga Krebs
Scales: Not specified
This is a working copy, still many changes to come.
Creator: Wolfgang Müller
Submitter: Wolfgang Müller
Scales: Not specified
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Scales: Not specified
Systems Biology is one of the most prominent newly emerging interdisciplinary science areas. By connecting fields such as genomics, proteomics, cell biology, medicine, molecular biology, biochemistry and genetics, with mathematics, bioinformatics, engineering and computation, it 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 are generated, which are
...
Country: Austria
City: Innsbruck