SysMO DB
OverviewThe 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 utility of data generated by SysMO;
* provides an integrated platform for the dissemination of the results of the SysMO projects to the scientific community; and
* facilitates standardization of practices in Systems Biology for the interfacing of modelling and experimentation.
We follow several key principles: * exploit what is already available, both within the consortium and outside it, and do not reinvent; * identify the least we can do to make a benefit and do this incrementally.
Programme: SysMO
SEEK ID: https://demo.fairdomhub.org/projects/12
Public web page: http://www.sysmo-db.org/
Organisms: Saccharomyces cerevisiae, Lactic acid bacteria
FAIRDOM PALs: Stuart Owen
Project created: 15th Jan 2009
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Projects: SysMO DB
Institutions: HITS gGmbH
Projects: SysMO DB
Institutions: HITS gGmbH
Projects: SysMO DB
Institutions: HITS gGmbH
Projects: SysMO DB, FAIRDOM training
Institutions: HITS gGmbH
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
I am leader of the SDBV group at the EML Research gGmbH.
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 ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB
Web page: http://sysmo.net/
Describet here is the ivnestigation
Submitter: Guest
Studies: This is the study of the investigation of today
Assays: This is the first assay of the study of the investigation of today
Investigating moths
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
Submitter: Katy Wolstencroft
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
This Investigation was performed by SySMO DB team together with PALS in order to crete methods and best practices for capturing experimental data.
Submitter: Katy Wolstencroft
Studies: No Studies
Assays: Computer Practicals "Data management in practice" Advanced Lecture Cours..., Transcriptional profiling
It also is described, but as a study
Submitter: Guest
Investigation: An Investigation Today
Assays: This is the first assay of the study of the investigation of today
Studying moths
Comprehensive high-throughput analyses at the levels of mRNAs, proteins, and metabolites, and studies on gene expression patterns are required for systems biology studies of cell growth [4,26-29]. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth ...
Submitter: Katy Wolstencroft
Investigation: Growth control of the eukaryote cell: a systems...
This study examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes.
Submitter: Katy Wolstencroft
Investigation: Growth control of the eukaryote cell: a systems...
A study which combines mathematical modelling and experimental measurements to determine the effects of redox charge on glycolytic flux
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
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
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
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
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
Investigation: Growth control of the eukaryote cell: a systems...
Study: 1 hidden item
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
Investigation: Growth control of the eukaryote cell: a systems...
Glycolysis in Saccharomyces cerevisiae
Submitter: Guest
Biological problem addressed: Metabolism
Investigation: Growth control of the eukaryote cell: a systems...
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External Link
The Assmus model taken from JWS Online at - http://jjj.mib.ac.uk/models/assmus/
The 2nd version has been modified, to demonstrate use of the BiVeS tool for comparison ( https://sems.uni-rostock.de/projects/bives/ )
To view the comparison, you need to be logged in (you can login as guest), and click the button for the version you wish to compare with the current displayed version in the box below...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: JWS Online
This model is for a paper that examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In non-growing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under ...
Creator: Stuart Owen
Submitter: Stuart Owen
Model type: Not specified
Model format: SBML
Environment: Not specified
Detailed kinetic model for glycolysis of L. lactis. The model is basically the same model as that published by Hoefnagel et al 2002 (Mol. Biol. Reports 29, 157-161). The change made to the model is to make external glucose a variable such that a glucose pulse can be simulated.
Creators: Jacky Snoep, Ana Rute Neves
Submitter: Katy Wolstencroft
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
MCA of Glycerol Synthesis in Saccharomyces cerevisiae
Creators: Jacky Snoep, Garth R. Cronwright, Johann M. Rohwer, and Bernard A. Prior
Submitter: Katy Wolstencroft
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: 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
The procedure describes the preparation of fluorescent DNA probes from human mRNA or total RNA.
Creator: Olga Krebs
Submitter: Olga Krebs
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
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
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
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
Abstract (Expand)
Authors: Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère
Date Published: 27th Oct 2011
Publication Type: Not specified
An example of add a presentation hosted from SlideShare.
Creator: Stuart Owen
Submitter: Stuart Owen
Hand on for Computer Practical04 Data management in praxis : Day 1 _ ISA in SEEK
Creator: Olga Krebs
Submitter: Olga Krebs
This is a working copy, still many changes to come.
Creator: Wolfgang Müller
Submitter: Wolfgang Müller
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
