41 Works

test doi

Quyen Nguyen

Modelling of M. pneumoniae metabolism

Niels Zondervan
1. To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae 2. To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M. hyopneumoniae for vaccine optimization 3. To deploy the metabolic model(s) to: 1) the rational design and optimization of the vaccine chassis; 2) aid the development of a higher-growth rate chassis; 3) assist the development of a nutrient optimized a serum-free growth medium and; 4) assess, at...

Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition

Malte Herold & Antoine Buetti-Dinh
Supplementary files for the publication: Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Andrew Millar, Daniel Seaton & Katja Baerenfaller
Data, model and analysis for Daniel Seaton et al. biorXiv 2017 https://doi.org/10.1101/182071 and Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962. Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.

Enzymatic Growth Model

Henning Lindhorst
A minimal model showing the core of resource allocation models as it can either be invested in enzymatic machinery or single biomass components with the best yield. The model is written in SBML using the RAM extension for use in deFBA. Compatible python software for simulation can be found at https://tinyurl.com/yy8xu4v7

Carbon Core deFBA Model

Henning Lindhorst & Steffen Waldherr
A small model representing the core carbon network in each cell. For more detail on the model creation see [1]. The model is written in SBML using the RAM extension for use in deFBA. Compatible python software for simulation can be found at https://tinyurl.com/yy8xu4v7 [1] S. Waldherr, D. A. Oyarzún, A. Bockmayr. Dynamic optimization of metabolic networks coupled with gene expression. In: Journal of Theoretical Biology, 365(0): 469 - 485.

Yeast_deFBA Model

Henning Lindhorst & Alexandra-M. Reimers
This SBML file uses the RAM extension and contains a minimal genome scaled model for Saccharomyces cerevisiae. The model is based of Yeast 6.06 and was published first in A.-M. Reimers Thesis "Understanding metabolic regulation and cellular resource allocation through optimization".

Resource Allocation Model

Henning Lindhorst
This model was created to showcase all functions of the SBML extension RAM. The model can be unr in deFBA with the python software deFBA-Python. The software is freely available at at https://tinyurl.com/yy8xu4v7

Metabolic analysis of effects of sucrose translocation on phenotypic traits of plants

Maksim Zakhartsev, Olga Krebs & Waltraud Schulze
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 into efflux exporters (SWEET family)...

MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection

Ziva Ramsak, Tjasa Stare, Maja Križnik & Kristina Gruden
Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.

Metabolic analysis of effects of sucrose translocation on phenotypic traits of Arabidopsis thaliana

Maksim Zakhartsev & Olga Krebs
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 into efflux exporters (SWEET family)...

Creating data sheet template for 'omics data

Olga Krebs
This investigation contains spreadsheet templates and examples for SEEK users to download and use for structuring experimental data. These templates were developed by the SysMO-DB team and the SysMO PALs

ZucAt: multi-compartment metabolic model of growing Arabidopsis thaliana

Maksim Zakhartsev, Olga Krebs, Waltraud Schulze, Yuriy Orlov & Irina Medvedeva

Modelling of M. pneumoniae metabolism

Niels Zondervan
1. To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae 2. To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M. hyopneumoniae for vaccine optimization 3. To deploy the metabolic model(s) to: 1) the rational design and optimization of the vaccine chassis; 2) aid the development of a higher-growth rate chassis; 3) assist the development of a nutrient optimized a serum-free growth medium and; 4) assess, at...

Glucose metabolism in Plasmodium falciparum trophozoites

G. Penkler, F. Du Toit, W. Adams, M. Rautenbach, D. C. Palm, D. D. Van Niekerk & J. L. Snoep

iNS142 RobOKoD Redesigned Butanol Producing.

Natalie Stanford
Butanol producing iNS142, redesigned using RobOKoD.

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Andrew Millar, Daniel Seaton & Katja Baerenfaller
Data, model and analysis for Daniel Seaton et al. biorXiv 2017 https://doi.org/10.1101/182071 and Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962. Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.

Metabolic analysis of effects of sucrose translocation on phenotypic traits of plants

Maksim Zakhartsev, Olga Krebs & Waltraud Schulze
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 into efflux exporters (SWEET family)...

G3PDH Kinetic data

David Van Niekerk & Jacky Snoep

Registration Year

  • 2014
    3
  • 2015
    7
  • 2016
    8
  • 2017
    5
  • 2018
    9
  • 2019
    9