Investigations

We develop macrophage logical models to represent the activation/polarization of this immune cell. Interactions are manually curated with available macrophage literature. The models are mainly built and analyzed in GINsim. But other resources are used to integrate specific pathways or small modules (CasQ software) and to analyze the logical models (CoLoMoTo Notebooks).

The COVIDminer text mining project (https://rupertoverall.net/covidminer/) reads the published literature concerning SARS-CoV-2 and COVID-19 to extract statements about (primarily molecular) interactions. Using the API associated with this project, putative interactors can be automatically retrieved for the existing COVID-19 Disease Maps. New interactions are prioritised based on their frequency in the literature and the topological importance of the interaction targets to provide a focussed set ...

Frequency doubling in the cyanobacterial circadian clock

Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.

Here we collect curated data to be integrated into public repositories

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 ...

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.

One of these activities is antibiotic production and is widespread in streptomycetes ...

The aims of this investigation is to quantify metabolites associated with pathways involved in stress responses for parameterising models of oxidative stress metabolism; the measurement of metabolic fluxes of metabolites of interest with intracellular concentrations

Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.

User metadata is an essential part of experimental data. Scientists need to understand underlying conditions and experimental procedures in order to model or investigate relevant biological questions. Currently, only a small fraction of the High Content SCreening (HCS) investigations are deposited for reuse by the community, and an even smaller fraction of that data is standards-compliant. For reusing data, scientists need to be able to understand how data was generated, under which experimental ...

Understanding how liver function arises from the complex interaction of morphology, perfusion, and metabolism from single cells up to the entire organ requires systems-levels computational approaches.

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.

All the files available are published under the CC BY 4.0 license.

A further investigation of the variation of FNR number in E.coli Cyo/Cyd mutants is carrying out at different oxygen supply levels. The agent-based FNR and ArcBA model is going to be used for this prediction. The number of Cyo or Cyd and other unrelated agents would be set as ‘0’ at the initial XML file with which the model starts. According to the restrictions of supercomputer ‘Iceberg’ (serviced provided by the University of Sheffield), certain parameters, such as memory per node, would be ...

A key insight, emerging from discussions and data between the projects PIs, was the importance of switching rates in bistable systems. While the existence of multiple steady states in bistable systems can be described by universal models (that do not differ between different systems), switching rates from one stable state to another depend on the molecular details of the system under consideration.

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 genome scale, the metabolic ...

Automated model building using Taverna workflows from KEGG-Database

Collection of models submitted to PLaSMo by Robert Muetzelfeldt and automatically transferred to FAIRDOM Hub.

Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".

High salinity chemostat cultivation, multiomics sampling (proteome, transcriptome, metabolome, fluxome) and modelling of carbon core metabolism of Bacillus subtilis 168.