Projects

Research programme in the Takato Imaizumi lab, with multiple collaborators. Published in Song et al. Nature Plants 2018; Kinmonth-Schultz et al., in silico Plant 2019.

Storage of thermophysical properties (e.g. density, viscosity, thermodynamic activity of water, conductivity) using Chemical Markup Language (CML).

This project aims to develop an agent based model using the Netlogo package which can then be used for outreach in schools and the wider community. This model represents the development of breast cancer with the potential for users to explore the effects of combination treatments in silico.

The COLOSYS project aims to develop a deeper understanding of colon cancer networks and convert them into computer models with which it will be better to predict response to treatment. The combination of computational, experimental and clinical testing will provide understanding of drug resistance mechanisms, and allow personalised treatment of colon cancer.

Web application developed using RStudio-Shiny for outreach. Incorporates information, videos and images, worksheets and simulations surrounding breast cancer development and therapy. Incorporates NetLogo simulation from "Outreach - Simulation of breast cancer development using an agent based modelling approach" project.

testing fairdomhub

The gut–brain axis (GBA) provides a bidirectional homeostatic communication between the gastrointestinal tract and the central nervous system. The interdisciplinary collaboration is going to fully explore a first comprehensive GBA cross-disease map of genetic, expression and regulatory changes associated with ulcerative colitis and schizophrenia disease entities.

Dysfunction of this axis can have pathophysiological consequences. Genome-wide association studies (GWAS) have identified >300 ...

documents for use with RStudio-Shiny and java API testing

testing fairdom API in Java and R programming language for use in Breast cancer outreach project

Exploiting native endowments by re-factoring, re-programming and implementing novel control loops in Pseudomonas putida for bespoke biocatalysis. The EmPowerPutida project aims to engineer the lifestyle of Pseudomonas putida to generate a tailored, re-factored chassis for the production of so far non-accessible biological compounds. Pseudomonas putida is a bacterium with a highly versatile metabolism, including the capability to degrade or produce organic chemicals.

NAD phylogeny

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This projects seeks to uncover how phytochrome signalling modulates leaf architecture

How light control development

BIOMICRO PROJECT TEST

The goal of the project is to establish a new biotechnological platform for the production of hydroxy-amino acids, since the current production of these important building blocks is very expensive. Enzyme engineering, systems biotechnology and metabolic engineering will be used in a synthetic biology approach.

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.

This investigation is published under the CC BY 4.0 license.

INBioPharm - Integrated Novel Natural Product Discovery and Production Platform for Accelerated Biopharmaceutical Innovation from Microbial Biodiversity project will develop a new, generic technology platform for the more efficient discovery of novel bioactive compounds with improved prospects to become medical products. A unique national collection of marine microorganisms at SINTEF/NTNU will be used as the basis for the development of different new, complementary molecular biology, analytical ...

We will systematically analyse large datasets of multiple types to: (i) identify key components affected by age or experimental perturbation; (ii) establish networks of interaction; (iii) develop dynamic computational models based on these networks; (iv) use model selection methods to discriminate between alternative network topologies and generate predictive models. To characterise the data, we will apply an ensemble of methods, including frameworks in R/Bioconductor and toolboxes connected via ...

What is PlaSMo? PlaSMo stands for Plant Systems-biology Modelling Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

Our aims

To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost

To represent these models in a declarative XML-based format, which is closer to the systems biology standard SBML To evaluate the behaviour ...

Extremophiles metabolsim

There is an urgent need for novel antibiotics to fight life-threatening infections and to counteract the increasing problem of propagating antibiotic resistance. Recently, new molecular genetic and biochemical tools have provided insight into the enormous unexploited genetic pool of environmental microbial biodiversity for new antibiotic compounds. New tools for more efficiently lifting this hidden treasure are needed to strengthen competitiveness of European industry, as well as for a cost-saving ...

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.

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 ...