Projects

This is a sandbox where DigiSal members can learn to use the SEEK.

Tutorial document: http://tinyurl.com/seek-ds17

The SEEK is a web interface to a database of research "assets" organised in a hierarchical "ISA structure" (investigation-study-assay) [1].
These are further organised into projects and programmes.

* Programme = Overarching research theme (The Digital Salmon)
* Project = Research grant (DigiSal, GenoSysFat)
* Investigation = a particular biological process, phenomenon or thing
...

Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining
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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.

Programme: Breast Cancer Simulation

Public web page: Not specified

Start date: 1st Jun 2019

End date: 1st Aug 2019

documents for use with RStudio-Shiny and java API testing

Programme: API_testing_projects

Public web page: Not specified

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

Programme: API_testing_projects

Public web page: Not specified

Background- Thermophilic organisms are composed of both bacterial and archaeal species. The enzymes isolated from these species and from other extreme habitats are more robust to temperature, organic solvents and proteolysis. They often have unique substrate specificities and originate from novel metabolic pathways. Thermophiles as well as their stable enzymes (‘thermozymes’) are receiving increased attention for biotechnological applications.

The proposed project will establish thermophilic in
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Amino alcohol moieties are found in highly diverse classes of natural products that are of great importance due to their bioactivity, and they function as chiral building blocks for the synthesis of pharmaceuticals and agrochemicals. The chemical synthesis of stereoisomerically pure amino alcohols is difficult and typically requires uneconomical steps for protective group manipulations. Conventional syntheses in the chemical industry often use hazardous substances, consume large amounts of energy
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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.

PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.

Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease
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Programme: This Project is not associated with a Programme

Public web page: http://polimer-itn.eu/

NAD phylogeny

Programme: This Project is not associated with a Programme

Public web page: Not specified

Start date: 30th May 2019

SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.

Programme: NIBSys

Public web page: http://susphire.info/susphireproject/

Start date: 1st Apr 2018

End date: 31st Mar 2021

Rhodolive

Programme: Era CoBioTech

Public web page: Not specified

Our world is changing fast! Key global trends are rapid urbanisation, growing and ageing populations, and increased prosperity. This results in depletion of natural and petrochemical resources and climate change, which affects the quality of the environment and people's lives. Therefore, developing a bio-based economy is key to sustain our planet in the long term. Raw materials will have to be recruited from renewable sources.

Industrial biotechnology is potentially a very powerful technology in
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No description specified

Programme: COMBINE (Computational Modeling in Biology Network)

Public web page: Not specified

to complete

Programme: Independent Projects

Public web page: Not specified

Centre for Digital Life Norway (DLN) project 'OXYMOD - Optimized oxidative enzyme systems for efficient conversion of lignocellulose to valuable products'

Bioprocesses for the optimized, integrated production of butyl esters from sustainable resources (BESTER)

Industrial Biotechnology is a key enabling technology to produce a plethora of different bio-based products from sustainable resources and a driver for developing the bio-based economy in Europe. Systems biology and Synthetic biology are recent additions to the biotechnology toolbox that in interplay with bioprocess and chemical process technology can help developing competitive industrial
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to complete

Programme: Independent Projects

Public web page: Not specified

Start date: 11th May 2019

Most biological processes require energy and are tightly regulated. Energy is extracted from food supplies and eventually transformed into ATP, the universal energy carrier of the cell. These pathways consist of many reactions which involve NAD or NADP, small molecules which serve as intermediate energy transmitters.
Vitamin B3 is essential for the synthesis of these nucleotides. Interestingly, the key molecules in energy transduction also have important roles in the regulation of all vital
...

Programme: Independent Projects

Public web page: Not specified

Start date: 11th Mar 2018

End date: 28th Feb 2022

please complete description

Programme: Independent Projects

Public web page: Not specified

This projects seeks to uncover how phytochrome signalling modulates leaf architecture

Programme: Halliday Lab

Public web page: http://hallidaylab.bio.ed.ac.uk/

Start date: 10th Jan 2017

How light control development

Programme: Modelling Light Control of Development

Public web page: Not specified

Start date: 1st Nov 2017

End date: 30th Nov 2021

No description specified

Programme: Independent Projects

Public web page: Not specified

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.

MESI-STRAT: Systems Medicine of Metabolic-Signaling Networks -A New Concept for Breast Cancer Patient Stratification.
Breast cancer is a complex disease with high prevalence in the European Union and world-wide. 75%-80 of the patients have estrogen receptor-positive (ER)-positive tumors and are treated with endocrine therapies. Endocrine therapies, which block ER-driven tumor growth, show high efficacy. Yet, a significant proportion of the patients will eventually relapse with metastatic breast
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Programme: This Project is not associated with a Programme

Public web page: http://www.mesi-strat.eu

ScyCode

Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)

Public web page: Not specified

Start date: 30th Apr 2019

Coastal zones and oceans constitute an essential fundament for Norway’s history as well as current economy, providing ecosystem services for fisheries, aquaculture, transport, tourism, and recreation. The petroleum activities in Norwegian waters have been crucial for Norway’s financial growth and in financing the Norwegian welfare state. As the pressure on the oceans continuously increases, both the petroleum industry and the seafood industries have acknowledged that awareness and actions are
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The project addresses the generation and establishment of programmed pacemaker cells for an in vitro drug testing possibility to perform predictive tests. This may lead to an improved treatment of cardiac arrhythmias or an accurate identification of potential drug molecules at a very early stage of development. Important benefits will arise in verifying the safety of a wide variety of medicines while reducing animal testing.

This project is funded by the European Social Fund (ESF) program of the
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Programme: Independent Projects

Public web page: Not specified

ERACoBioTech project

Programme: Era CoBioTech

Public web page: https://www.ntnu.edu/c1pro

A joint NTNU and SINTEF project to establish a knowledge platform on DHA synthesis and lipid accumulation in the native DHA-producing thraustochytrids, and to develop these into high productivity omega-3 fatty acid producing cell factories.

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