Projects

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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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.

The Systems Biology Service Center of de.NBI (de.NBI-SysBio) provides bioinformatics support and a standards-based data management for systems biology projects, with focus on the provenance of experimental results and on the reproducibility of modeling experiments, as well as high-quality curated biochemical data to modelers and experimentalists.
The node concentrates on two tools for the data management in life sciences research: SEEK, a catalogue for storage, registration and exchange of data
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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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SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.

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

pISA-tree: Standard project directory tree (ISA compliant)

Development of support for standardization of directory trees to suport ISA framework of research organization. We are developing a set of batch/make files to enable creation of trees for storage of assets (data/presentations/protocols/scripts) and description files that hold associated metadata for Investigation / Study / Assay levels.

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.

The project “Rational development of anti-cancer combinations” focuses on precision medicine for cancer by pursuing novel insight into cancer disease mechanisms, combinatorial drug treatment in order to enable selection of the best treatment for the individual patient. The aim is to develop and integrate computational, experimental and analytical approaches to predict and validate anti-cancer drug combinations and produce an integrated pipeline for rational screening of synergistic drugs and for
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In the project “Crossover Research 2.0 – Well constructed Knowledge Commons” the domain of precision medicine is explored as a key visionary driver for developing the Knowledge Commons and the enabling of Systems Biology approaches to innovate healthcare. In particular, we seek to engage stakeholder concerns in investigating and establishing strategies for DrugLogics to contribute to the Knowledge Commons in an RRI mode.

Short-chain fatty-acids (SCFA) are produced from dietary fibres by the intestinal microbiota. They protect humans against obesity. The fate of SCFA and their impact on human fat metabolism is complex and dynamic. To optimally apply prebiotic (fibre) and probiotic (microbial) supplements, a better understanding of their mode of action is required. Our aim is to construct, infer, and analyse a dynamic, multiscale computational model predicting how dietary fibres affect the balance between fat intake
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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
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Salmon farmed on modern feeds contains less of the healthy, long-chain fatty acids (EPA and DHA) than before. Up until the turn of the millennium, farmed salmon were fed fish oil as a replacement for their omega-3 rich natural prey. However, fish oil is now a scarce resource, and more than half of the fat in modern feeds comes from plant oils that are inexpensive, but devoid of long-chain omega-3 fatty acids. How can we increase the omega-3 content of salmon on sustainable feeds?

One option is
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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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The project "INtegrative COllaborative modeling in systems MEdicine" aims at connecting different heterogenous datasets and individual models within systems medicine.

SAFE-Aqua (SustainAble Farming for Effective Aquaculture) is an international consortium research project, consisting of a group of multidisciplinary experts from leading research institutes in France, UK, Thailand and a private-company in Spain.

Glycon proposal preparation

Test

Translating Systems Virology data into broad-spectrum antiviral Drugs

The MycoSynVac project AIMS at using cutting-edge synthetic biology methodologies to engineer Mycoplasma pneumoniae as a universal chassis for vaccination.
Designing a universal Mycoplasma chassis that can be deployed as single- or multi-vaccine in a range of animal hosts. Annually, infections caused by Mycoplasma species in poultry, cows, and pigs result in multimillion Euro losses in the USA and Europe.
There is no effective vaccination against many Mycoplasmas that infect pets, humans and farm
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Andrew Millar's research group, University of Edinburgh

Tobacco as sustainable production platform of the natural biopolymer cyanophycin as co-product to oil and protein

EPSRC project with Exeter, SynthSys and EPCC