Projects

Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you!

At our users meeting you can:

- Learn why data and model management is
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Increasing temperature in the European wine producing regions is having a negative impact on this key sector. Climate change results in a lack of balance between technological and phenolic ripening of wine grapes and, as a consequence, alcohol increase in wines. This trend is of great concern for the European wine industry because it has a negative impact on wine quality, becomes a hurdle for international trade, and jeopardizes compatibility of moderate wine consumption with a healthy lifestyle.
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Here we share resources and best practices to develop a disease map for COVID-19. The project is progressing as a broad community-driven effort. We aim to establish a knowledge repository on virus-host interaction mechanisms specific to the SARS-CoV-2. The COVID-19 Disease Map is an assembly of molecular interaction diagrams established based on literature evidence.

This generic project bundles information about COVID-19 related studies and tools in Germany. It intends to provide an information hub for the different initiatives, their aims, their processes, standards and study protocols, as well as their available data and metadata.
It is initiated by the German National Research Data Infrastructure for Personal Health Data (NFDI4Health), a consortium that plans to establish a concept for a federated research data infrastructure for personal health data in
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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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Microalgae Microbiomes: A natural source for the prevention and treatment of diseases in aquaculture

Aquaculture is one of the fastest growing food sectors in the world. In order to guarantee continuous, efficient and sustainable production and to safeguard the growth of this important sector, its protection from biological threats is crucial.
Within the AquaHealth project, an international consortium of highly experienced partners will assemble and apply an advanced meta’omics toolbox on the
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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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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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WooBAdh project aims to study the feasibility of replacing formaldehyde in wood adhesives by natural components derived from wood or other vegetable matter. The consortium will develop new bioadhesives which are able to provide a holistic solution to the current emissions challenges facing the wood-based composites industry. The proposed solution is focused on different modifications of polyphenols, namely lignin and tannins, for producing bioadhesives that do not contain formaldehyde in its
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Sustainable co-production is the short form of the research project “Tobacco as sustainable production platform of the natural biopolymer cyanophycin as co-product to oil and protein”. It combines plant and industrial biotechnology to increase the value of commercially grown tobacco with products that can sustainably substitute fossil raw materials. We aim to establish a new economically feasible production system for the biopolymer cyanophycin (CGP) as a by-product of tobacco without relevant
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CEPOPA envisions a sustainable cascade one-pot process for the synthesis of optically pure amines from alcohols and/or alkynes, using enzymes immobilized onto catalytically active nanomaterials. In the framework of the project, efficient chemoenzymatic processes will be developed for the synthesis of a set of amines that can be used as building blocks for pharmaceuticals or biomaterials.

Designing 3D metamaterials

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 cellular senescence in skin with the potential for users to explore the effects of combination treatments in silico.

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

Overall, we will measure in-vitro and model in-silico the short-term biochemical network dynamics of extra cellular matrix maintenance (ECM) in populations of young, old and senescent dermal fibroblasts. We have shown in previous work that differences in network dynamics are highly informative and provide a means to identify parts of the network that could be targeted to restore healthy function.

The work will be first carried out in 2D culture of human dermal fibroblasts then extended to a novel
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In this project we use mechanism based modelling .... (complete later)

The group around Nicole Radde specializes in the modeling, analysis, and simulation of biochemical systems. This especially includes parameter optimization and identification.

This project gathers all biomics projects submitted to biomics.pasteur.fr

project: _p_stRT
Short Name: stRT
Title: Solanum tuberosum Reference Transcriptomes
Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
pISA projects path: ../pISA-Projects
Local pISA-tree organisation: National Institute of Biology
pISA project creation date: 2019-10-22
pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek
Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636,
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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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SMART Plants for Tomorrow’s Needs

Plants enable life on Earth through the conversion of solar energy into chemical energy. Beginning with the Neolithic Revolution, the domestication of plants provided the basis for human population growth and, subsequently, the evolution of highly developed civilizations. However, the growing food demands imposed by an increasing population and the effects of anthropogenic climate change pose huge challenges for sustainable food production and ecosystem maintenance.
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The main objective of SynBio4Flav is to go further in the standardization of high complexity synthetic biological parts, and to demonstrate the development of a standardized, and systematic platform for flavonoids production based on synthetic microbial consortia (SMCs).

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

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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Using MCA to understand which enzymes have higher impact in Acetyl-coa production in P. putida