The INFECT consortium takes on a novel systems biology approach towards necrotizing soft tissue infection (NSTI). NSTI is an aggressively progressing bacterial infection that usually starts from a small wound. The diagnosis of this infection is often challenging due to clinical heterogeneity like presence of comorbidities. The INFECT consortium takes on a novel systems biology approach by integrating clinical data with the underlying molecular data in order to understand infection specific molecular mechanisms.

LifeGlimmer is involved as a computational partner in the consortium. We integrate interactions with experimental omics data to pinpoint disease-specific molecular mechanisms and develop statistical methods to reveal associations between clinical parameters (for example comorbidities, age, or BMI) and infection types. Furthermore, we develop effective classification methods to identify patient subgroups from a heterogeneous patient cohort aiming for a better diagnosis and ultimately treatment.

The partners of SysmedIBD are working towards a systems medicine approach of Inflammatory Bowel Disease. Mathematical experts develop models describing the process of chronic inflammation starting with one central pathway present in each cell type, the NF-kb pathway. Biologists with expertise in animal models generate data to validate the mathematical models and samples from patients are used to match experimental data to patient cohorts. Within the consortium, specialists in chemical computing will suggest potential drugs to treat chronic inflammation.

LifeGlimmer provides advanced statistical methods in differential expression analysis of time series RNA sequencing. We implement an interactive database that integrates the data produced during the project and allows users to perform differential expression analysis with their own data. Health medical records from follow-up cohorts are digitalised, anonymised and mined with specific text-mining tools to reveal information that was not systematically collected before. We investigate new characterisation of patients with those new data using machine learning algorithms.

The overarching aim of IBISBA is to create a coordinated network of research infrastructure facilities and thus provide a novel and timely response to the main challenges that are currently hampering the development of industrial biotechnology (IB) as a key enabling technology of Europe’s bioeconomy.

Building upon its expertise in large-scale functional annotation, analysis and integration of heterogeneous data sets (in particular omics), semantic technologies and metabolic modeling, Lifeglimmer participates in various WPs, in particular on the development and deployment of computational workflows for biocatalyst and process design, semantic analysis and integration of data using a decision support system.

In silico analysis of algal metabolism for industrial application is often a challenge due to the fact that algae are in general less understood in the research field than plants or bacteria. In the SPLASH project LifeGlimmer is involved in genome-scale metabolic modelling and analysis of the green microalga Botryococcus braunii which is capable of overproducing long-chain hydrocarbons, botryococcenes, and exopolysaccharides etc. Microalgae are promising new renewable feedstocks for chemicals and plastics. They can be cultivated on non-arable land and can yield valuable compounds for chemical industries. If microcalgae can be sustainably utilized at an industrial scale this will provide new opportunities for decreased dependency on fossil feedstocks and potentially contribute to climate mitigation and reduced pressure on land resources.

The Marie Curie Initial Training Network PerFuMe (PERoxisome Formation, Function, Metabolism) is an interdisciplinary and intersectoral initial stage training network (ITN) at the interface of medicine, plant and fungal biology, devoted to understanding the principles of peroxisome biology.

EmPowerPutida answers current market needs by the thorough application of Synthetic Biology. This industrially driven project will pave the way to the production of so far non-accessible biological compounds. Therefore, the lifestyle of Pseudomonas putida, a bacterium with remarkable metabolic endowment and stress tolerance, will be engineered. The guiding idea is to embed optimised biosynthetic pathways into an optimised chassis offering new functionalities. We have the ambition to establish Pseudomonas putida as the major European platform of choice for industrial, large-scale whole-cell biocatalysis directed at the sustainable biotechnological production of bulk and specialty chemicals.

As part of the project LifeGlimmer engages in data management and dissemination activities. Intensive interaction with relevant stakeholder groups contributes to the public debate on Synthetic Biology and maximises the socio-economic impact of the project.

The Chromatin3D project explores the molecular, cellular and systems level biology of chromatin through the cross-disciplinary expertise of academic and non-academic partners. Chromatin is a key component of the cell nucleus and the destabilization of regulatory mechanisms that act on the chromatin structure are implicated in pathologies, such as cancer. The aim of this project is to gain mechanistic insight of the dynamic assembly and modification of chromatin during developmental processes and its deregulation during the onset of disease.

The aim of NORM-SYS is to incorporate established community standards for data and in silico models in systems biology into generalized concepts that enable easy communication between expert groups and standardization organisations.

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