Projects

BaCell-SysMO 2
Modelling carbon core metabolism in Bacillus subtilis – Exploring the contribution of protein complexes in core carbon and nitrogen metabolism.

Bacillus subtilis is a prime model organism for systems biology approaches because it is one of the most advanced models for functional genomics. Furthermore, comprehensive information on cell and molecular biology, physiology and genetics is available and the European Bacillus community (BACELL) has a well-established reputation for applying
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Programme: SysMO

Public web page: http://www.sysmo.net/index.php?index=53

tba.

Programme: COLOSYS

Public web page: Not specified

Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves

CropClock - Increasing Crops Biomass by Uncovering the Circadian Clock Network Using Dynamical Models

The circadian clock is an internal timing system that allows plants to predict daily and seasonal changes in light and temperature and thus to adapt photosynthesis, growth, and development to external conditions. The core oscillator is well understood in the model plant Arabidopsis, however, relatively little is known about the dynamic effects of the clock on agronomic behaviour of crop plants.
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Programme: ERASysAPP

Public web page: Not specified

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

Public web page: Not specified

No description specified

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

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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No description specified

Programme: LiSyM - Systems Medicine of the Liver

Public web page: Not specified

No description specified

Programme: Independent Projects

Public web page: Not specified

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.

ErasysApp Funders

Programme: ERASysAPP

Public web page: Not specified

Public showcase and collection of training material

The aim of the project is bioprospecting, isolation and characterization of novel secondary metabolites, produced by extremophilic microorganisms. The project is dedicated to a poorly investigated problem of antagonistic interactions between extremophilic microorganisms in their communities, namely, to the investigation of the ability of extremophiles to produce secondary metabolites with biocidic, cytotoxic and cytostatic activities. Working out this problem will fulfill an important applied
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Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)

Public web page: Not specified

FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.

Programme: FAIRDOM

Public web page: http://fair-dom.org/

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 the meeting you will:

- Learn why data and model management is
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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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Glycon proposal preparation

Programme: This Project is not associated with a Programme

Public web page: Not specified

Aim of HUMET Startup Project is to make an inventory of expertise, research goals, resources etc. of the HUMET Coaliytion of the Willing.

Programme: HUMET

Public web page: Not specified

Despite the intensive use of agrochemicals, plant pathogens are responsible for huge yield losses worldwide. Understanding the interaction between plant and pathogens is crucial to ensure long lasting and environmentally friendly system of plant protection. Therefore research of the most important human food crops in combination with their pathogens is one of the highest priorities for sustainable agriculture.

The aim of the proposed research project is to bring new perspective into understanding
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Programme: NIBSys

Public web page: http://projects.nib.si/hyp/

Systems Biology studies the properties and phenotypes that emerge from the interaction of biomolecules where such properties are not obvious from those of the individual molecules. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex
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Programme: Independent Projects

Public web page: http://www.icysb.se/

IMOMESIC - Integrating Modelling of Metabolism and Signalling towards an Application in Liver Cancer

One of the most challenging questions in cancer research is currently the interconnection of metabolism and signalling. An understanding of mechanisms that facilitate the physiological shift towards a proliferative metabolism in cancer cells is considered a major upcoming topic in oncology and is a key activity for future drug development. Due to the complexity of interrelations, a systems biology
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Programme: ERASysAPP

Public web page: Not specified

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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The workshop focuses on the publication, curation, retrieval, and usage of kinetic data from the reaction kinetics database SABIO-RK and on the use of data in modeling. There will be experience reports from scientists who successfully used experimental data to formulate or verify biological hypotheses with the computer, and you will experience how experimental data can be used with computational models.

Ion and solute homeostasis in enteric bacteria: an integrated view generated from the interface of modelling and biological experimentation

Programme: SysMO

Public web page: http://www.sysmo.net/index.php?index=56

Escherichia coli is a well-established and the most widely used organism for the production of recombinant proteins (used in medical and industrial applications, as molecular biology reagents, etc.). Production of proteins is the most resource exhaustive process for the cells and therefore needs to be optimized to achieve maximal productivities. Natural environment of E. coli is much harsher compared to the near optimal growth conditions used in production processes. In order to survive cells
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No description specified

Programme: LiSyM - Systems Medicine of the Liver

Public web page: Not specified

This is a repository of logical models created within the COLOSYS consortium, by the NTNU and Curie groups (and possibly others).

Programme: COLOSYS

Public web page: Not specified

No description specified

Programme: This Project is not associated with a Programme

Public web page: Not specified

No description specified

Programme: Independent Projects

Public web page: Not specified

Systems biology of bacterial methylotrophy for biotechnological

Andrew Millar's research group, University of Edinburgh

The Molecular Systems Biology project holds information for reproducing simulation figures in the journal. This can include experimental data files, model files and manuscript information.

Programme: Journals

Public web page: http://msb.embopress.org

MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.

Programme: SysMO

Public web page: http://www.moses.sys-bio.net/

No description specified

Programme: MS_DILI

Public web page: Not specified

We will contribute to the LiSyM Research Network an open source, freely available and reproducible multiscale model of the human liver from single cell metabolism to whole liver function. The model will be available in existing standards of systems biology, provide standardized interfaces for data integration and be fully annotated to available biological, medical and computational ontologies. All data, models and source code will be shared within the LiSyM Research Network and made available to
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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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Bistable switches are the key elements of the regulatory networks governing cell development, differentiation and life-strategy decisions. Transcriptional noise is a main determinant that causes switching between different states in bistable systems. By using the human pathogen Streptococcus pneumoniae as a model bacterium, we will investigate how transcriptional fidelity and processivity influence (noisy) gene expression and participate in bistability. To study this question, we will use both
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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.

Programme: NIBSys

Public web page: http://ablejec.nib.si/doc

Systems analysis of process-induced stresses: towards a quantum increase in process performance of Pseudomonas putida as the cell factory of choice for white biotechnology.

The specific goal of this project is to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that increase its performance through a systems biology understanding of key metabolic and regulatory parameters that control callular responses to key stresses generated
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Programme: SysMO

Public web page: http://www.psysmo.org/

Microbial strains used in biotechnological industry need to produce their biotechnological products at high yield and at the same time they are desired to be robust to the intrinsic nutrient dynamics of large-scale bioreactors, most noticeably to transient limitations of carbon sources and oxygen. The engineering principles for robustness of metabolism to nutrient dynamics are however not yet well understood. The ROBUSTYEAST project aims to reveal these principles for microbial strain improvement
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Programme: ERASysAPP

Public web page: Not specified

No description specified

Programme: ERASysAPP

Public web page: Not specified

Multi-level mathematical modeling of erythropoiesis for optimized expansion of erythroid progenitor cells and improved treatment regimes

Programme: e:Bio

Public web page: http://sbepo.de/

Systems Biology of a genetically engineered Pseudomonas fluorescens with inducible exo-polysaccharide production: analysis of the dynamics and robustness of metabolic networks

Programme: SysMO

Public web page: http://www.sysmo-alginate.net/

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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We are modelling ROS management and mitochondrial dysfunction. Mitochondria produce both energy and reactive oxygen species (ROS), and suffer from ROS. Experimental data from University Milan-Bicocca.

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

Cystic Fibrosis (CF)- lethal autosomic disease CFTR - Cystic Fibrosis Transmembrane Regulator

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

Pesticides, plastics, cosmetics, electrical transformers and many other products contain Endocrine disruptors (EDCs). EDCs interfere with natural hormone functions and may cause the disease.

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

The SilicoTryp project aims at the creation of a “Silicon Trypanosome”, a comprehensive, experiment-based, multi-scale mathematical model of trypanosome physiology.
Trypanosomes are blood-stream parasites transmitted by tsetse flies; they cause African sleeping sickness in humans and livestock. Currently available drugs have severe side effects, and the parasites are rapidly developing resistance.
In this project, we collect a wide range of new experimental data on the parasite in its various
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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.

Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Programme: SysMO

Public web page: http://sulfosys.com/

Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.

Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012)
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Programme: e:Bio

Public web page: http://www.sulfosys.com/

"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling
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Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base.

The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising
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Designer microbial communities for fermented milk products: A Systems Biology Approach

Programme: ERASysAPP

Public web page: Not specified

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
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Programme: SysMO

Public web page: http://www.sysmo-db.org/

No description specified

Programme: SysMO

Public web page: http://www.sysmo.net/

Comparative Systems Biology: Lactic Acid Bacteria

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
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This project provides a space for storing, annotating and publishing Systo models.

Programme: Independent Projects

Public web page: Not specified

Translating Systems Virology data into broad-spectrum antiviral Drugs

Programme: ERASysAPP

Public web page: Not specified

No description specified

Programme: LiSyM - Systems Medicine of the Liver

Public web page: Not specified

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.

Programme: NIBSys

Public web page: Not specified

No description specified

Programme: Model repository for M4 (Make Me My Model) clients of ISBE

Public web page: Not specified

Gene interaction networks and models of cation homeostasis in Saccharomyces cerevisiae

Programme: SysMO

Public web page: http://www.translucent-network.org/

No description specified

Hypoglycaemia and lactic acidosis are key diagnostics for poor chances of survival in malaria patients. In this project we aim to test to what extent the metabolic activity of Plasmodium falciparum contributes to a changed glucose metabolism in malaria patients. The approach is to start with detailed bottom up models for the parasite and then merge these with more coarse grained models at the whole body level.

GMO free systems optimization of wine yeast for wine production by massive scale directed evolution

Programme: ERASysAPP

Public web page: Not specified

WURSynBio

Programme: This Project is not associated with a Programme

Public web page: Not specified

D-xylose is a major component of lignocellulose and is after D-glucose the most abundant monosaccharide on earth. However, D-xylose cannot be naturally utilised by several industrially relevant microorganisms. On the way to a strong bio-based economy in Europe, this widely available feedstock has to be made accessible for the sustainable microbial synthesis of value-added chemical building blocks to be used in a broad range of applications. The project aims at engineering Corynebacterium glutamicum
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ZucAt - Sucrose (from german Zucker) translocation in Arabidopsis thaliana. Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the
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Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)

Public web page: Not specified

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