Projects
What is a Project?Filters
testing project to evaluate capabilities of SEEK
Programme: Multicomponent Therapy for Age-related Skin Stem Cell Deficiency
Public web page: Not specified
New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Project
Public web page: Not specified
This project collects and maintains metadata templates designed and used at the UMass Chan BioImage DMS Core and built in collaboration with the CBI Open Science Project. The templates are based on the REMBI recommendations and on the NBO-Q Microscopy Metadata specifications. These templates contribute to FAIR bioimaging data in North America, and are meant to be utilized to support image data annotation in the OMERO database.
Programme: Independent Projects
Public web page: Not specified
This project stored supplementary files that we didn't include in the paper ' Exploring the Evolution of the Gene Ontology and itsImpact on Enrichment Analysis'
Programme: Hallmarks of cancer
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Ionizing radiation (IR) leads to DNA double-strand breaks and can therefore be used as cancer treatment. However, some tumors are less responsive to radiation treatment because of their underlying molecular profile. Our ultimate goal is to understand the reaction of lung cancer cells with different phenotypes to IR on a molecular level to then provide the best therapy options for lung cancer patients with IR therapy.
Programme: This Project is not associated with a Programme
Public web page: https://www.sbi.uni-rostock.de/research/projects/detail/74
Start date: 1st Aug 2023
End date: 31st Dec 2027
About
This project houses all the publicly available datasets generated by the Hi-IMPAcTB consortium over the course of its 7+ years.
What is Hi-IMPAcTB?
Hi-IMPAcTB is an ambitious endeavor bringing together a team of international, interdisciplinary researchers to improve our understanding of host-pathogen interactions in the context of tuberculosis (TB). Funded by a multi-center contract from the NIH, the long-term goal of the consortium is to enable principled vaccine design by improving ...
Programme: IMPAcTB
Public web page: https://grantome.com/grant/NIH/75N93019C00071-0-9999-1
FUNCEMM is a project bringing together 2 teams from France and Austria focusing on synthetic methylotrophy.
Programme: Independent Projects
Public web page: Not specified
Model-based design of a biorefinery platform to valorise agrifood organic waste into odd-chain volatile fatty acids integrating technical and environmental criteria
The conversion of organic wastes by anaerobic fermentation (the so-called carboxylate platform) is one of the promising emerging biorefineries that allows valorising organic carbon to volatile fatty acids (VFA), which can be further processed as chemicals, biopolymers and biofuels. A major obstacle to the widespread of the carboxylate ...
Programme: Targeted VFA production from (waste) waters - Biogroup
Public web page: https://biogroup.usc.es/ODDITY
Start date: 1st Dec 2022
End date: 30th Nov 2024
The BioRECIPE (Biological system Representation for Evaluation, Curation, Interoperability, Preserving, and Execution) knowledge representation format was introduced to facilitate seamless human-machine interaction while creating, verifying, evaluating, curating, and expanding executable models of intra- and intercellular signaling. This format allows a human user to easily preview and modify any model component, while it is at the same time readable by machines and can be processed by a suite ...
Programme: Independent Projects
Public web page: https://melody-biorecipe.readthedocs.io/en/latest/introduction.html
Programme: Independent Projects
Public web page: Not specified
Mission: We perform cutting-edge research on data generated by novel biomolecular technologies to address questions in pneumology. Towards this, we use biological high-throughput data, i.e., OMICs data, to gain insights into molecular and phenotypic traits and diseases using computational methods. We combine data, methodology and their applications in pneumology through interdisciplinary collaboration with mathematicians, computer scientists, biologists and physicians.
Programme: Research Center Borstel
Public web page: https://fz-borstel.de/index.php/en/sitemap/service/data-science
Real-time smart monitoring of bioprocesses for efficient conversion of organic carbon to volatile fatty acids
Programme: Targeted VFA production from (waste) waters - Biogroup
Public web page: https://biogroup.usc.es/WATCHER
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: Applied Lipidomics Göttingen
Public web page: Not specified
nfdi4health aims to create the most comprehensive inventory of German epidemiological, public health and clinical trial data to date. It builds a centralised data catalogue with elaborate search functionalities, sophisticated data access management, and a data analysis toolbox, while respecting stringent requirements for privacy concerning personal health data. Standardisation services ensure a high degree of interoperability. Use cases covering prototypical study types and areas of research show ...
Programme: nfdi4health - German National Research Data Infrastructure for Personal Health Data
Public web page: https://www.nfdi4health.de
Start date: 1st Jul 2020
SDBV group using Hub
Programme: Independent Projects
Public web page: Not specified
Based on the combination of sensor and big data revolutions, PHENET (HE INFRA-TECH) will equip crop and ecosystems RI with innovative services based on tools and methods developed in the frame of the project and allowing enhanced capacity to future-proofing agroecosystems. These services will be excellent tools for users addressing environmental and societal challenges such as climate change adaptation / mitigation and agroecology transition.
Programme: Independent Projects
Public web page: https://www.phenet.eu/en
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Further proteomic data and ATP calculation
Programme: BaPro
Public web page: Not specified
Development of a lactic acid centred biorefinery scheme to valorize flexibly organic waste streams into biochemicals
Programme: Targeted VFA production from (waste) waters - Biogroup
Public web page: Not specified
Testing out FAIRDOM-Seek
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis. Theyhad and have tremendous influence on the biogeochemical cycles on Earth. Recently,cyanobacteria are increasingly investigated as cell factories for a sustainableeconomy. Despite their global, environmental and rising economic importance, ourknowledge on the regulation of their primary metabolism is fragmented.Cyanobacteria switch between photoautotrophic and heterotrophic modes ofmetabolism during day/night cycles or ...
Programme: DFG founded projects
Public web page: https://gepris.dfg.de/gepris/projekt/397695561
Start date: 1st Sep 2018
Public web page: Not specified
MESI-Review 2024
Programme: Independent Projects
Public web page: Not specified
The group around Nicole Radde specializes in the modeling, analysis, and simulation of biochemical systems. This especially includes parameter optimization and identification.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: https://www.ist.uni-stuttgart.de/research/group-of-nicole-radde/
Start date: 11th Feb 2020
Programme: Independent Projects
Public web page: Not specified
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 ...
Programme: This Project is not associated with a Programme
Public web page: http://www.mesi-strat.eu
Cell biological and proteogenomic study of the chloroplast of the marine, bloom-forming dinoflagellate P. cordatum
Programme: Independent Projects
Public web page: Not specified
Start date: 4th Jul 2023
End date: 31st Aug 2024
This data contains fish data such as fish abundance, fish community structure data, fish species data obtained in the study, fish productivity and also fish length-weight relationships.
Programme: Independent Projects
Public web page: Not specified
This research discusses what is the status of fisheries provisioning services in Jatigede Reservoir and what anthropogenic pressures in the form of community activities affect the status of fisheries provisioning services.
Programme: Independent Projects
Public web page: Not specified
MESI-STRAT Review
Programme: Independent Projects
Public web page: Not specified
-engineering next level photosynthesis-PhotoBoost is a 4-year research and innovation action that aims to significantly improve the efficiency of photosynthesis in plants. The optimisation of photosynthesis will be achieved by capitalising on multidisciplinary approaches including computational biology, metabolic modelling, systems biology, enzyme and pathway engineering, synthetic biology, and the multigene transformation of two major C3 crops: potato and rice. The PhotoBoost project will deliver ...
Programme: Independent Projects
Public web page: http://www.photoboost.org
Programme: Independent Projects
Public web page: Not specified
This project aims to streamline the integration of Japanese plant research data into the global data ecosystem using the FAIR Data-finder for Agronomic Research (FAIDARE) and Breeding API (BrAPI) standards. Despite the large and diverse datasets generated in plant research, there are significant barriers to efficient data use due to findability and interoperability issues. Our initiative addresses these challenges by adopting the Minimum Information About Plant Phenotyping Experiments (MIAPPE) ...
Programme: Japanese Data in Global Plant Research
Public web page: Not specified
A fundamental and enduring challenge for ecosystem managers developing risk and impact assessment tools is to predict the extent of impact that spilled oil can have on the immediate fish populations and on future generations. Modelling approaches are important tools for these assessments, but they currently suffer from two major shortcomings: 1) the failure to acknowledge that effects can be transferred through several generations and 2) the assumption that a small group of toxic compounds, ...
Programme: Independent Projects
Public web page: https://uit.no/project/toxigen
Start date: 17th Sep 2023
End date: 31st Dec 2027
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 ...
Programme: This Project is not associated with a Programme
Public web page: http://polimer-itn.eu/
The mission of the Virtual Human Platform is to improve the prediction of the potential harmful effects of chemicals and pharmaceuticals based on a holistic, interdisciplinary definition of human health by developing the Virtual Human Platform and accelerating the transition from animal-based testing to innovative safety assessment. The Virtual Human Platform integrates data on human physiology, chemical characteristics and perturbations of biological pathways, for the first time in an inclusive ...
Programme: Independent Projects
Public web page: https://www.sciencrew.com/c/6586?title=VHP4Safety
The current project is created as a potential repository for resources resulting from the Virtual Human Platform for Safety Assessment (VHP4Safety) project.
Programme: VHP Programme
Public web page: Not specified
the Supplementary materials for Journal of Clinical Endocrinology and Metabolism
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Independent Project
Programme: Independent Projects
Public web page: Not specified
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).
Programme: Systems Biology Programme
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Test case for porting sampleBD to fairdom-seek
Programme: SampleDB_programme
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: BaPro
Public web page: Not specified
PROMISEANG is a 48-month project that aims to develop novel alternative proteins from marine underexploited sources (marineinvertebrate and macroalgae discards and industrial biowastes) through biomass fermentation (solid-state and submerge processes),generating new microbial protein biomass, meeting market requirements for food, feed, and non-food (biomedicine, pharma andcosmetic) bio-based applications. A technically and economically viable biorefinery for microbial-based protein production ...
Programme: Independent Projects
Public web page: Not specified
The PETzyme project's objective is to develop an enzymatic technology for recycling polyethylene terephthalate (PET) wastes using free and immobilized PET hydrolases. We aim to obtain biocatalysts with enhanced thermostability, and we will take advantage of all recent works where protein engineering was used to improve the stability and catalytic efficiency of these enzymes, thus increasing the competitiveness of this recycling process.
Programme: WooBAdh
Public web page: Not specified
Programme: IBG-1
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: IBG-1
Public web page: Not specified
Programme: IBG-1
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Start date: 12th Aug 2023
End date: 12th Aug 2023
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
IntraCellular Pathway Modeling at KTH
Programme: Independent Projects
Public web page: https://github.com/icpm-kth
Transcription bursting and stochastics
Programme: Thermodynamics and kinetics for Biology
Public web page: Not specified
Start date: 24th Jun 2023
End date: 24th Jun 2023
Programme: Era CoBioTech
Public web page: https://www.ufz.de/cell4chem/
Start date: 1st Jul 2021
End date: 30th Jun 2024
The project is aimed at integrated analysis of multi-omics TCGA data. We are going to use multiSOM approach.
Programme: TCGA-reanalysis
Public web page: Not specified
Test data amaizing
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: Metabolic Modeling
Public web page: Not specified
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 ...
Programme: BlueBio ERA-NET COFUND
Public web page: https://aquahealth-project.com/
Start date: 1st May 2020
End date: 30th Apr 2023
Programme: Independent Projects
Public web page: Not specified
LIMAQUA results in an innovative process for converting and recirculating aquaculture side-streams (sludge and wastewater) in algae (Galdieria sulphuraria)-based feed production for aquacultures. In conventional aquaculture, feed production is responsible for 50% of greenhouse gas (GHG) emission. The aim is to substantially reduce GHG emission by considering geographic and site-specific characteristics (temperature, sunshine duration etc.) and to design site-specific phototrophic or heterotrophic ...
Programme: Independent Projects
Public web page: https://www.foscera.net/en/foscera/projects/climaqua.htm
Programme: Independent Projects
Public web page: Not specified
Project Overview
Databases of biomedical knowledge are rapidly proliferating and growing, with recent advances (such as the RTX-KG2 knowledge-base that we have recently developed; (Wood et al. 2022)) increasingly focusing on integration of knowledge under a standardized schema and semantic layer (i.e., controlled vocabularies for types of concepts and types of relationships, for example, the Biolink standard (Unni et al. 2022)). The rise of standardized knowledge-bases sets the stage for the ...
Programme: Independent Projects
Public web page: https://github.com/RTXteam/RTX
Start date: 1st Jan 2020
End date: 28th Nov 2023
Test
Programme: 2017 Upload Test
Public web page: Not specified
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 ...
Programme: FAIRDOM
Public web page: Not specified
Programme: Independent Projects
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This 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 Germany. ...
Endometriosis research done by the Griffith lab (MIT) and the Goods lab (Dartmouth)
Programme: Independent Projects
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Trabajo de Fin de Master
Programme: Independent Projects
Public web page: Not specified
Programme: Metastasis Network
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: COMBINE (Computational Modeling in Biology Network)
Public web page: https://multicellml.org/
Programme: COMBINE (Computational Modeling in Biology Network)
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Up-regulation of glycolytic flux (glucose to lactate conversion), also known as the “Warburg effect”, has been associated with 90% of cancers. We implemented a systems biology approach in order to improve the overall understanding of the “Warburg effect” as well as identifying drug targets within the glycolytic pathway.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
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: 30th Sep 2021
supplementary materials
Programme: Independent Projects
Public web page: Not specified
Developing a placenta on a chip
Programme: Independent Projects
Public web page: https://www.iplacenta.eu/
Start date: 1st Jan 2018
End date: 31st May 2022
Programme: Independent Projects
Public web page: Not specified
This work aims to identify the biochemical pathways of THP-1 human monocytes infected by different Leishmania infantum clinical isolates from patients with either resistance or with TF outcome, using whole cell differential Mass Spectrometry proteomics. Network enrichment analysis was adopted to integrate the transcriptomics and the proteomic results of infected cells studies. Transferrin Receptor C and Nucleoside Diphosphate Kinase 3 were discovered as overexpressed proteins in THP-1 cells ...
Programme: Independent Projects
Public web page: Not specified
The placenta remains the key to maternal diseases such as Pre-eclampsia (PE) and Intrauterine growth restriction (IUGR), however the pathophysiology of these disorders remains elusive. The aim of this study is to characterize the key proteomic variations between PE and IUGR, to better understand the pathoetiology of these diseases.Term placentas each were collected from PE, IUGR pregnancies, and age and BMI matched healthy controls. Quadrupole-orbitrap mass spectrometer was used in data dependent ...
Programme: iPlacenta: A European Union Horizon 2020 innovative training network (ITN)
Public web page: Not specified
Placental dysfunction has been associated with various pregnancy complications leading to both maternal and fetal death and long-term consequences, however, the placenta is one of the least studied organs within the human body. In this pilot study, protein signature of three healthy placentae was measured using label free quantification mass spectrometry. Each placenta was sampled in five sample sites and three sub-anatomical regions. Differentially expressed proteins were identified considering ...
Programme: iPlacenta: A European Union Horizon 2020 innovative training network (ITN)
Public web page: Not specified
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Programme: This Project is not associated with a Programme
Public web page: Not specified
The project "INtegrative COllaborative modeling in systems MEdicine" aims at connecting different heterogenous datasets and individual models within systems medicine.
Programme: e:med
Public web page: Not specified
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. ...
Programme: CoolWine
Public web page: Not specified
The main idea of MIX-UP (MIXed plastics biodegradation and UPcycling using microbial communities) is to showcase a novel approach for plastic recycling and therefore addresses one of the greatest challenges of our time: the establishment of a circular (bio)-economy for plastics. The continuing demand for plastic products, the lack of appropriate recycling and the ubiquitous pollution of the environment with plastic waste pose a global challenge. An ambitious vision and considerable efforts are ...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: https://www.mix-up.eu/
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Corona virus epidemic. The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that ...
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Start date: 1st Mar 2020
End date: 24th Mar 2023
In this proposal, we aim the sequential multivalorization of apple pomace towards the extraction of polyphenolics, the production of enzymes and its biological conversion into acetone-butanol-ethanol (ABE)
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 ...
Programme: ERASysAPP
Public web page: Not specified
Storage of thermophysical properties (e.g. density, viscosity, thermodynamic activity of water, conductivity) using Chemical Markup Language (CML).
Programme: This Project is not associated with a Programme
Public web page: Not specified
Programme: ERNEST - European Research Network on Signal Transduction
Public web page: Not specified
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
What is PlaSMo? PlaSMo stands for Plant Systems-biology Modelling Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.
Our aims
To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost
To represent these models in a declarative XML-based format, which is closer to the systems biology standard SBML To evaluate the behaviour ...
Programme: SynthSys
Public web page: Not specified
This project aims to characterise the mechanisms through which microRNAs and small non-coding RNAs act to regulate cellular processes focusing on Naïve CD4 T cell activation and viral replication - namely HIV - and to explore their potential use as a therapeutic co-adjuvant agents or targets.
Programme: RNA Systems Biology Lab
Public web page: http://flysmals.campus.ciencias.ulisboa.pt
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 ...
Programme: Era CoBioTech
Public web page: https://www.cobiotech.eu/call-information
Start date: 1st Apr 2018
End date: 31st Mar 2021
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.
Programme: SynthSys
Public web page: https://faculty.washington.edu/takato/
to complete
Programme: Independent Projects
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 ...
Programme: Independent Projects
Public web page: https://digitallifenorway.org/gb/projects/inbiopharm
The GMDS project group bundles activities for health-related FAIR data infrastructures in the fields of biomedical research, clinical data management and medical informatics in Germany. It aims at providing a platform for information exchange about best practice for and implementation of FAIR data management in these fields and constructing a network of FAIR data managements providers in these fields. Through bridging between providers and potential users of such data management platforms within ...
Programme: German Association for Medical Informatics, Biometry and Epidemiology (GMDS)
Public web page: https://gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukturen-fuer-die-biomedizinische-informatik/
Start date: 28th Feb 2019
End date: 27th Feb 2022
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.
Programme: Auromega
Public web page: https://digitallifenorway.org/prosjekter/auromega
We will systematically analyse large datasets of multiple types to: (i) identify key components affected by age or experimental perturbation; (ii) establish networks of interaction; (iii) develop dynamic computational models based on these networks; (iv) use model selection methods to discriminate between alternative network topologies and generate predictive models. To characterise the data, we will apply an ensemble of methods, including frameworks in R/Bioconductor and toolboxes connected via ...
Programme: Newcastle University Systems Modelling of Ageing
Public web page: Not specified
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 ...
Programme: ERASysAPP
Public web page: http://sysmetex.eu/index.html
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
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 ...
Programme: ERASysAPP
Public web page: Not specified
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 ...
Programme: Independent Projects
Public web page: http://www.mycosynvac.eu/
Programme: e:med
Public web page: http://www.mi.med.uni-goettingen.de/en/content/research/307.html
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 ...
Programme: ERASysAPP
Public web page: https://www.erasysapp.eu/calls/2nd-call/xylocut
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.
Programme: Independent Projects
Public web page: http://www.empowerputida.eu/
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 ...
Programme: ERASysAPP
Public web page: https://www.erasysapp.eu/calls/2nd-call/systeract
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Programme: LiSyM - Systems Medicine of the Liver
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 ...
Programme: LiSyM - Systems Medicine of the Liver
Public web page: https://livermetabolism.com
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.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.h-its.org/event/kinetics-on-the-move/
Multi-level mathematical modeling of erythropoiesis for optimized expansion of erythroid progenitor cells and improved treatment regimes
Programme: e:Bio
Public web page: Not 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.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Translating Systems Virology data into broad-spectrum antiviral Drugs
Programme: ERASysAPP
Public web page: Not specified
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 ...
Programme: Independent Projects
Public web page: http://www.icysb.se/
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 ...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
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
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 ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=163
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 ...
Programme: SysMO
Public web page: http://silicotryp.ibls.gla.ac.uk/wiki/Main_Page
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
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.
Programme: SysMO
Public web page: Not specified
As an Innovative Training Network (ITN) , our approach to bringing about innovation is via education. The 15 Early Stage Researchers that join our project will gain multidisciplinary and cutting-edge expertise from our hosting institutions and associated partners, which is required to manipulate biological catalysts for meeting tomorrow’s demanding challenges in sustainable production processes.
CC-TOP is focused on exploiting the potential benefits of C-C bond forming enzymes (“carboligases”) ...
Programme: EU Projects
Public web page: https://cc-top-itn.eu/
Start date: 1st Mar 2021
End date: 30th Mar 2024
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 ...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
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 ...
Programme: WooBAdh
Public web page: http://www.usc.es/biogroup/woobadh
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
The goal of the project is to establish a new biotechnological platform for the production of hydroxy-amino acids, since the current production of these important building blocks is very expensive. Enzyme engineering, systems biotechnology and metabolic engineering will be used in a synthetic biology approach.
Programme: SARCHI: Mechanistic modelling of health and epidemiology
Public web page: Not specified
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
We used the Neo4j graph database approach to integrate the content of the COVID-19 Disease Map diagrams to efficiently access, query and manage the content of these diagrams and enable communication with external resources, such as Reactome and Recon, that already provide support via a similar environment. This work complements the efforts on exploring COVID-19 disease mechanisms within the COVID-19 Disease Map Project.
Programme: C19DM-Neo4j
Public web page: Not specified
Start date: 1st Sep 2020
End date: 31st Dec 2022
Programme: Independent Projects
Public web page: Not specified
Collection of training material for SEEK/FAIRDOMHub
Programme: FAIRDOM
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Just a test
Programme: Independent Projects
Public web page: Not specified
Public web page: Not specified
This is a project for testing
Programme: NIBSys
Public web page: Not specified
BIODYNAMICS approach will aim to demonstrate that multipurpose microbial cell factories based on a standardized, modular plug-andplay synthetic biology pipeline are a real possibility for quicker, cheaper and more effective bioproduction. To this end, we will develop novel hybrid (data-driven and mechanistic) modelling and characterization methods and tools for advanced metabolic engineering biology. In particular, it will consider the design, implementation and analysis of optimal synthetic ...
Programme: Wellcome Trust Development Grant - Unshackling membrane proteins ...
Public web page: Not specified
Programme: M-era.Net 3D4D2
Public web page: Not specified
Start date: 9th Aug 2021
End date: 8th Aug 2024
LEADER: StU (prof. B. Klumperman)
PARTNERS: StU & SU
OBJECTIVES:
• Optimization of antimalarial drug encapsulation for fast release.
• Development of transmission blocking drug encapsulation for slow release.
DELIVERABLES:
**07.2022 D ...
Programme: M-era.Net 3D4D2
Public web page: Not specified
Start date: 1st Jul 2021
End date: 1st Jan 2024
LEADER: prof. L-M. Birkholtz
PARTNERS: UP & WITS & SU & StU
OBJECTIVES:
• Evaluation of the ability of the novel polymer-drug systems to kill the transmissible gametocytes.
• Validation using treatment of anopheline mosquitoes in a membrane feeding assay.
...
Programme: M-era.Net 3D4D2
Public web page: Not specified
Start date: 1st Jul 2021
End date: 30th Jun 2024
Programme: Independent Projects
Public web page: Not specified
This project collects and maintains minimum information metadata templates designed and used in the National NL-Bioimaging initiative. The templates are based on the REMBI standards and contribute to FAIR bioimaging data in the Netherlands, together with data management in the OMERO database.
Programme: NL-Bioimaging: FAIR-DM
Public web page: http://eurobioimaging.nl/
A project for the Digital Salmon use case in BT8121 - Transdisciplinary biotechnology - a Digital Life Norway course.
Programme: The Digital Salmon
Public web page: https://www.ntnu.edu/studies/courses/BT8121
WARNING: THIS IS A TEST PROJECT CREATED FOR TESTING THE UPLOAD TO FAIRDOMHUB USING seekr AND SEEK API
pISA-tree: Standard project directory tree
A set of batch files is used to create standard directory tree for research projects. Batch files are provided to make standardized nested directories in accordance with the ISA Abstract Model levels (Investigation/Study/Assay).
https://github.com/NIB-SI/pISA-tree
Linked resources:
- R support for pISA-tree DOI ...
Programme: NIBSys
Public web page: http://ablejec.nib.si/doc
Programme: Independent Projects
Public web page: Not specified
LEADER: UL (prof. J.C. Simon)
PARTNERS: UL & IPF & SU & StU
OBJECTIVES:
• Validation of biocompatibility of the drug delivery systems with the skin.
• Testing of the drug delivery into and through the skin.
DELIVERABLES ...
Programme: M-era.Net 3D4D2
Public web page: Not specified
Start date: 1st Jul 2021
End date: 30th Jun 2024
Programme: Independent Projects
Public web page: Not specified
Programme: MIT Superfund Research
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
BBSRC sLoLa grantThe spread of antimicrobial resistance (AMR) is a slow-moving pandemic that has been identified by the WHO as one of the top 10 threats facing humanity. Plasmids and other MGEs play a key role in the dissemination of AMR, but we have only a rudimentary understanding of the factors that determine if and how MGEs spread through microbial communities. It is generally assumed that bacterial immune systems are a major determinant, but existing studies are limited to only a few stand-alone ...
Programme: MultiDefence - sLoLa
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 ...
Programme: The Digital Salmon
Public web page: http://tinyurl.com/digisal
The project brings comprehensive study of diversity in Clostridium beijerinckii, solvent-producing species with potential use in industrial biotechnology.
Programme: Clostridium beijerinckii
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
Rationale: Individuals with a cancer predisposition due to a mutation in the paradigm tumor suppressor gene RB1, have a high risk to develop the childhood cancer retinoblastoma (Rb). Biopsies are not possible in Rb, before treatment selection. Heritable Rb patients have also a high risk to develop other types of second primary, either childhood or adult, malignancies (SPMs), notably sarcomas and melanomas. Remarkably, SPMs are now the leading cause of death in heritable-Rb-survivors. Unfortunately, ...
Public web page: Not specified
LEADER: IPF (prof. A. Lederer)
PARTNERS: IPF & StU
OBJECTIVES:
• Determination of stability, degradation and drug release kinetics.
• Mathematical modelling of response to treatments of infectious diseases.
DELIVERABLES
10.2022 M 3.1 ...
Programme: M-era.Net 3D4D2
Public web page: Not specified
Start date: 1st Jul 2021
End date: 30th Jun 2024
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.
Programme: Disease Maps
Public web page: http://doi.org/10.17881/covid19-disease-map
Investigation regarding the impact of periportal steatosis on selected parameters of drug metabolism.
Programme: Experimental Transplantation Surgery
Public web page: https://qualiperf.de/
Programme: Impact of hepatic perfusion on drug metabolism
Public web page: Not specified
Start date: 1st Apr 2020
Programme: M-era.Net 3D4D2
Public web page: Not specified
Start date: 1st Jul 2021
End date: 30th Jun 2023
Cells of P. cordatum adapted to growth at 20 °C and constant light:dark conditions were shifted to growth at 26 °C and 30 °C, respectively, with similar illumination conditions. During exponential and stationary growth, cells were collected for transcriptomic, proteomic and metabolomic analyses.
Programme: Independent Projects
Public web page: Not specified
experimental data; middle ear transfer functions
Programme: Independent Projects
Public web page: https://www.ercd.net
By intelligent use of existing registries and health data, DeCipher aims to develop a data-driven framework to provide a personalized time-varying risk assessment for cancer initiation and identify subgroups of individuals and factors leading to similar disease progression. By unveiling structure hidden in the data, we will develop novel theoretically grounded machine learning methods for the analysis of large-scale registry and health data.DeCipher consists of an excellent multidisciplinary ...
Programme: Independent Projects
Public web page: https://www.simula.no/research/projects/decipher
Standard ASO design is based on the sequence complementarity of the oligo to its target. However, the degree of target knockdown that ASOs can achieve varies strongly between different ASOs having full complementarity to the target. To determine which factors affect the ASOs’ activity, Secarna has used a novel approach: the Company has designed and screened 51 multi-specific ASOs with a common target (IDO1, a gene involved in tryptophan metabolism), and varying numbers of diverse other targets ...
Programme: RNA-seq
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
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 ...
Programme: The Digital Salmon
Public web page: http://tinyurl.com/genosysfat
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 ...
Programme: The Digital Salmon
Public web page: http://www.nmbu.no/prosjekter/digisal
Assessing different tools for RDM
Programme: MPIB
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 ...
Programme: Era CoBioTech
Public web page: https://www.cobiotech.eu/call-information
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, ...
Programme: NIBSys
Public web page: http://www.nib.si/eng/index.php/systems-biology
Start date: 1st Dec 2017
End date: 1st Jan 2020
Programme: Independent Projects
Public web page: Not specified
FAIR data storage and annotation for LiceVault
Programme: Independent Projects
Public web page: https://www.digitallifenorway.org/research/licevault/
For plants, light is a signal that carries information about the environment, and a source of energy for photosynthesis. PHYTOCAL focuses on the interaction between phytochrome signalling and photosynthesis, and seeks to understand fundamental processes that make carbon (C) and nitrogen (N) resources available for plant growth. These unexplored connections underlie biomass production and plasticity, which contribute significantly to yield variability in the field.
Programme: SynthSys
Public web page: http://hallidaylab.bio.ed.ac.uk/node/1
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. For more information you may visit our project website at ...
Programme: Independent Projects
Public web page: https://irhythmics.med.uni-rostock.de/
This is a project servicing Anna Maria Colangelo of UNIMIB to make models for neural differentiation and the effects of NGF addition and NGF withdrawal
Programme: ISBE.NL service programme
Public web page: Not specified
This is the FAIRDOM hub for the Make Me My Model part of ISBE.NL. Various models for ISDBE.NL clients are stored here.
Programme: Innate immunity
Public web page: http://isbe.nl/
The Integrated Platform for Endocrine Disruptor Risk Assessment (SNAPPER) project will propose solutions based around three core philosophies: Integrated Science: Integration of knowledge from a complete pipeline of systems biology into a holistic yet mechanistic framework that enhances the understanding both of endocrine biology and of adverse effects due to externally induced disruption of the body’s endocrine system. The pipeline includes in vivo, in vitro, and in silico data resulting both ...
Programme: This Project is not associated with a Programme
Public web page: Not specified
CLIMAQUA results in an innovative process for converting and recirculating aquaculture side-streams (sludge and wastewater) in algae (Arthrospira platensis)-based feed production for aquacultures. In conventional aquaculture, feed production is responsible for 50% of greenhouse gas (GHG) emission. The aim is to substantially reduce GHG emission by considering geographic and site-specific characteristics (temperature, sunshine duration etc.) and to design site-specific phototrophic or heterotrophic ...
Programme: CLIMAQUA
Public web page: https://www.foscera.net/en/foscera/Projects/CLIMAQUA.htm
Start date: 1st Jun 2021
End date: 31st May 2024
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 ...
Programme: Era CoBioTech
Public web page: https://www.cobiotech.eu/call-information
Identification of genomic variation in perennial ryegrass
Programme: ILVO test
Public web page: Not specified
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 ...
Programme: dCod 1.0: decoding systems toxicology of cod
Public web page: http://www.uib.no/en/dcod
Programme: ILVO test
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
From thermodynamics through kinetics and non equilibrium thermodynamics to control analysis
Programme: Thermodynamics and kinetics for Biology
Public web page: http://sysba.nl/
Start date: 8th Apr 2021
End date: 8th Apr 2031
Chapter on non equilibrium thermodynamics. The chapter discusses both phenomenological and mechanistic non equilibrium thermodynamics. The phenomenological part has as asset compared to earlier treatments that it also considers the phenomenological stoichiometry as a parameter that may be adjusted by systems to attain optimal performance. In the mechanistic part, this feature of variable stoichiometry and 'slips' as well as redistribution of fluxes over parallel branches of metabolism is discussed. ...
Programme: Thermodynamics and kinetics for Biology
Public web page: http://sysba.nl/
Start date: 8th Apr 2021
End date: 8th Apr 2031
A chapter on generalized thermodynamics. The chapter is not specifically about biology although it uses many examples in biology due to the richness of the topic. It deals with the first and second law of thermodynamics, catalysts, and engines. This includes heat engines, heat pumps, and protonmotive ATP synthase.
Programme: Thermodynamics and kinetics for Biology
Public web page: http://sysba.nl/
Start date: 8th Apr 2021
End date: 8th Apr 2031
Most systems biology deals with Life as we know it on this planet (Earth). This project will focus on how (nonsynthetic) Life may differ from mainstream Life. The ultimate focus thereby rests on extraterrestrial Life, but for lack of definitive evidence of this, the project studies Life found under conditions that may be similar to extraterrestrial conditions enabling Life. The focus is herewith on the systems biology in remote environments on Earth. The project deals both with the systems cell ...
Programme: ISBE.NL service programme
Public web page: http://isbe.nl/
Start date: 8th Apr 2021
End date: 8th Apr 2035
Investigation 1: An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure ...
The purpose of this project is to exchange public and private research data that is not attached to "normal" projects together with SDBV via the FAIRDOMHub.
Programme: Independent Projects
Public web page: Not specified
to test the api
Programme: Independent Projects
Public web page: Not specified
The main goal of this project is to create a null-CO2 foot-printing and robust biotechnological platform based on microbial consortia to produce sustainable bio-based compounds using CO2 and light as the sole sources of carbon and energy, respectively.
Programme: Independent Projects
Public web page: Not specified
The data that support the findings of this study are available from the corresponding author upon reasonable request.
Programme: JUANGMC
Public web page: https://mail.qq.com/cgi-bin/frame_html?sid=Ae7IqEp1D610uBh5&r=4617f5b0ff0ad873c810afdb0ee5e6be
Programme: Public
Public web page: Not specified
Programme: iPlacenta: A European Union Horizon 2020 innovative training network (ITN)
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
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 ...
Programme: Era CoBioTech
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Programme: NORCE Environment Test
Public web page: Not specified
BioCreative VII
Programme: Independent Projects
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 ...
Programme: NIBSys
Public web page: https://indie.cebitec.uni-bielefeld.de/
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.
Programme: Hellenic Foundation for Research and Innovation - Supporting academic Staff and Researchers
Public web page: Not specified
Start date: 24th Feb 2020
End date: 23rd Aug 2023
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
to complete
This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.
Programme: NIBSys
Public web page: http://projects.nib.si/rnainval/
Start date: 1st Nov 2014
End date: 31st Oct 2017
Programme: Independent Projects
Public web page: Not specified
Programme: Aneurinibacillus thermoaerophilus CCM 8960 metabolic pathways model
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
The New Medicines for Trypanosomatidic Infections - NMTrypI project aimed at obtaining new candidate drugs against Trypanosomatidic infections with appropriate efficiency from the lead phase to the final preclinical phase that are more accessible to patients.
Programme: Drug development for neglected parasitic diseases
Public web page: https://fp7-nmtrypi.eu/
Start date: 1st Feb 2014
End date: 31st Jan 2017
In the CoVIDD project, we aim at unravelling interactions of viral proteins with the cellular factors and the host pathways involved in SARS-CoV-2 infection by a combination of modern technologies, genomics, proteomics, structural biology, chemoinformatics and drug discovery. To effectively search for drugs that could modify viral replication we need to know what human proteins and viral proteins interact. Thus, a comprehensive virus-host protein interaction network will help us to identify the ...
Programme: This Project is not associated with a Programme
Public web page: Not specified
Programme: Cancer drug discovery preclinical research
Public web page: Not specified
tba
Programme: iPlacenta: A European Union Horizon 2020 innovative training network (ITN)
Public web page: Not specified
Rhodolive
Programme: Era CoBioTech
Public web page: Not specified
To systematically evaluate the general efficacy of nape acupuncture combined with rehabilitation training for the treatment of post-stroke dysphagia and in the recovery of swallowing function.
Programme: The Effect of Nape Acupuncture Combined with Rehabilitation Training on Dysphagia After Stroke
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
Systems Biology as we know it is mostly terrestrial, i.e. it deals with mainstream Life on planet Earth. There are two exceptions. One is synthetic systems biology that designs other types of Life. The other exception studies the systems that may exist on other planets, or that exists at remote locations on planet Earth. Xenosystems Biology refers to the latter exception. At present this runs projects that deal with Life as found at remote locations on Earth, which are held representative of other ...
Programme: ISBE.NL service programme
Public web page: http://isbe.nl/
Start date: 8th Apr 2021
End date: 8th Apr 2031
Old versions of files that cannot be deleted because they have been published.
Programme: ISBE.NL service programme
Public web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Four ppt lecture files that are part of a UvA course on 'How to design an alien'. They correspond to four lectures given by Hans V. Westerhoff, September - October 2021
Programme: ISBE.NL service programme
Public web page: Not specified
ONT+Illumina bacterial genome assembly project
Programme: Independent Projects
Public web page: Not specified
Oxidative stress is an important mechanism of cerebral ischemia-reperfusion injury. Ferroptosis caused by iron overload after cerebral ischemia-reperfusion is considered a common cause of oxidative stress. A large number of recent studies have shown that electroacupuncture (EA) can regulate the expression of inflammatory factors, and the use of electroacupuncture preconditioning can produce a protective effect, which can reduce injury after cerebral ischemia and reperfusion. We aimed to assess ...
Public web page: Not specified
ORHIZON IS A PROPOSAL FOR A HORIZON EUROPE PROJECT (RIA) AIMED AT DELIVERING SOLUTIONS FOR ROOT AND RHIZOSPHERE TRAITS BASED BREEDING IN THE CONTEXT OF LOW INPUT AGRICULTURE AND CLIMAT CHANGE
Programme: Independent Projects
Public web page: Not specified
Study on the mechanism of acupuncture combined with treadmill in treating apoplexy
Public web page: Not specified
With aging comes cellular senescence, and (multi-)morbidity. Cellular senescence is a key driver of an interconnected disease network including cancer and stroke. We wish to utilize systems modeling and bioinformatics, learning from omics and other lab data, to design and develop a biomarker + software kit with a focus on measuring and interpreting senescence-related signatures for precise (and early) diagnosis, prognosis, and, ultimately, therapy, of pancreatic cancer and ischemic stroke/thromboembolism. ...
Programme: Independent Projects
Public web page: https://www.sbi.uni-rostock.de/research/projects/detail/66
Collection of coastal data via telemetry and sensors
Programme: Independent Projects
Public web page: https://www.afbini.gov.uk
genetical innovation
Programme: Independent Projects
Public web page: Not specified
Programme: Testing 1, 2, 3
Public web page: Not specified
Programme: Supplemental Data for "Why did the eyewall replacement cycle in Trami terminate rapidly? "
Public web page: Not specified
Start date: 29th Apr 2021
End date: 31st Aug 2021
Programme: Cancer drug discovery preclinical research
Public web page: Not specified
The Hippo signalling is a metabolic control pathway of cells proliferation and apoptosis, thus represents an emerging topic in tumour suppression regulation and regenerative medicine. This pathway is activated by anti-proliferative signals which come from the extracellular environment received by membranes proteins. In the cytosol compartment, the pathway is regulated by a phosphorylation cascade of four main proteins with Serin-Treonin kinase activity. At the end-point of this cascade the ...
Programme: Cancer drug discovery preclinical research
Public web page: Not specified
OBJECTIVE: To summarise an overview of existing evidence between Chinese medicine and polycystic ovary syndrome (PCOS),and to evaluate the strength and validity of these associations. METHODS: We retrieved systematic evaluations and meta-analyses of randomized controlled trials(RCT) evaluating Chinese herbal interventions in polycystic ovaries, including the use of decoctions or Chinese patent medicines. The quality of these systematic evaluations was evaluated using AMSTAR2 tools, while ovulation ...
Programme: An overview of systematic reviews of treatment of polycystic ovary syndrome with Chinese medicine
Public web page: Not specified
Start date: 1st Dec 2020
End date: 1st May 2021
Programme: e:med
Public web page: https://kohlbacherlab.org
Centre for Digital Life Norway (DLN) project 'OXYMOD - Optimized oxidative enzyme systems for efficient conversion of lignocellulose to valuable products'
Programme: DLN - OXYMOD
Public web page: https://digitallifenorway.org/gb/projects/oxymod
Programme: Covid-19 disease map - Bioinformatics analysis and computational modelling
Public web page: Not specified
Start date: 1st May 2020
In this project, we integrate COVID19 Disease Maps curated regulatory information in a macrophage logical model. This allows logical simulations of the effects of acute inflammation caused by the SARS-CoV-2 virus, both in general and in a cell-specific perspective. Moreover, understanding the regulatory network behavior of macrophages following infection opens new ways to test and predict drug and drug combination effects, as a first step towards the development of new treatments.
Data and experimental methods to support the work in the following paper:
Establishing Consensus Annotation for the Hallmarks of Cancer, 2020, Yi Chen, F.J.Verbeek and K.Wolstencroft, in submission
Programme: Hallmarks of cancer
Public web page: Not specified
In this project, the involved partners are trying to develop the knowledge base that will enable the breeding of new potato varieties, tolerant to multiple environmental stressors.
Programme: NIBSys
Public web page: https://adapt.univie.ac.at/
Start date: 1st Jul 2020
End date: 30th Jun 2024
Modelling COVID-19 epidemics : the training course organized by ISBE-NL, ELIXIR-LU, and EOSC-Life
Programme: Independent Projects
Public web page: https://elixir-luxembourg.org/events/2020_11_30_COVID19_modelling_training
Start date: 30th Nov 2020
End date: 31st Jan 2021
Programme: Skin Ageing and Senescence
Public web page: Not specified
Valorization of mussel processing water into bioplastics
Programme: FAIR Biocatalysis
Public web page: Not specified
Programme: FAIR Biocatalysis
Public web page: Not specified
Programme: FAIR Biocatalysis
Public web page: Not specified
optogenetic control of plant signaling
Programme: Systems Brewology
Public web page: Not specified
Programme: Von Hippel-Lindau (VHL) Tumor Suppressor research programme
Public web page: Not specified
Start date: 2nd Jan 2020
End date: 1st Apr 2025
NA
Hidden project
Programme: Test program
Public web page: Not specified
Programme: This Project is not associated with a Programme
Public web page: Not specified
Testing project creation
Programme: Test program
Public web page: Not specified
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Collaboration with Miltos Tsiantis for reconstructing RCO transcriptional regulation
improvement of PULSE, derivation of tools for ontogenetic control of interesting pathways
Modulation of light, temperature and time networks using prime editing and mathematical modelling
Test project to see Fairdom capabilities.
Programme: Test program
Public web page: Not specified
Programme: Test program
Public web page: Not specified
Start date: 1st Jul 2020
End date: 4th Sep 2020
Designing 3D metamaterials
Programme: 3DMM2O
Public web page: https://www.3dmattermadetoorder.kit.edu/metamaterials.php
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.
Programme: Newcastle University Systems Modelling of Ageing
Public web page: Not specified
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.
Programme: Newcastle University Systems Modelling of Ageing
Public web page: Not specified
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 ...
This project gathers all biomics projects submitted to biomics.pasteur.fr
Programme: Biomics Platform
Public web page: https://biomics.pasteur.fr/projects
Using MCA to understand which enzymes have higher impact in Acetyl-coa production in P. putida
Programme: Pseudomonas putida metabolism
Public web page: Not specified
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: Not specified
Programme: DiaPhotosynth
Public web page: Not specified
Start date: 3rd Feb 2020
End date: 31st Aug 2023
Programme: DiaPhotosynth
Public web page: Not specified
Start date: 1st Sep 2020
End date: 31st Aug 2023
DeepHyperSpec: Combining spectral and image information in the analysis of hyperspectral imaging data Infrared microspectroscopic imaging is a new technique for rapid, label-free and automated diagnosis of various types of cancer. The technique is expected to enter clinical routine analysis in the years coming.
Programme: BioSpec
Public web page: Not specified
Understanding the molecular basis of diseases can shed light into new methods to manage and cure diseases. Exploring the common or unique molecular mechanisms among a group of diseases may enhance our understanding of each disease or uncover therapeutic approaches that can be effective in multiple diseases. In this project we develop methods that use biological networks and known gene-disease associations to identify common molecular mechanisms associated across multiple diseases.
Testing stuff
Programme: Data_Management_lessons
Public web page: Not specified
Centre for Environment-friendly Energy Research Research in the past decade has shown that biomass conversion into energy fuels and other value added products, in contrast to traditional refineries, requires highly integrated versatile plants. In most cases, such plants will need to produce a portfolio of products that together secure economic sustainability. The Centre for Environment-friendly Energy Research aims to develop innovative technology and support industries to realize economic and ...
Programme: BioSpec
Public web page: Not specified
Bioconversion of low-cost fat materials into high-value PUFA-Carotenoid-rich biomass The project aims at upgrading Norwegian animal slaughter fat by-products to high-value fatty acids by fungal fermentation processes.
Programme: BioSpec
Public web page: Not specified
generation of a toggle switch based on a non-cooperative network
Programme: BioZEment
Public web page: https://digitallifenorway.org/gb/projects/biozement-2-0
A project created for demonstration
Programme: This Project is not associated with a Programme
Public web page: Not specified
Programme: RNA Systems Biology Lab
Public web page: Not specified
Programme: RNA Systems Biology Lab
Public web page: Not specified
This is a placeholder
Programme: Interface MIAPPE / BrAPI
Public web page: Not specified
ERACoBioTech project
Programme: Era CoBioTech
Public web page: https://www.ntnu.edu/c1pro
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
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.
Programme: Druglogics
Public web page: http://www.colosys.org/
Programme: LiSyM - Systems Medicine of the Liver
Public web page: Not specified
Web application developed using RStudio-Shiny for outreach. Incorporates information, videos and images, worksheets and simulations surrounding breast cancer development and therapy. Incorporates NetLogo simulation from "Outreach - Simulation of breast cancer development using an agent based modelling approach" project.
Programme: Breast Cancer Simulation
Public web page: Not specified
testing fairdomhub
Programme: GPSLab testing Programme
Public web page: Not specified
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
NAD phylogeny
Programme: This Project is not associated with a Programme
Public web page: Not specified
Start date: 30th May 2019
please complete description
Programme: Independent Projects
Public web page: Not specified
This projects seeks to uncover how phytochrome signalling modulates leaf architecture
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
Programme: Independent Projects
Public web page: Not specified
BIOMICRO PROJECT TEST
Programme: KOCH
Public web page: Not specified
Programme: Thesis AHG 2019
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.
This investigation is published under the CC BY 4.0 license.
Programme: NIBSys
Public web page: Not specified
Extremophiles metabolsim
Programme: Independent Projects
Public web page: Not specified
Programme: The Novo Nordisk Foundation Center for Biosustainability
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 ...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Research group of Guillaume Lobet
Programme: Earth and Life Institute
Public web page: http://www.rosi.science
Glycon proposal preparation
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
MicroRNAs are a recently discovered group of factors that control cell behaviour. There are thousands of microRNAs, but specific ones control the behaviour of cartilage cells and have key roles in osteoarthritis. Changing the level of a single microRNA can alter osteoarthritis, but we know that several microRNAs change during disease. The group has identified four microRNAs which have key roles in cartilage. This programme seeks:
to show that these microRNAs have a role in osteoarthritis in the ...
Programme: Newcastle University Systems Modelling of Ageing
Public web page: http://dunhillmedical.org.uk/project/david-young-programme/
Detection of pathogenic mutation in the patients with non-coronary heart diseases
Programme: Laboratory of the /cytoplasmic/ heredity (Institute of Genetics and Cytology, NAS Belarus)
Public web page: Not specified
Programme: Proteome Centre Tuebingen
Public web page: Not specified
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 ...
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
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 ...
Programme: NIBSys
Public web page: http://projects.nib.si/hyp/
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 ...
Programme: Druglogics
Public web page: https://www.ntnu.edu/health/druglogics
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.
Programme: Druglogics
Public web page: http://www.ntnu.edu/crossover-research
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 ...
Programme: Independent Projects
Public web page: https://www.nwo.nl/en/research-and-results/research-projects/i/75/29175.html
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.
Programme: SAFE-Aqua
Public web page: http://safeaqua-project.net
Programme: Mathematical modelling of the morphological transition of Pseudomonas aeruginosa
Public web page: Not specified
EPSRC project with Exeter, SynthSys and EPCC
Programme: SynthSys
Public web page: Not specified
EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015. "TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."
Programme: SynthSys
Public web page: http://timing-metabolism.eu/
Programme: LiSyM - Systems Medicine of the Liver
Public web page: https://www.fairdomhub.org/events/96
Public showcase and collection of training material
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: http://www.denbi.de
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
WURSynBio
Programme: This Project is not associated with a Programme
Public web page: Not specified
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 ...
Programme: ERASysAPP
Public web page: https://www.bioprocess.tu-berlin.de/menue/research/projects/leanprot/
tba.
Programme: Druglogics
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
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. ...
Programme: ERASysAPP
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
Programme: Model repository for M4 (Make Me My Model) clients of ISBE
Public web page: Not specified
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
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
Programme: This Project is not associated with a Programme
Public web page: Not specified
This project provides a space for storing, annotating and publishing Systo models.
Programme: Independent Projects
Public web page: Not specified
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) ...
Programme: e:Bio
Public web page: http://www.sulfosys.com/
GMO free systems optimization of wine yeast for wine production by massive scale directed evolution
Programme: ERASysAPP
Public web page: Not specified
Designer microbial communities for fermented milk products: A Systems Biology Approach
Programme: ERASysAPP
Public web page: Not specified
ErasysApp Funders
Programme: ERASysAPP
Public web page: Not specified
Systems biology of bacterial methylotrophy for biotechnological
Programme: ERASysAPP
Public web page: http://www.sintef.no/projectweb/metapp/
Comparative Systems Biology: Lactic Acid Bacteria
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=57
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 ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=53
Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=54
"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 ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=55
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 ...
Programme: SysMO
Public web page: http://www.psysmo.org/
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/
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/
Gene interaction networks and models of cation homeostasis in Saccharomyces cerevisiae
Programme: SysMO
Public web page: http://www.translucent-network.org/
Programme: SysMO
Public web page: http://www.sysmo.net/