Programmes

Biomedizinische Informatik und Data Science

Biorefineries are set to become an important agent in the shift towards a circular economy due to their potential to valorize organic wastes into marketable products. Anaerobic fermentations yielding volatile fatty acids (VFA) are a key process in this biorefinery paradigm as VFA act as intermediates between the organic wastes and the final biorefinery products. However, the development of a new bioprocess based on mixed-culture fermentation is an extremely challenging task. Targeting the desired ...

Creative Biolabs has developed proprietary procedures for Hi-Affi™ recombinant antibody production, with optimized library construction and screening processes using hybridoma or phage display technology.

This Programme is created as a repository for the Virtual Human Platform for Safety Assessment (VHP4Safety) project.

The recent COVID19 pandemic infection has undisclosed long-standing issues in the translation of drugs from animals to humans or vice-versa. Nearly 75% of emerging human infections worldwide originated from animals; existing drugs for human and animal (H&A) vector-borne diseases (VBD) are scarce, with limited efficacy, toxicity, and finite resources. Emerging environmental problems in pharmaceutical use/manufacturing increase attention in the field. The two drug pipelines are developed ...

NL-BioImaging AM is a distributed research infrastructure aimed at promoting progress in the most cutting edge microscopy technologies and providing open access to these technologies to a broad community of academic and industrial users. All Netherlands bio(medical) microscopy centers participate.

FAIR (Findable Accessible, Interoperable and Reusable) data management is a challenge for the optical microscopy community due to a high diversity in participating research fields and methodologies, ...

The Snoep Lab’s core research efforts are in Computational Systems Biology; a combined experimental, modeling and theoretical approach to quantitatively understand the functional behavior of Biological Systems resulting from the characteristics of their components. Our main focus is on metabolism, of human pathogens such as Plasmodium falciparum, Mycobacterium tuberculosis, but also of breast cancer cell lines, and on modelling disease states such as glucose homeostatis in type 2 diabetes, and ...

Synthetic Biology and Biosystems Control Lab (SB2CL). We focus our research on applications of systems engineering and control to Systems and Synthetic Biology, and Bioprocesses estimation and control. Our group is member of the Institute for Automatica and Industrial Informatics (ai2) at the Universitat Politècnica de València (Spain).

Our main interests are in:

• Dynamic regulation of gene expression for control of variability in gene expression and regulation of novel routes to obtain complex ...

Background. RB1 is a paradigm gene for heritable cancer. Almost all RB1 mutation-carriers develop retinoblastoma (heritable-Rb-patient) during childhood and many heritable-Rb-survivors develop second primary malignancies (SPMs; notably sarcomas and melanomas) throughout life, which are often fatal. To date, no standard protocols are available for early detection of SPMs. Recently, blood-based cancer tests have opened up encouraging new possibilities for surveillance. We have developed novel ...

RNA-Seq projects from SECARNA

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.

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 ...

The principal research aim of iPLACENTA is to improve our ability to study, model and visualise the placenta. This will contribute to developing diagnostic tests and therapies for pregnancy complications such as preeclampsia and intrauterine growth restriction (IUGR). Placental defects are thought to be the cause of many major pregnancy complications, such as preeclampsia and intra-uterine growth restriction. Preeclampsia affects between 5 and 8 out of every 100 pregnant women and claims the lives ...

The Deutsche Forschungsgemeinschaft (DFG) is the self-governing organisation for science and research in Germany. It serves all branches of science and the humanities. In organisational terms, the DFG is an association under private law. Its membership consists of German research universities, non-university research institutions, scientific associations and the Academies of Science and the Humanities.

Work of the Gygli group...

This is research programme towards the production of a collection of Chapters for a book on thermodynamics, kinetics and systems biology that is being written by Hans V. Westerhoff. This book will be a successor to 'Thermodynamics and control of biological free-energy transduction, Elsevier, Amsterdam (1987) by Westerhoff, H.V. & Van Dam, K.

This is the home programme for the Infrastructure Systems Biology @ NL activity of assisting clients with systems biology

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. 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 rate, pregnancy ...

Infection management requires the development of research programs that operate with the logic of network medicine for implementation of complex strategies to make the best use of availability of "omics-based" technologies, development of systems diagnostics, possibility of using innovative (and at the same time extremely expensive) drugs. This study group is composed by many experts with high knowledge in infectious diseases and “omics” competences at at Italian National Institute for Infectious ...

This page is dedicated to the bioinformatics analysis and computational modelling related to Covid-19 disease map pathways.

We develop macrophage logical models to represent the activation/polarization of this immune cell. Interactions are manually curated with available macrophage literature. The models are mainly built and analyzed in GINsim. But other resources are used to integrate specific pathways or small modules (CasQ software) and to analyze the logical models (CoLoMoTo Notebooks).

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 is personal project

Inactivation of the VHL tumor suppressor gene is linked to the development of several different tumor types in humans, including hemangioblastomas of the retina and central nervous system, clear cell renal carcinoma, pancreatic cysts, pheochromocytoma. Biochemical studies revealed that pVHL interacts with several different proteins serving as a multipurpose adaptor protein that engages in multiple protein-protein interactions to control diverse transcriptional-dependent and transcriptional-independent ...

IDPfun is an international consortium aiming to extend our knowledge on the functions of intrinsically disordered proteins (IDPs). Starting from available state of the art computational tools and databases, which have been mostly developed by IDPfun participants, it aims to drive a new level of IDP characterization.

This is a test programme, which will be used to learn how to use and evaluate Fairdom Hub for NORCE Environment's purposes, as part of the SIS-OMICS project.

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 ...

COST Action CA18133

BlueBio ERA-NET COFUND on the Blue Bioeconomy

The Hellenic Foundation for Research and Innovation is a new institution through which a profound reforming effort is being undertaken in the field of Research and Innovation in the country. The Organization supports unrestricted research (the systematic inquiry born of scientific curiosity) and new researchers by providing scholarships for doctoral candidates, as well as research projects for post-doctoral students, Researchers and Faculty Members. Through H.F.R.I., the research and academic ...

Bringing 3D Additive Manufacturing from the macroscale to the micro-, nano-, and eventually to the molecular scale and at applying these technologies

The aim is to bundle the information about the manifold of COVID-19 centered initiatives offering tools and studies.

The Disease Maps Project is designed as a large-scale community effort. It is a network of groups that work together in order to better understand disease mechanisms. The project exchanges best practices, share information, develop tools to make it easier for all the involved groups to achieve their goals.

ERA CoBioTech is an ERA-Net Cofund Action under H2020, which aims to strengthen the European Research Area (ERA) in the field of Biotechnology through enhanced cooperation and coordination of different national and regional research programs, promoting systems biology and synthetic biology as technology driversto speed up research and innovation in industrial biotechnology.

› By maximizing synergies between current mechanisms of biotechnology research funding in Europe; › By fostering the exchange ...

Using kinetic models to study the central carbon metabolism in pseudomonas putida, both for metabolite production and understanding the impact of certain perturbations.

Opening future biotechnological possibilities by revealing the acclimation and biogenesis of the photosynthetic apparatus in marine algae.

The primary objective of the project is to determine the molecular mechanisms that facilitate regulation and biogenesis of the photosynthetic machinery of the most significant group of eukaryotic phytoplankton, represented here by the model diatom Phaeodactylum tricornutum.

The main objective of the ERANET proposal Systems Biology Applications - ERASysAPP (app = application = translational systems biology) is to promote multidimensional and complementary European systems biology projects, programmes and research initiatives on a number of selected research topics. Inter alia, ERASysAPP will initiate, execute and monitor a number of joint transnational calls on systems biology research projects with a particular focus on applications - or in other words so called ...

Program for lessons data management

general working environment for the Genomics Platform

The Biospectroscopy and Data Modeling Group at the Faculty of Science and Technology is carrying out research related to spectroscopy in life and environmental sciences.

A study of the systems biology of innate immunity

The RNA Systems Biology Lab Programme compiles the different research projects developed in our lab. The RNA Systems Biology Lab is a collaborative research lab headed by PIs Margarida Gama-Carvalho and Francisco Pinto at the Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, and integrates the BioSystems and Integrative Sciences Institute (BioISI) Gene Expression and Regulation Group, headed by Margarida Gama-Carvalho. Our research brings together computational ...

This is a placeholder Programme for the future development of the interface Project. At the moment we are creating spaces and testing features.

Development of a NetLogo simulation and RStudio-Shiny web application surrounding cellular senescence for outreach. Aimed at GCSE/A-level students

Testing of FAIRDOMHUB functionality and APIs

testing access to fairdom hub documents. data files etc via the API in various programming languages

A small application which simulates the development of breast cancer

Plant development is strongly influenced by external light cues, yet we know very little of how this is mediated at a molecular level. This BBSRC funded project seeks to determine how phytochrome light receptor signalling connects with the developmental pathways to control plant architecture.

The objective of this project is to overcome current limitations for antibody production that are inherent to the extant immune system of vertebrates. This will be done by creating an all-in-one artificial/synthetic counterpart based exclusively on prokaryotic parts, devices and modules. To this end, ARISYS will exploit design concepts, construction hierarchies and standardization notions that stem from contemporary Synthetic Biology for the assembly and validation of (what we believe is) the ...

PhD Thesis of Angeles Hueso Gil

The GMDS (Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie) is the German Association for Medical Informatics, Biometry and Epidemiology and is the only scientific organization in this field in Germany. It is the official national member society within the EFMI and IMIA and closely cooperates with related scientific societies.

The coordinated project TREASURE has as main objective the development and evaluation of a modular treatment train comprising two lines operated in parallel to valorize and treat the wastewater (WW) produced in the fish-canning industry.

Biogroup will be responsible for the Sub-Project 1 TECHNOSALT "Unravelling salt and temperature effects on the performance of an integrated modular system for fish canning wastewater treatment and valorization" Its objective is the development and evaluation of ...

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 ...

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. ...

Modeling of presynaptic dopamine homeostasis

The computational identification of Zinc Finger genes in genomes. The computational identification of the DNA binding profile of Zinc Finger genes.

Earth and Life Institute at UCLouvain

Systems modelling molecular mechanisms of ageing

A storage of the data #for the first time

projects difference in non-chromosomal genomes of the alloplasmic lines of barley & detection of pathogenic mutations in the patients with non-coronary heart diseases through NGS using

This programme will provide infrastructure to several projects performed by the team of the proteome centre tuebingen. Our team and collaborators will be able to share/homogenise protocols, methods and raw data from genomics and proteomics measurements.

The DrugLogics initiative comprises a number of different subprojects, all geared towards the development of personalised medicine, or precision medicine

SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).

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

SBRC Nottingham focuses on the sustainable and economically viable production of platform/speciality chemicals through SynBio-engineered, gas fermenting microbes capable of using single carbon (C1) feedstocks.

This is the exchange platform of the COMBINE network.

COMBINE is an initiative to coordinate the development of various community standards and formats for computational models: BioPax, CellML, NeuroML, Synthetic Biology Open Language (SBOL), Systems Biology Graphical Notation (SBGN), Systems Biology Markup Language (SBML), Simulation Experiment Description Markup Language (SED-ML).

My lab studies how plants sense and respond to their environment. We specialise in signal integration. Learn more about what we do by exploring the web pages.

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.

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. The Digital Salmon will be an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted ...

The Collaborative Research Center / Transregio 124 Pathogenic fungi and their human host: Networks of Interaction - FungiNet studies the interaction of the human pathogenic fungi Candida albicans and Aspergillus fumigatus with their host using a Systems Biology approach. The yeast Candida albicans and the filamentous fungus Aspergillus fumigatus are by far the most important causes of life-threatening invasive mycoses in Europe. Despite the increasing incidence of these infections, the current ...

ISBE-Light provides M4 service (Make Me My Mode) where non modelers can request (assistance with) the making of a computational model of their biological system. These models are deposited here.

LiSyM (Liver Systems Medicine) represents a research network of German centers and institutions, brought together by a 20 Million Euro funding program of the German Government, in which mathematicians, modelers, pharmacologists, molecular biologists and clinical scientists work together to develop a Systems Medicine approach to study early and advanced liver disease. The aim of this unique research program is to acquire and use new experimental data and data from existing data bases to build ...

The goal of the dCod-project is to combine the competencies in environmental toxicology, biology, bioinformatics and mathematics across the traditional department boundaries, to create a deeper understanding of cods' adaptations and reactions to stressors in the environment. Building on the thoroughly studies and mapping of the cod genome at UiO and the long research traditions on cod at the Department of Biology at UiB, the dCod project will expand our knowledge with methods based on genomics; ...

FAIRDOM is establishing a support and service network for European Systems Biology. FAIRDOM is a joint action of ERA-Net ERASysAPP and European Research Infrastructure ISBE to establish a data and model management service facility for Systems Biology. Our prime mission is to support researchers, students, trainers, funders and publishers by enabling Systems Biology projects to make their Data, Operating procedures and Models, Findable, Accessible, Interoperable and Reusable (FAIR).

The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...

BioModelKit is a database for modular modeling, where modules describe the functionality of single biomolecular entities and their interactions with other molecules in terms of Petri nets. All modules adhere to the guidelines of the modular Petri net modeling concept, which has been developed in need of a sophisticated reconstruction of growing biomolecular models. The database allows to browse to single modules and to intuitively gather the functionality of a biomolecular entity by its corresponding ...

Genomics, proteomics and molecular epidemiology of avian influenza.

National Institute of Biology, Department of Biotechnology and Systems Biology projects

Consortium of European research groups that aim to develop - in the forthcoming 10 years - a cluster of interlinked models that describe the whole-body human energy metabolism and its multi-dimensional regulation. Regulation includes interations with the brain, the immune system and the gut.

Research of Computational Systems Biology Group, Institute of Microbiology and Biotechnology, University of Latvia and Biosystems group at Latvia University of Agriculture is funded by several programmes in several projects. This program is an umbrella for the projects.

This programme is used to store published data files that are not available in other FAIRDOM projects. We specifically store information for journals that we collaborate with for technical curation of mathematical models. These files are used in COMBINE archives to reproduce journal figures.

Projects that do not fall under current programmes.

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

e:Bio - Innovations Competition Systems Biology