Programmes
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Chronic non-healing skin ulcers are a source of considerable suffering worldwide, particularly in rapidly growing aging populations. Why skin becomes fragile and heals poorly as we age remains unclear, although current research indicates that a major reason may reside in defective “stem cells” in skin that normally fuel its renewal and regeneration in order to maintain healthful and youthful function and appearance. Our findings indicate that stem cell pathways involving cell metabolism, DNA ...
Projects: test project for RNAseq of mouse skin samples
Web page: Not specified
Projects: Proteogneomics of Desulfobacteraceae members
Web page: Not specified
Biomedizinische Informatik und Data Science
Projects: Not specified
Web page: Not specified
Projects: Group Data Science, Group Microbial Interface Biology, Core Facility Fluorescence Cytometry
Web page: https://fz-borstel.de
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 ...
Projects: ODDITY, WATCHER, VIALACTEA
Web page: https://biogroup.usc.es/programme32
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.
Projects: Not specified
Web page: https://www.creativebiolabs.net/hi-affi-tm-recombinant-antibodies.htm
Projects: Japanese Data in Global Plant Research: A FAIDARE and BrAPI Project
Web page: Not specified
This Programme is created as a repository for the Virtual Human Platform for Safety Assessment (VHP4Safety) project.
Projects: VHP project
Web page: Not specified
Projects: Catabolic network of the gut bacteria P. vulgatus, Bioreactor/Omics Phocaeicola vulgatus
Web page: Not specified
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 ...
Projects: WG1 - Compound libraries coordination and integration of compound design, WG2 - Integration of early phase studies and low environmental impact actions, WG3 - Coordination of in vitro-to-in vivo translation of OneHealth leads and candidates, WG4 - Integration of R&D process-environmental studies and translation in informed whitepaper, WG5 - Promote dissemination, WG6 - Promote the transfer of knowledge
Web page: https://onehealthdrugs.com/
Projects: We learn to fairdomhub @IBG, Beads analysis, Optimizing biocatalytic flow reactors via inline NMR-analysis
Web page: Not specified
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, ...
Projects: NL-Bioimaging FAIR Metadata Templates
Web page: http://eurobioimaging.nl/
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 ...
Projects: Whole body modelling of glucose metabolism in malaria patients, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications, Glucose metabolism in cancer cell lines
Web page: http://www.sun.ac.za/english/faculty/science/biochemistry/research/snoep-group
Projects: Not specified
Web page: https://www.up.ac.za/malaria-parasite-molecular-laboratory-m2pl
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 ...
Projects: BioDynamics
Web page: http://sb2cl.ai2.upv.es
Projects: Unshackling Membrane Protein Research: New Amphiphilic Copolymers for Extraction of Stable, Active Membrane Proteins, WP1 - Structure-activity relationships of amphiphilic copolymers, WP2.1 - Mono-chain-end functional amphiphilic copolymers, WP2.2 - Hetero di-chain-end functional amphiphilic copolymers, WP2.4 - Block copolymers for tethering to surfaces, WP2.3 - Meta-stable amphiphilic copolymers, WP2.5 - Fusion of SMALPs, WP2.6 - SMALPs for photosynthetic research, WP3 - Scalability of polymer production process, WP4 - Community engagement and technical advice
Web page: Not specified
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 ...
Projects: NIRBTEST
Web page: Not specified
Projects: SteaPKMod
Web page: https://www.uniklinikum-jena.de/avc/Forschung/Experimentelle+Chirurgie.html
Web page: Not specified
RNA-Seq projects from SECARNA
Projects: Investigation of the activity of antisense oligonucleotides targeting multiple genes
Web page: Not specified
Projects: Testing tools for research data management
Web page: Not specified
Projects: Aneurinibacillus thermoaerophilus CCM 8960 metabolic pathways model
Web page: Not specified
Projects: WP 1: Biodegradable and responsive polymer matrix, WP 2: Antimalarial drug encapsulation, WP 3: Drug release kinetics study, WP 4: Evaluation of drug activity against multiple life cycle stages of malaria parasites, WP 5: Intradermal 3D drug device administration, Project Coordination
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.
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 ...
Web page: Not specified
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 ...
Projects: Molecular characterization and angiogenic properties of extracellular vesicles in healthy and preeclamptic amniotic fluid, Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved, Comparative Proteome Profile of Placental Sub-anatomical regions, The deregulated interplay of complement system and antioxidant activity as a driver of adverse pregnancy outcomes
Web page: https://www.iplacenta.eu/
Web page: Not specified
Web page: Not specified
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.
Web page: https://www.dfg.de/en/index.jsp
Projects: Supplemental Data for "Why did the eyewall replacement cycle in Trami terminate rapidly? "
Web page: Not specified
Work of the Gygli group...
Projects: Test Project (dummy), Towards Reproducible Enzyme Modeling
Web page: Not specified
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.
Projects: Thermodynamics, Non equilibrium thermodynamics, Book on Thermodynamics, and kinetics, Stochastics and bursting
Web page: https://isbe.nl
This is the home programme for the Infrastructure Systems Biology @ NL activity of assisting clients with systems biology
Projects: Xenosystems biology, Xenophiles Systems Biology, Teaching Alien Biology, Outdated material, Fusion-fission-mitophagy
Web page: https://isbe.nl
Projects: Mass spectrometry proteomics for biomarker discovery, TEAD-(YAP) structure, function and inhibition, Thymidylate synthase dimer dissociation
Web page: Not specified
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 ...
Projects: An overview of systematic reviews of treatment of polycystic ovary syndrome with Chinese medicine
Web page: Not specified
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 ...
Projects: Not specified
Web page: Not specified
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This page is dedicated to the bioinformatics analysis and computational modelling related to Covid-19 disease map pathways.
Projects: Covid-19 Interferon pathway modelling and analysis
Web page: Not specified
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).
Projects: C19DM - Macrophage logical model
Web page: Not specified
Projects: Hi-IMPAcTB
Web page: https://www.niaid.nih.gov/research/immune-mechanisms-protection-mycobacterium-tuberculosis
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.
Projects: C19DM-Neo4j
Web page: Not specified
Projects: Consensus Hallmark Annotation, The evolution of Gene Ontology
Web page: Not specified
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this is personal project
Projects: Not specified
Web page: Not specified
Projects: EnzymeML, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling
Web page: Not specified
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Web page: Not specified
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 ...
Projects: Towards a mechanistic understanding of von Hippel-Lindau syndrome in different tissues
Web page: https://protein.bio.unipd.it/research
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.
Projects: BiocompUP Test Project
Web page: https://idpfun.eu/
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.
Projects: AGENSI
Web page: Not specified
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
Web page: https://cordis.europa.eu/programme/id/FP7_HEALTH.2013.2.3.4-2
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 ...
Projects: COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data
Web page: https://www.nfdi4health.de
Projects: Testing FairdomHub functionality, Study of Pleiomorphic Ensembles, Hidden project, Hidden project 2
Web page: Not specified
BlueBio ERA-NET COFUND on the Blue Bioeconomy
Projects: AquaHealth (ERA-BlueBio)
Web page: https://bluebioeconomy.eu/
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 ...
Web page: http://www.elidek.gr/en/homepage/
Bringing 3D Additive Manufacturing from the macroscale to the micro-, nano-, and eventually to the molecular scale and at applying these technologies
Projects: Thrust C2
Web page: https://www.3dmm2o.de
The aim is to bundle the information about the manifold of COVID-19 centered initiatives offering tools and studies.
Projects: Not specified
Web page: Not specified
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.
Projects: COVID-19 Disease Map
Web page: https://disease-maps.org
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 ...
Projects: Sustainable co-production, BESTER, Rhodolive, HOTSOLUTE, TRALAMINOL, C1Pro, Cell4Chem
Web page: https://www.cobiotech.eu/
Using kinetic models to study the central carbon metabolism in pseudomonas putida, both for metabolite production and understanding the impact of certain perturbations.
Projects: Acetyl-coa production in Pseudomonas putida
Web page: Not specified
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.
Projects: Finding interaction partners of thylakoid membrane insertase, Characterization of P. tricornutum chloroplast protein mutants
Web page: Not specified
Projects: Perennial ryegrass, Genetic diversity and forage yield of perennial ryegrass
Web page: Not specified
Projects: RDM awareness
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 ...
Projects: SysVirDrug, SysMilk, SysMetEx, MetApp, IMOMESIC, WineSys, CropClock, SYSTERACT, XyloCut, RootBook, ROBUSTYEAST, LEANPROT, ErasysApp Funders
Web page: https://www.cobiotech.eu/about-cobiotech/erasysapp
Projects: Not specified
Web page: Not specified
Program for lessons data management
Projects: Test Project
Web page: https://www.howest.be/nl/opleidingen/banaba/bio-informatica
general working environment for the Genomics Platform
Projects: Not specified
Web page: http://www.ilvogenomics.be
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.
Projects: Lipofungi, DeepHyperSpec, Bio4Fuels, LIGNOLIPP
Web page: https://www.nmbu.no/en/faculty/realtek/research/groups/biospectroscopy
Projects: Toggle switch, Reduce Complexity (RCO) reconstruction, Model Driven Prime Editing, PULSE 2.0, Plant optogenetics
A study of the systems biology of innate immunity
Projects: Make Me My Model
Web page: http://sysba.nl
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 ...
Projects: CF transcriptome, miRiAD - exploring the role of microRNAs in T cell function and anti-viral defence, ComPASs - Common Pathways in Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA), LungCARD - Blood test for clinical therapy guidance of non-small cell lung cancer patients, UnCentre - Unlocking satellite DNA and centromere structure in vertebrate chromosomes, Mapping Disease Modules Overlaps in Biological Networks
Web page: Not specified
This is a placeholder Programme for the future development of the interface Project. At the moment we are creating spaces and testing features.
Projects: Interface MIAPPE / BrAPI
Web page: Not specified
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Web page: Not specified
Development of a NetLogo simulation and RStudio-Shiny web application surrounding cellular senescence for outreach. Aimed at GCSE/A-level students
Projects: Not specified
Web page: Not specified
testing access to fairdom hub documents. data files etc via the API in various programming languages
Projects: Fairdom Hub documents, RStudio-Shiny and Java_API connection testing
Web page: Not specified
A small application which simulates the development of breast cancer
Projects: Outreach - Simulation of breast cancer development using an agent based modelling approach, Outreach - Breast Cancer RStudio-Shiny application
Web page: Not specified
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.
Projects: Light and plant development
Web page: http://hallidaylab.bio.ed.ac.uk
Projects: Not specified
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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 ...
Projects: Not specified
Web page: https://cordis.europa.eu/project/rcn/107706/factsheet/es
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.
Projects: GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"
Web page: https://gmds.de
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 ...
Projects: Not specified
Web page: http://www.usc.es/biogroup/treasure
Projects: Not specified
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 ...
Projects: Environmentally-friendly bioadhesives from renewable resources (WooBAdh), Ultreia, MPW-Val, Enzymatic biorecycling of PET (PETzyme)
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. ...
Projects: CoolWine
Web page: Not specified
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Modeling of presynaptic dopamine homeostasis
Projects: Not specified
Web page: Not specified
Projects: Escherichia coli chemical product tolerance
Web page: http://biosustain.dtu.dk
The computational identification of Zinc Finger genes in genomes. The computational identification of the DNA binding profile of Zinc Finger genes.
Projects: Not specified
Web page: Not specified
Systems modelling molecular mechanisms of ageing
Projects: Systems modelling age-related changes in the maintenance of dermal extra-cellular matrix: mechanisms and interventions, Are microRNAs key mediators of cartilage destruction in osteoarthritis?, Dynamic interplay between nuclei and mitochondria in ageing cells, Outreach - Senescence RStudio-Shiny application, Outreach - Simulation of cellular senescence using an agent based modelling approach
Web page: https://www.ncl.ac.uk/camb/staff/profile/darylshanley.html
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
Projects: DCM
Web page: Not specified
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.
Projects: Proteogenomics of melanoma
Projects: SynBio4Flav
Web page: http://www.cnb.csic.es/index.php/en/research/research-departments/systems-biology
The DrugLogics initiative comprises a number of different subprojects, all geared towards the development of personalised medicine, or precision medicine
Projects: CausalDB, Colosys, Crossover Research 2.0, NTNU Health Druglogics
Web page: http://druglogics.eu/
Projects: Not specified
Web page: Not specified
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).
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Web page: http://www.synthsys.ed.ac.uk
Centre for Digital Life Norway (DLN) project OXYMOD - Optimized oxidative enzyme systems for efficient conversion of lignocellulose to valuable products
Projects: OXYMOD
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.
Projects: Not specified
Web page: http://sbrc-nottingham.ac.uk/
Projects: Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa
Web page: Not specified
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).
Projects: COMBINE Multicellular Modelling, ModeleXchange initiative
Web page: http://co.mbine.org
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.
Projects: Light control of leaf development
Web page: http://hallidaylab.bio.ed.ac.uk/
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.
Web page: http://www.safeaqua-project.net
Projects: Not specified
Web page: Not specified
Projects: WG Infrastructure for Translational Research, INCOME, Translational Bioinformatics, Medical Biometry, Epidemiology, Medical Informatics
Web page: Not specified
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 ...
Projects: GenoSysFat, DigiSal, SEEK tutorial for DigiSal, DigiSal-BT8121
Web page: http://tinyurl.com/digisal
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 ...
Projects: Not specified
Web page: http://www.funginet.de/
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.
Projects: Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation, ROS detailed model for MSB manucript, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population
Web page: http://www.isbe.nl
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 ...
Projects: Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), FAIRDOM & LiSyM & de.NBI Data Structuring Training, New LiSyM project
Web page: http://www.lisym.org
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; ...
Projects: Systems toxicology of Atlantic cod
Web page: http://dcod.no
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).
Projects: FAIRDOM, FAIRDOM user meeting, FAIRDOM Community Workers
Web page: http://fair-dom.org
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 ...
Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, SABIO-VIS
Web page: http://www.denbi.de
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 ...
Projects: Not specified
Web page: http://www.biomodelkit.de
Genomics, proteomics and molecular epidemiology of avian influenza.
Projects: Not specified
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
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.
Projects: HUMET Startup
Web page: Not specified
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.
Projects: Not specified
Web page: http://biosystems.lv/
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: Molecular Systems Biology
Web page: Not specified
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Endometriosis, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, icpm-kth, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG, URGI, Matsutake, UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 2022, Semantic Table Interpretation in Chemistry, MS identification of L infantum proteins related to their drug resistance patterns for new drug targets identification and ecotoxicological evaluations of their environmental and interspecies impact, the Supplementary materials for paper, ToxiGen - Reproductive toxicity and transgenerational effects of petroleum mixtures in fish, PhotoBoost, Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia, FIsh data on 2022 in the Jatigede Reservoir, ImmPort - data sharing, MESI-Review 2024, REWIRED: comparative RNA-seq and ATAC-seq in six salmonids and six outgroup telest fishes, REWIRED, Data Repository, APPN Test Project, Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation, BIDS, BioRECIPE representation format, UMass Chan BioImage DMS Core_FAIR Metadata Templates, Function, control and engineering of microbial methylotrophy, Pectobacterium pangenome, New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration, Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species
Web page: Not specified
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 ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
e:Bio - Innovations Competition Systems Biology
Projects: SulfoSys - Biotec, SBEpo - Systems Biology of Erythropoietin
Web page: http://www.fona.de/en/14276