FAIRDOMHub

19 items tagged with 'Copasi'.

Projects: SysMO-LAB, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation

Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, Warsaw University of Technology

https://orcid.org/0000-0003-3979-0364

Expertise: Microbiology, Molecular Biology, Systems Biology, Biochemistry

Tools: Biochemistry and protein analysis, Metabolic Engineering, Molecular biology techniques (RNA/DNA/Protein), Transcriptomics, Fluorescence and confocal microscopy, Flux balance analysis, Copasi

https://www.academia-net.org/profile/malgorzata-adamczyk/87232

Kristaps Berzins

Projects: Rhodolive

Institutions: Latvia University of Agriculture

Expertise: Stoichiometric modelling

Tools: Copasi, COBRA toolbox, Matlab

Agris Pentjuss

Projects: LEANPROT, Rhodolive

Institutions: Latvia University of Agriculture

Expertise: Python, Systems Biology, Dynamic modelling, Mathematical modelling

Tools: COBRA toolbox, cobrapy toolbox, Python, SBML, Copasi, Computational Systems Biology

Raju Prasad Sharma

Projects: Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), EraCoBiotech 2 nd call proposal preparation, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation

Institutions: VU University Amsterdam, Universitat Rovira i Virgili

https://orcid.org/0000-0001-9103-9127

Expertise: PBPK modeling, Pharmacology, Pharmacokinetics, Mechanistic Modelling

Tools: R, Berkeley Madonna, Copasi, Cell designer

Niels Zondervan

Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, WURSynBio

Institutions: Wageningen University & Research

https://orcid.org/0000-0001-7049-5334

Expertise: Bioinformatics, Systems Biology, Agent-based modelling, Dynamic modelling, Python, Java, R, pathogen host interaction, Molecular Biology

Tools: Copasi, libRoadrunner, Python, R, semantic web

I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model. I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation ...

Egils Stalidzans

Projects: LEANPROT, FAIRDOM user meeting, Rhodolive

Institutions: Latvia University of Agriculture, Institute of Microbiology and Biotechnology, University of Latvia

https://orcid.org/0000-0001-6063-0184

Expertise: Kinetic modelling, optimization, Parameter estimation

Tools: Copasi, COBRA toolbox

Melanie Stefan

Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map

Institutions: Kinetics on the move Workshop at HITS, University of Edinburgh

https://orcid.org/0000-0002-6086-7357

Expertise: Calcium signalling, learning, memory, cooperativity

Tools: Copasi, multi-state modelling, MCell

Eduard Kerkhoven

Projects: SilicoTryp, SYSTERACT, SynBio4Flav

Institutions: University of Glasgow, Chalmers University of Technology

https://orcid.org/0000-0002-3593-5792

Expertise: genome-scale modeling, Kinetic modelling, metabolism, Metabolomics, Metabolic Engineering, Transcriptomics, Microbiology, Data Integration

Tools: R, Matlab, COBRA toolbox, Copasi, RNAseq, Bioreactor experiments, Metabolomics, Dynamic modelling

Anastasiya Lapytsko

Projects: ICYSB 2015 - International Practical Course in Systems Biology

Institutions: Institute for Experimental Internal Medicine

Expertise: Mathematical modelling, Image processing

Tools: Matlab, Copasi, c++, Mathematica

I am a PhD student in the field of Systems Biology. In my PhD project I apply mathematical modelling to understand the role of time delay in biological systems containing delayed negative feedbacks.

Natalie Stanford

Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.

David Knies

Projects: SUMO

Institutions: University of Stuttgart

Tools: Matlab, Copasi, Flux balance analysis, Dynamic modelling

I recently joined the Institute for System Dynamics as a PhD student. I'm currently working on a dynamic model of nitrate respiration in E. coli.

Mark Musters

Projects: SysMO-LAB

Institutions: Wageningen University & Research

I'm a modeller, specialized in kinetic modeling of biochemical networks. My focus in the SysMO-LAB consortium is on creating models of Lactococcus lactis glycolysis and couple this to other related lactic acid bacteria like Streptococcus pyogenes and Enterococcus faecalis. Besides kinetic modeling, I'm also interested in combining various modeling techniques (genome-scale modeling, qualitative modeling).

Deepa Damodaran

Projects: SysMO-LAB

Institutions: University of Heidelberg

Expertise: Bioinformatics, Databases

Tools: Copasi

I am working on the development of algorithms for Comparative Systems Biology.

Jennifer Levering

Projects: SysMO-LAB

Institutions: University of Heidelberg

Expertise: Bioinformatics, Streptococcus pyogenes, Mathematical modeling

Tools: SBML, ODE, Copasi, JWS Online, Matlab, Mathematica, Computational Systems Biology, Dynamic modelling, SABIO-RK http://sabio.villa-bosch.de/, SYCAMORE

I am working on a kinetic model of the central metabolism as well as on a genome wide model of Streptococcus pyogenes.

Ursula Kummer

Projects: SysMO-LAB, Kinetics on the move - Workshop 2016, de.NBI-SysBio

Institutions: University of Heidelberg

Expertise: Mathematical modelling of biological systems, Mathematical modelling; Nonlinear Dynamics; Time Series Analysis; network theory

Tools: Copasi

Ursula Kummer is heading the dept. "Modeling of Biological Processes" at the University of Heidelberg.

Afsaneh Maleki-Dizaji

Projects: SUMO

Institutions: University of Sheffield

Expertise: Bioinformatics, Agent-based modelling, Microarray Data Analysis

Tools: Java, Copasi, Taverna, Bioconductor Packages in R

I am a research associate in the department of computer science at the University of Sheffield since January 2008. My research is primarily involved with using agent-based modelling techniques and mathematical modelling techniques to model Escherichia coli K-12 Respiratory Adaptation. My research interests also include, development of workflows to analyze Microarray Data.

Absolute units for proteins in Arabidopsis clock models up to U2020.5

Millar group

(Show All)

The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025.

Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet ...

Submitter: Andrew Millar

Studies: Construction of NanoLUC-tagged plants, Estimating DNA-binding affinities for Arabidopsis proteins, Measuring absolute levels of clock proteins with calibrated NanoLUC assays, Predicting absolute levels of clock proteins with a simple model, Recalibrating the clock models for absolute protein levels, to create mo..., Reproducibility documentation

Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, Gatway maps of genomic regions of clock genes, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi..., Jupyter notebook Predicting Protein Numbers, Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Protein level time series, Python packages, Reproducibility tool set, Selection of complemented transgenic lines, TiMet RNA timeseries data, promoter binding affinity calculations on the genome based on PBMs and E...