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SysMO9 Independent Projects4 ERASysAPP4 de.NBI Systems Biology Service Center (de.NBI-SysBio)4 Era CoBioTech4 FAIRDOM2 SARCHI: Mechanistic modelling of health and epidemiology1 The Digital Salmon1 Model repository for M4 (Make Me My Model) clients of ISBE1 COMBINE (Computational Modeling in Biology Network)1 Systems Biology Programme1 Disease Maps1 FAIR Biocatalysis1 More...

SysMO-LAB5 Kinetics on the move - Workshop 20163 Rhodolive3 SUMO2 ICYSB 2015 - International Practical Course in Systems Biology2 SYSTERACT2 LEANPROT2 de.NBI-SysBio2 FAIRDOM user meeting2 SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation2 SysMO DB1 SilicoTryp1 Whole body modelling of glucose metabolism in malaria patients1 Manchester Institute for Biotechnology1 FAIRDOM1 iRhythmics1 GenoSysFat1 DigiSal1 Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW)1 MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine1 WURSynBio1 EraCoBiotech 2 nd call proposal preparation1 COMBINE Multicellular Modelling1 BESTER1 SynBio4Flav1 EnzymeML1 OLCIR: Optimization of Lung Cancer Therapy with Ionizing Radiation1 COVID-19 Disease Map1 Standardization of enzyme-catalyzed reaction measurement1 Standardization of enzyme-catalyzed reaction modelling1 SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke1 More...

University of Heidelberg4 Latvia University of Agriculture3 Manchester Centre for Integrative Systems Biology, University of Manchester2 Wageningen University & Research2 VU University Amsterdam1 University of Rostock1 University of Sheffield1 University of Stuttgart1 University of Manchester - Department of Computer Science1 Chalmers University of Technology1 University of Glasgow1 University of Edinburgh1 Universitat Rovira i Virgili1 Institute for Experimental Internal Medicine1 Kinetics on the move Workshop at HITS1 Institute of Microbiology and Biotechnology, University of Latvia1 Warsaw University of Technology1 More...

Germany8 United Kingdom5 Latvia3 Netherlands3 Spain1 Poland1 Sweden1 More...

Copasi17

Copasi18 Molecular Biology61 Matlab61 R57 Python56 Molecular biology techniques (RNA/DNA/Protein)53 Transcriptomics52 Biochemistry and protein analysis50 Microbiology42 Bioinformatics41 ODE35 Data Management34 Computational Systems Biology34 SBML33 Genetic modification30 Fermentation28 Dynamic modelling28 Biochemistry27 Computational and theoretical biology27 Databases25 Microarray analysis24 Proteomics23 Java23 Genetics22 Systems Biology19 Genomics17 Metabolomics17 Mathematica15 Fluorescence and confocal microscopy15 Parameter estimation15 linux13 Stochastic models13 Metabolic Engineering13 Data Integration13 Cytoscape12 Chromatography11 Proteomics (2D-PAGE)11 qRT-PCR11 CellDesigner11 Cell and tissue culture9 qPCR9 Fluorecence based reporter gene analyses/single cell analyses9 Mass spectrometry (LC-MS/MS)9 COBRA toolbox9 Genetic analysis8 Perl8 MySQL8 Deterministic models8 Cell culture8 Cell biology7 Cytometry and fluorescent microscopy7 differential algebraic equations7 continuous cultivation7 Enzyme assay7 molecular biological techniques (RNA/DNA techniques7 Flow cytometry7 network theory7 microbiology techniques7 Machine Learning7 Model organisms6 Partial differential equations6 Workflows6 Web services6 Mass spectrometry6 SQL6 fluorescence spectroscopy6 quantitative western blot analysis6 Flux balance analysis6 HPLC6 Neo4J6 Kinetic Modeling6 Spectroscopy and structural analysis5 Single Cell analysis5 PCR5 Ruby on Rails5 Ontologies5 stimulus response experiments5 data modeling5 quantitative western blot analyses5 Molecular biology techniques (RNA/DNA)5 HTML5 NMR5 semantic web5 Javascript5 SBGN5 c++5 bash5 Data Science5 SBGN-ED5 Jupyter5 pathvisio5 Pharmacology and toxicology4 Cell designer4 PHP4 Material balance based modeling4 Protein chemical methods (protein overproduction4 enzymatic analyses4 C programming4 time lapse microscopy4 2-D Gel Electrphoresis4 Bioconductor Packages in R4 GC and LC analysis of metabolites4 Western blot analyses4 stochastic methods4 enzyme kinetics4 RNAseq4 SED-ML4 Statistics4 cobrapy toolbox4 wikipathways4 SEEK4 Isolation purification and separation3 Algebraic equations3 JWS Online3 Chip-chip3 Taverna3 evaluation of process dynamics3 mutant strain generation3 XPPAUT3 FACS3 Membrane protein biochemistry3 Site-directed mutagenesis3 Data analysis3 DNA technology RNA technology Protein analysis Fermentation Mutagenesis3 Fluorescence microscopy3 molecular biological techniques (RNA/DNA techniques)3 In silico Metabolic Network Analysis3 Chemostat culture3 RNA / DNA Techniques3 Mutant and Strain Construction3 Enzyme assays3 reporter gene analyses3 DNA3 Proteins3 Gaschromatographic analysis3 analysis of functional genomics data3 interaction analysis techniques especially SPR measurements3 Statistical tools3 Pathway Tools3 model prediction testing3 Molecular Dynamics3 transcription analysis3 RNA interference3 protein purification3 metabolic network visualization3 FBA3 High Performance Computing3 libSBML3 Compucell3D3 Latex3 Shell scripting3 Knowledge Management3 Modeling3 Linear equations2 rtPCR2 qtPCR2 Ruby2 MIRIAM2 DIVA2 quantitative Western analyses)2 Northern analyses)2 cultivation2 northern blot analysis2 including: - Dynamic modelling - Parameter estimation - Optimal experimental design - Dynamic optimization2 including:- Dynamic modelling- Parameter estimation- Optimal experimental design- Dynamic optimization2 Biochemistry of substrate transport. molecular biological techniques (RNA/DNA techniques analyses of transport across cell membranes heterologous expression of transporters2 Chemical cross-linking2 PDE2 transcriptional analysis (Northern blots2 Optimal experimental design2 Proteomics (Glycoproteins)2 BioMart2 Comparative Genomics2 GC and LC analysis of metabolites | Analysis of signal molecules | Handling of anaerobic bacteria |2 isothermal titration calorimetry2 SubtiWiki2 time-resolved microarray analysis2 protein-DNA interactions; gel shifts; footprints; in vitro transcription protein ligan interactions2 metabolic labeling2 absolute quantification2 Immunofluorescence2 protein interaction studies2 fed-batch cultivation2 bacterial chemostat culture2 Bioreactor experiments/Fermentation (batch2 spectroscopy2 site-directed and random mutagenesis2 Mutant and Strain Construction; RNA / DNA Techniques; RT-RealTime-PCR; 2D-Gels; Metabolite Analysis; Bioreactor Experiments; Flow Cyometry; Microscopy; Single Cell analysis2 Chemostats2 Multiscale and multiphysics modelling2 molecular biology techniques2 gel-based and gel-free proteomics2 shotgun proteomics2 in vivo crosslinking2 PIPSA2 SYCAMORE2 fortran2 CUDA2 Perl programming2 phage techniques2 PySCeS2 GC and LC/MS analysis of metabolites2 Reactome2 standards2 Model selection2 Identifiability analysis2 life-cell imaging2 imaging2 web development2 ChIP-seq2 tellurium2 SABIO-RK2 Boolean modeling2 Animal models2 mouse models2 immunohistochemistry2 Petri Nets2 libRoadrunner2 cloning2 Docker2 photobiology2 jupyter notebooks2 AMICI2 Stata2 unix2 GINsim2 Cell Collective2 Newt Editor2 DisGeNET2 ODE Modelling2 Spectrophotometry2 In vivo bioluminescence imaging2 Antimony2 Immunological techniques1 Agent-based modelling1 Spring1 semanticSBML1 ProMOT1 J2EE1 pulsed - FRAP1 purification1 molecular biological techniques (RNA/DNA techniques analyses of transport across cell membranes heterologous expression of transporters1 Biochemistry of substrate transport. molecular biological techniques (RNA/DNA techniquesanalyses of transport across cell membranesheterologous expression of transporters1 FRAP1 Fluorescence and confocal microscopy FRAP/FLIP1 genomic array footprinting1 gene regulation1 The Membrane Enzymology group focuses on the molecular mechanisms of transport and signalling across biological membranes. In other words: How do molecules permeate biological membranes and how at the level of protein molecules are environmental signals s1 engineering principles and approaches from molecular biology and synthetic chemistry are applied. Confocal microscopy and various spectroscopic methods are used to analyze processes at the single cell or even single molecule level.1 C programing1 quantitative RT-PCR); quantitative Western blot analysis; protein purification; reconstitution of membrane-integrated proteins; Biochemistry of substrate transport; Fluorecence based reporter gene analyses/single cell analyses1 surface plasmon resonance spectroscopy; site-directed spin labeling and EPR analysis;1 Dynamic optimization1 sensitivity analysis1 Time-lapse fluorescence microscopy Flow cytometry1 EnsEMBL1 XML1 Phylogenetics1 methods of nonlinear time series analysis1 programming in C1 site-directed spin labeling and EPR spectroscopy1 Biophysics1 SPINE1 bacterial two-hybrid system1 bacterial chamostat culture1 GeLC-MS/MS1 AQUA1 Logical modelling1 trac (wiki for data management)1 model reduction1 Fluxomics1 transposon mutagenesis1 Time-lapse fluorescence microscopy1 FLAME - Flexible Large-scale Agent-based Modelling Framework.1 GFP expression1 live cell array1 X-ray crystallography electron microscopy Biochemistry and protein analysis1 Chemostat)1 2D-PAGE1 plasmon resonance spectroscopy1 phage transduction1 Molecular biology techniques (DNA/Protein)1 Chemostat culture GC and LC analysis of metabolites1 asymptotic methods1 model reduction.1 RNA1 Gaschromatography1 Creation of Mutants1 stress experiments1 Groovy1 Protein1 Mutant construction1 2-D Gel Electrophoresis1 Chemostat cultures Molecular biology techniques (RNA/DNA) 2-D Gel electrophoresis Gaschromatography Protein overexpression/purification1 molecular biological1 microbiological and immunological techniques1 surface plasmon resonance spectroscopy1 reporter gene analysis1 X-ray crystallographyelectron microscopyBiochemistry and protein analysis1 Maple1 Clustering softwares1 affinity copurification/precipitation1 reverse engineering1 computational platform development1 metabolic netwlrk visualization1 gPROMS1 SABIO-RK http://sabio.villa-bosch.de/1 molecular modeling and simulation1 Protein and RNA structure prediction1 Homology Modelling1 Programming in perl and tcl1 Grails web development framework1 iTRAQ for quantitative proteomics1 madonna1 genetics of hyperthermophilic archaea1 phylogeny1 metagenomics1 GPU1 Thermodynamics1 SABIO-RK database1 in vitro transcription1 DNA affinity chromatography1 EMSA1 RightField1 Bayesian inference1 immunoblot1 Physiology1 graphdatabase1 Enzyme assays Molecular Biology, Biochemistry1 Protege1 Protein Arrays1 Excemplify1 standard bioinformatic tools1 Surface sensitive techniques1 octave1 Scilab1 Individual-based models1 protein analysis1 CalMorph1 GLM1 Activity-based Protein Profiling1 pulse SILAC1 Microbial Ecology1 micro-Computed Tomography1 omics1 fluorescence1 Bioreactor experiments1 AWS1 Research Objects1 energy metabolism1 Maxquant1 SILAC1 high-throughput sequencing1 Vaadin1 Numerical modells1 Comsol1 R package1 analytics1 multi-state modelling1 MCell1 roadrunner1 13C-MFA1 High-throughput phenotyping1 Integrative modeling1 Liquid handling systems1 Automation1 quantitative microscopy1 yEd Graph Editor1 antiSMASH1 CloneManager1 artemis1 indirect calorimetry1 human metabolic research1 geneXplain platform1 BioUML1 stable isotopes1 lipidomics1 Integrative physiology1 Glucose metabolism1 Lipid metabolism1 LPS measurments1 Gut microbiota analysis1 Isotope Ratio Mass Spectrometry1 Confocal Immunofluorescence microscopy1 In vivo measurement of susbstrate fluxes in humans1 Visualisation of muscle and microvascular metabolism in muscle sections1 hyperinsulinemic clamp in rats1 stereotactic surgery1 Morpheus1 GWAS1 WES/WGS1 patient interventions1 gene transfer tools1 metabolic phenotyping1 SBGNViz1 cBioPortal1 PathwayMapper1 ChiBE1 RNATrap1 cre mice and rats1 feeding behaviors1 Fluorescence and confocal microscopyFRAP/FLIP1 MS imaging1 FT-ICR-MS1 Field Flow Fractionation1 IHC1 ISH1 ChiP1 Snoopy1 Marcie1 Charlie1 CSS1 editors1 Intravital immaging1 CBMPy1 F-A-M-E1 Supervised Leadning1 Berkeley Madonna1 gpgpu computing1 evolutionary computation1 swarm intelligence1 Plant biology1 Metabolic modelling1 DNA/RNA isolation1 RACE pcr1 GoldenGate1 C. elegans biology1 NeuroML1 pbpk1 1D and 2D SDSPAGE1 ELISA Techniques1 oral food challenge matrix preparation for food allergy research1 data analysis and data management1 food allergen characterisation1 recombinant protein production1 Data2Dynamics1 PESTO1 HMMER1 genome engineering1 plant transformation1 Bifurcation analysis1 Gromacs1 Solid-state fermentation1 Galaxy1 lattice boltzmann1 REX1 AspenPlus1 JMP1 ICAS1 electrophysiology1 super resolution microscopy1 iPSC culture1 Photoactivated localization microscopy1 Bioreactors operation1 Gas exchange measurements1 screening assays1 enzymatic synthesis1 enzyme engineering1 biomarkers1 biomarkers1 In silico Mining1 CRISPR/Cas91 CRISPR/Cas91 experimental tools1 NetworkX1 Protein2GO1 BioNetGen1 ProcessDB1 VANTED1 MetaCrop1 TEAMwISE1 NaviCell1 Literature mining1 Literature mining1 CaSQ1 SBGNML1 JSBML1 SBSCL1 InSilico1 Text Mining1 Data Modelling1 constraint programming1 model checking1 Prolog1 yEd1 bridgedb1 sparql1 Jena1 Pentaho1 C#1 metadata1 NMR spectroscopy1 OmniPath1 pypath1 Adobe Illustrator1 GraphPad Prism1 Adobe Photoshop1 SBGN-ML1 sbgntikz1 pint1 clingo1 omics analysis1 Qualitative Methods1 Participatory Reseach1 Julia1 AlternatingConditionalExpectation1 PEtab1 Constraint-based analysis1 Ordinary differential equations1 Multiscale modeling1 dynamic light scattering1 COBRApy1 pycharm1 rstudio1 slurm1 Molecular docking and simulation1 sensors1 high throughput phenotyping1 MaBoSS1 TAILS1 PICS1 ATOMS1 Protease assays1 MALDI-TOF/TOF1 LC-MS/MS1 Animal modes1 X-ray crystallography1 recombinant technology1 MIAPPE1 Model-data integration1 Tissue Forge1 CC3DML1 Light Microscopy1 Snakemake1 Economics1 Molecular microbial ecology tools1 basico1 More...