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Organisms

Acidithiobacillus caldus
SysMetEx, Kinetics on the move - Workshop 2016

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/33059

Synonyms: Thiobacillus caldus

Arabidopsis thaliana
ZucAt, Kinetics on the move - Workshop 2016, Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/3702

Synonyms: thale-cress, mouse-ear cress

Bacillus methanolicus
MetApp

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/1471

Bacillus subtilis
BaCell-SysMO, Kinetics on the move - Workshop 2016

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1423

Brassica rapa
PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/3711

Chikungunya virus
SysVirDrug

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/37124

Clostridia Sp.
BESTER

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/186801

Clostridium acetobutylicum
COSMIC

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1488

Corynebacterium glutamicum
XyloCut

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/1718

Synonyms: Brevibacterium glutamigenes, Brevibacterium lactofermentum, Brevibacterium seonmiso, Brevibacterium chang-fua, Brevibacterium thiogenitalis, Micrococcus maripuniceus, Brevibacterium saccharolyticum, Corynebacterium lilium, Corynebacterium lactofermentum, Micrococcus glutamicus, Brevibacterium divaricatum, Brevibacterium taipei

Coxsackievirus
SysVirDrug

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/12066

Danio rerio
GenoSysFat, DigiSal

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/7955

Synonyms: Cyprinus rerio, Danio frankei, zebra danio, Brachydanio rerio frankei, Danio rerio frankei, Brachydanio rerio

Dengue virus
SysVirDrug

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/12637

Enterococcus faecalis
SysMO-LAB

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1351

Escherichia coli
SUMO, KOSMOBAC, Manchester Institute for Biotechnology, LEANPROT, Millar group, SynBio4Flav

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_562

Escherichia coli K-12
SUMO

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_83333

Synonyms: Escherichia coli K12

Gadus morhua
Systems toxicology of Atlantic cod

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/8049

Hepatitis C virus
SysVirDrug

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/11103

Synonyms: post-transfusion hepatitis non A non B virus, human hepatitis C virus, hepatitis C virus HCV, human hepatitis virus C HCV, human hepatitis C virus HCV

Homo sapiens
Whole body modelling of glucose metabolism in malaria patients, SysVirDrug, IMOMESIC, 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 user meeting, HUMET Startup, SBEpo - Systems Biology of Erythropoietin, 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), CausalDB, Colosys, MS_DILI, MESI-STRAT, INCOME, ROS detailed model for MSB manucript, Steroid biosynthesis

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/9606

Synonyms: man

Lactic Acid Bacteria
SysMO-LAB

Taxonomy URI: Not specified

Lactobacillus plantarum

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1590

Synonyms: Lactobacillus arizonae

Lactococcus lactis
SysMO-LAB

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1358

Leptospirillum ferriphilum
SysMetEx

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/178606

Methylobacterium extorquens
MetApp

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/408

Synonyms: Methylobacterium dichloromethanicum, Protomonas extorquens, Vibrio extorquens, Flavobacterium extorquens, Pseudomonas extorquens, Bacillus extorquens, Methylobacterium chloromethanicum

model organisms for unraveling human energy metabolism

Taxonomy URI: Not specified

Mus musculus
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), SBEpo - Systems Biology of Erythropoietin, MS_DILI

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/10090

Synonyms: mouse

Mycoplasma hyopneumoniae

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/2099

Synonyms: Mycoplasma suipneumoniae

Mycoplasma pneumoniae
MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/2104

Synonyms: Filterable agent of primary atypical pneumonia, Schizoplasma pneumoniae

Nicotiana benthamiana
SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/4100

Oncorhynchus mykiss
GenoSysFat, DigiSal

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/8022

Synonyms: Parasalmo mykiss, Oncorhynchus nerka mykiss, Salmo mykiss

Ostreococcus tauri
Millar group, TiMet

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/70448

Penaeus monodon
SAFE-Aqua

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/6687

Synonyms: tiger prawn, giant tiger prawn, Penaeus (Penaeus) monodon

Penicillium chrysogenum
SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/5076

Synonyms: Penicillium notatum

Planococcus citri
SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/170843

Plasmodium falciparum
Whole body modelling of glucose metabolism in malaria patients

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/5833

Synonyms: Plasmodium (Laverania) falciparum

Potato virus Y
HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/12216

Synonyms: potato virus Y PVY, potato virus Y PVY-H, potato virus Y, PVY

Pseudomonas aeruginosa
EmPowerPutida, Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/287

Synonyms: Bacterium aeruginosum, Pseudomonas pyocyanea, Bacterium pyocyaneum, Micrococcus pyocyaneus, Bacillus aeruginosus, Pseudomonas polycolor, Bacillus pyocyaneus

Pseudomonas fluorescens
SCaRAB, EmPowerPutida

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_294

Pseudomonas mendocina
EmPowerPutida

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/300

Pseudomonas putida
PSYSMO, EmPowerPutida, SynBio4Flav

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_303

Pseudomonas sp. PAO1
EmPowerPutida

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/1708767

Rattus norvegicus
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)

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/10116

Synonyms: Rattus sp. strain Wistar, brown rat

Rhodotorula glutinis
Rhodolive

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/5535

Synonyms: Cryptococcus glutinis

Saccharomyces cerevisiae
MOSES, TRANSLUCENT, WineSys, ICYSB 2015 - International Practical Course in Systems Biology, XyloCut, ROBUSTYEAST, SynBio4Flav

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_4932

Synonyms: yeast, lager beer yeast, brewer's yeast, baker's yeast

Salmo salar
GenoSysFat, DigiSal, SEEK tutorial for DigiSal

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/8030

SARS Coronavirus
SysVirDrug

Taxonomy URI: http://purl.bioontology.org/ontology/SNOMEDCT/415360003

Streptococcus pneumoniae
Noisy-Strep

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1313

Streptococcus pyogenes
SysMO-LAB

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1314

Streptomyces albus
SynBio4Flav

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/1888

Synonyms: Streptomyces griseus subsp. solvifaciens

Streptomyces coelicolor
STREAM, SYSTERACT, INBioPharm

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_1902

Sulfobacillus thermosulfidooxidans
SysMetEx, Glycon proposal preparation

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/28034

Sulfolobus acidocaldarius

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/2285

Sulfolobus solfataricus
SulfoSys, SulfoSys - Biotec

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_2287

Thermus thermophilus
HOTSOLUTE

Taxonomy URI: http://purl.bioontology.org/ontology/NCBITAXON/274

Synonyms: Thermus aquaticus flavus

Tiger Shrimp

Taxonomy URI: .

Trypanosoma brucei
SilicoTryp

Taxonomy URI: http://purl.obolibrary.org/obo/NCBITaxon_5691

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