Data files

data1140 pISA-tree543 pISA351 demo246 Docking46 Enzyme39 isothermal titration calorimetry33 Induced Fit29 caffeine28 Pharmacokinetics28 Binding22 Proteomics18 Drug discovery16 Kinetics12 Data Management8 Metabolomics8 Multiple Injection8 Transcriptomics8 UV-Vis Spectrophotometry8 Arabidopsis7 iTRAQ7 Sulfolobus solfataricus7 acetic acid6 chemostat6 KEGG6 Mass spectrometry6 Bacillus subtilis5 Homology modeling5 biomass4 chemical markup language4 deep eutectic solvents4 drug design4 Protein4 Python4 Selwyn test4 Specific Activity4 Validation4 70mM3 ADMET3 Arrhenius and Vogel–Fulcher–Tammann-Hesse models3 Bioinformatics3 Data Integration3 development3 dynamic light scattering3 enzyme kinetics3 FAIR3 fair data3 Homogeneity of Sample3 KEGG2SBTOOLBOX23 metadata3 microarray3 Modelling3 Pals3 pulse3 Reactome3 recurrent Single Injection3 sc-SynO3 scRNA-Seq3 SEEK3 Workflow3 acidogenesis2 allosteric regulation2 annotation2 API2 Automated Workflow2 butyric acid2 carbon sources2 clinical studies2 community2 Correlation analysis2 Cytoscape2 data retrieval2 environmental conditions2 Epidemiology2 FBA2 gene annotation2 HPLC2 in silico2 ISA2 literature2 M. pneumoniae2 Matlab2 mRNA decay2 public health studies2 R2 RNAseq2 SBTOOLBOX22 Sequence alignment2 sequencing2 SPINE2 Taverna2 Template2 Thermodynamics2 WQJR2 100mM1 50mM1 80mM1 absolute values1 aerobiosis1 Affymetrix1 amino acid1 Amino acid uptake1 anaerobic1 Arabidopsis thailana1 Arrhenius model1 butanol producing strain e.coli1 CAC1 Clock1 Clocks1 Clostridium1 cofactor1 coil length1 combine1 Comparative modeling1 comparison1 continuous culture1 Control Analysis1 COVID-191 Data analysis1 data and model management1 data citation1 Data Dictionary1 Data logger1 DES1 dynamic model1 electrostatics1 Enyzme Kinetics1 enzyme activity measurement1 enzymes1 epidemic1 Escherichia coli1 Evaluation Script1 experiment1 fair publishing1 FDJR1 feed composition1 feed switch1 figures; Tables1 fluxes1 GC-MS1 gel1 gene co-expression analysis1 gene expression1 Graph Analysis1 high content screen1 hplc thiol analysis1 input1 intera1 interaction partner1 kcat1 Km1 l-fucose1 lactate dehydrogenase1 LC MS1 leaf area1 lepto1 LXX1 Master file1 MCAD1 membrane transport1 metabolic shift1 Metadata table1 mice1 Microbial Ecology1 Microbiology1 mineral1 mitochondrial carrier1 mitochondrial transporter1 model curation1 Modeling1 Molecular Dynamics1 NAD1 NAD+ transporters1 Network Analysis1 networking1 oxygen1 PAINS1 pathway1 PC1 PDB1 PFL1 PGK1 pH-shift1 phosphorylation1 PIPSA1 Protocol development1 pyruvate kinase1 quenching temperature1 reactions1 relative measurements1 Report1 repression1 respiration1 RNA1 RobOKoD redesigned1 SBML1 seek tutorial1 SLC25A511 solute carrier family 251 solventogenesis1 space science1 step1 Stickland reactions1 stoichiometric equation1 Stressosome1 Systems Biology1 T. brucei1 TCA1 Training Data1 transcriptiption regulation1 Transcriptome1 transformer1 transport1 tutorial1 viscosity1 vmax1 Vogel–Fulcher–Tammann-Hesse model1 workshop1 yeast1 More...

Marko Petek894 Andrej Blejec249 BioData SynthSys130 Charles Demurjian110 Maja Zagorscak92 Ina Poehner62 Gudrun Gygli58 Malte Herold43 Ziva Ramsak42 Dikshant Pradhan34 Dawie van Niekerk31 Sahar Hassani31 Yi Chen31 Matthias König30 Andrew Millar29 Jacky Snoep28 Karina Dale26 Jan-Willem Veening24 Zdenka Bartosova24 Daniel Seaton24 Niels Zondervan23 Maksim Zakhartsev22 Alexey Kolodkin22 Olga Krebs19 Sebastian Curth19 Jake Schissel17 Theresa Kouril16 Katy Wolstencroft14 Pasquale Linciano14 Martijn Bekker13 Natalia Gebara13 Julia Koblitz13 Xiaokang Zhang12 Praveen kumar Sappa11 Margrete Solheim11 Jacqueline Wolf11 Jon Olav Vik11 Marta Eide11 Mohamed Albadry11 Jana Kalvelage11 Leif Steil10 Markus Wolfien10 Ioannis Metaxas10 Helge Stark9 Yang Jin9 Runyu Liang9 James Wordsworth9 Graceline Tina Kirubakaran8 Julia Scheel8 Sarah Kirstein8 Patrick Becker8 Anette McLeod7 Lorenzo Tagliazucchi7 Lars Wöhlbrand7 Rohola Hosseini7 Paul Heusden6 Holger Janssen6 Wolfgang Müller6 Dong-Hyun Kim6 Hannah O'Keefe6 Anne-Marie Galow6 Sebastian Höpfl6 Katja Bettenbrock5 Hans V. Westerhoff5 Sonja Steinsiek5 Ulf Liebal5 Sandra Maass5 Anna Feldman-Salit5 Jurgen Haanstra5 Thomas Rimpf5 Natalie Stanford5 Fatemeh Zamanzad Ghavidel5 Jennifer Zehner5 Gabriela Loscalzo5 Jay Moore4 Hanna Meyer4 Abeer Fadda4 Franco du Preez4 Daniel Hönicke4 Koen van Grinsven4 Stefan Albaum4 Ulrike Wittig4 Martin Golebiewski4 Inga Leena Angell4 Dorothee Houry4 Theresa Bender4 Karel Sedlar4 Maja Rey3 Michael Kohlstedt3 Antoine Buetti-Dinh3 Fekadu Yadetie3 Evert Bosdriesz3 Christoff Odendaal3 Hong Yang3 Andi N.K.B.P Iskandar3 Matthew Rolfe2 Stefan Henrich2 Alejandro Leroux2 Federico Rojas2 Silvio Hering2 Araz Zeyniyev2 Quyen Nguyen2 Eivind Almaas2 Thomas Harvey2 Cornelius Erbelding2 Chloe Spalding2 Harald Kusch2 Flora D'Anna2 Xiangcheng Li2 Sofia Doello2 Faiz Khan2 Bas Teusink1 Vitor Martins dos Santos1 Michael Ederer1 Maike Bartholomae1 Fiona Achcar1 Antje Sieg1 John Raedts1 Wayne Aubrey1 Ron Henkel1 Fabian Grammes1 Vasundra Toure1 Magny Sidsel Thomassen1 Roel Van Driel1 Lutz Brusch1 Jasper Koehorst1 Huseyin Tas1 Mohamed El Hajjami1 Ines Heiland1 Baudoin Delépine1 Angeles Hueso-Gil1 DAVID RODRIGUEZ ESPESO1 Hannah Kinmonth-Schultz1 Petra Engele1 Ghadeer Mobasher1 PoLiMeR_user Martines_data1 Ahmed Hemedan1 Birger Wolter1 Maria Paola Costi1 Felix Ott1 Chris Wilson1 Sophie Klopfenstein1 Carsten Reuse1 Aaron Laier1 Shareefa AlGhamdi1 More...

TRANSLUCENT716 SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture543 _p_RNAinVAL351 _p_stRT338 PlaSMo model repository130 DigiSal82 NMTrypI - New Medicines for Trypanosomatidic Infections76 IMPAcTB74 MIT SRP59 Systems toxicology of Atlantic cod57 GenoSysFat54 SysMO-LAB52 Millar group50 Towards Reproducible Enzyme Modeling47 SysMetEx44 BaCell-SysMO43 MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection42 COSMIC35 EbN1 Systems Biology31 SUMO30 Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF)30 Consensus Hallmark Annotation29 SysMO DB26 SulfoSys - Biotec26 Noisy-Strep24 MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine23 SulfoSys22 Whole body modelling of glucose metabolism in malaria patients22 Molecular characterization and angiogenic properties of extracellular vesicles in healthy and preeclamptic amniotic fluid19 ROS detailed model for MSB manucript18 Endometriosis18 SilicoTryp17 TiMet17 iRhythmics16 SteaPKMod15 FAIRDOM14 ZucAt13 Computational pathway design for biotechnological applications13 The nucleus of Prorocentrum cordatum13 MOSES10 CML for thermophysical properties of mixtures10 CEPOPA - Development of sustainable chemoenzymatic processes for optically pure amines from alcohols or alkynes10 MetNet10 Molecular Systems Biology9 Selective Destruction in Ageing9 PoLiMeR - Polymers in the Liver: Metabolism and Regulation7 COVID-19 related studies and tools in Germany7 NL-Bioimaging FAIR Metadata Templates7 Working Group Nicole Radde6 Glucose metabolism in cancer cell lines6 de.NBI-SysBio5 BioZEment 2.05 MESI-STRAT5 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 Involved5 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"5 STREAM4 Kinetics on the move - Workshop 20164 Colosys4 NAMPT affinity4 Clostridium beijerinckii pan-genome4 Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum4 IMOMESIC3 pISA-tree3 EmPowerPutida3 Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population3 nfdi4health - German National Research Data Infrastructure for Personal Health Data3 Scalp Acupuncture and Treadmill Training Inhibits Neuronal Apoptosis Through Activating cIAP1 in Cerebral Ischemia Rats3 Electroacupuncture preconditioning reduces oxidative stress in the acute phase of cerebral ischemia-reperfusion in rats by regulating iron metabolism pathways3 Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia3 WineSys2 FAIRDOM user meeting2 WG Infrastructure for Translational Research2 Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa2 INCOME2 SCyCode The Autotrophy-Heterotrophy Switch in Cyanobacteria: Coherent Decision-Making at Multiple Regulatory Layers2 Outreach - Breast Cancer RStudio-Shiny application2 Outreach - Senescence RStudio-Shiny application2 Perennial ryegrass2 Mass spectrometry proteomics for biomarker discovery2 Xenophiles Systems Biology2 Book on Thermodynamics, and kinetics2 Supplemental Data for "Why did the eyewall replacement cycle in Trami terminate rapidly? "2 SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke2 The Effect of Nape Acupuncture Combined with Rehabilitation Training on Dysphagia After Stroke: A Meta-analysis2 Comparative Proteome Profile of Placental Sub-anatomical regions2 FAIR Functional Enrichment2 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 impact2 Manchester Institute for Biotechnology1 ICYSB 2015 - International Practical Course in Systems Biology1 Early Metabolic Injury (LiSyM-EMI - Pillar I)1 Chronic Liver Disease Progression (LiSyM-DP - Pillar II)1 Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III)1 LiSyM Core Infrastructure and Management (LiSyM-PD)1 Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV)1 Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP)1 The Hedgehog Signalling Pathway (LiSyM-JGMMS)1 Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM)1 HUMET Startup1 SEEK tutorial for DigiSal1 Training Hunfeld1 COMBINE Multicellular Modelling1 POP - the Parameter Optimisation Problem1 Regulation of flowering time in natural conditions1 Thesis1 C1Pro1 NAD phylogeny1 Outreach - Simulation of breast cancer development using an agent based modelling approach1 Outreach - Simulation of cellular senescence using an agent based modelling approach1 Simulation Foundries1 FAIRDOM Community Workers1 MIX-UP1 COVID-19 Disease Map1 Test Project (dummy)1 Covid-19 Interferon pathway modelling and analysis1 An overview of systematic reviews of treatment of polycystic ovary syndrome with Chinese medicine1 Thermodynamics1 Non equilibrium thermodynamics1 Coastal Data1 BioCreative VII1 Adaptation of Salmonella enterica1 UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 20221 More...

NIBSys1277 SysMO979 SynthSys184 Independent Projects141 The Digital Salmon92 Drug development for neglected parasitic diseases76 IMPAcTB74 MIT Superfund Research59 dCod 1.0: decoding systems toxicology of cod57 ERASysAPP49 Gygli Group48 SARCHI: Mechanistic modelling of health and epidemiology41 LiSyM - Systems Medicine of the Liver30 de.NBI Systems Biology Service Center (de.NBI-SysBio)29 Hallmarks of cancer 29 e:Bio26 iPlacenta: ​A European Union Horizon 2020 innovative training network (ITN)26 Model repository for M4 (Make Me My Model) clients of ISBE22 FAIRDOM16 Experimental Transplantation Surgery15 Hellenic Foundation for Research and Innovation - Supporting academic Staff and Researchers10 Metastasis Network10 Journals9 nfdi4health - German National Research Data Infrastructure for Personal Health Data9 NL-Bioimaging: FAIR-DM 7 BioZEment5 e:med4 Druglogics4 Clostridium beijerinckii4 Newcastle University Systems Modelling of Ageing3 Breast Cancer Simulation3 Thermodynamics and kinetics for Biology3 Combined therapy involving Scalp Acupuncture and Treadmill Training Inhibits Neuronal Apoptosis in Cerebral Ischemia Rats by regulating cIAP13 Electroacupuncture preconditioning reduces oxidative stress in the acute phase of cerebral ischemia-reperfusion in rats by regulating iron metabolism pathways3 Mathematical modelling of the morphological transition of Pseudomonas aeruginosa2 ILVO test2 Cancer drug discovery preclinical research2 ISBE.NL service programme2 Supplemental Data for "Why did the eyewall replacement cycle in Trami terminate rapidly? "2 DFG founded projects2 The Effect of Nape Acupuncture Combined with Rehabilitation Training on Dysphagia After Stroke2 HUMET1 COMBINE (Computational Modeling in Biology Network)1 Era CoBioTech1 Thesis AHG 20191 Disease Maps1 Covid-19 disease map - Bioinformatics analysis and computational modelling1 An overview of systematic reviews of treatment of polycystic ovary syndrome with Chinese medicine1 More...

Marko Petek895 Falko Krause327 Andrej Blejec248 Dani Valverde219 BioData SynthSys130 Charles Demurjian109 Maja Zagorscak92 Jost Ludwig83 Jacky Snoep69 Ina Poehner62 Rebecca Wade60 Lina Patricia Barreto Parra58 Gudrun Gygli57 Andrew Millar50 Felix Ott44 Malte Herold43 Yang Jin38 Fabian Grammes37 Jon Olav Vik34 Dawie van Niekerk31 Matthias König30 Theresa Kouril29 Dikshant Pradhan29 Yi Chen29 Yin Hoon Chew28 Daniel Seaton27 Per Bruheim26 Zdenka Bartosova26 Joanna Panecka-Hofman25 Jan-Willem Veening24 Hans V. Westerhoff23 Maksim Zakhartsev22 Alexey Kolodkin22 Sebastian Curth19 Thomas Harvey19 Karina Dale18 Olga Krebs17 Katy Wolstencroft16 Raju Prasad Sharma16 Sahar Hassani16 Praveen kumar Sappa15 Matthew Rolfe14 Pasquale Linciano14 Niels Zondervan13 Lu Shen13 Natalia Gebara13 Martijn Bekker12 Graceline Tina Kirubakaran12 Xiaokang Zhang12 Silvia Petrezselyova11 Margrete Solheim11 Jacqueline Wolf11 Markus Wolfien11 Mohamed Albadry11 Uta Dahmen11 Anne-Marie Galow10 Xinmeng Xu10 Paul Heusden9 Helge Stark9 Juergen Pleiss9 Runyu Liang9 Joerg Stuelke8 Phil Wright7 Holger Janssen7 Trong Khoa Pham7 Anette McLeod7 Rohola Hosseini7 Tomas Fiedler6 Sonja Steinsiek6 Wolfgang Müller6 Sandra Maass6 Dong-Hyun Kim6 Ulrike Wittig6 Gareth Gillard6 Virginie Mengin6 Hannah O'Keefe6 Julia Scheel6 Katja Bettenbrock5 Ulf Liebal5 Anna Feldman-Salit5 Jurgen Haanstra5 Thomas Rimpf5 Natalie Stanford5 Antoine Buetti-Dinh5 Inga Leena Angell5 Fatemeh Zamanzad Ghavidel5 Christian Bauer5 Ziva Ramsak5 Jennifer Zehner5 Pål A. Olsvik5 Dorothee Houry5 Theresa Bender5 Eleni Konia5 Ioannis Metaxas5 Lorenzo Tagliazucchi5 Gabriela Loscalzo5 Dietmar Schomburg4 Jaromir Zahrádka4 Hanna Meyer4 Abeer Fadda4 Barbara Bakker4 Alejandro Leroux4 Franco du Preez4 Michael Kohlstedt4 Daniel Hönicke4 Koen van Grinsven4 Stefan Albaum4 Magny Sidsel Thomassen4 Mohamed El Hajjami4 Marta Eide4 Karel Sedlar4 Jake Schissel4 David Hodgson3 Jay Moore3 Guido Hasenbrink3 Alexander Ter Beek3 Inge Jonassen3 Fekadu Yadetie3 Anders Goksøyr3 Evert Bosdriesz3 Odd André Karlsen3 Saptarshi Bej3 Christoff Odendaal3 Andi N.K.B.P Iskandar3 Michael Hecker2 Uwe Voelker2 Trond Ellingsen2 Stuart Owen2 Sara Jabbari2 Øyvind Jakobsen2 Per Bruheim2 Håvard Sletta2 Anders Øverby2 Sunniva Hoel2 Sven Even Borgos2 Michael Ederer2 Stefan Stagge2 Rick Lewis2 Alexander Wentzel2 Stefan Henrich2 Federico Rojas2 Silvio Hering2 Araz Zeyniyev2 Maja Rey2 Quyen Nguyen2 Ulrike Mäder2 Eivind Almaas2 Ansgar Poetsch2 Soeren Bellenberg2 Arne Gjuvsland2 Martin Golebiewski2 Sandve Simen2 Jacob Seilø Torgersen2 Cornelius Erbelding2 Luis Serrano2 Maria Lluch2 Eva Yus2 Alexander Graf2 Katja Baerenfaller2 Chloe Spalding2 Uriel Urquiza Garcia2 Ines Heiland2 Terry G.J. Derks2 Harald Kusch2 Matthias Löbe2 Ligia Akemi Kiyuna2 Carsten Oliver Schmidt2 Moritz Lehne2 Aliaksandra Shutsko2 Sebastian Höpfl2 Maria Paola Costi2 Xiangcheng Li2 Sofia Doello2 Faiz Khan2 Joost Aerts2 Meina Neumann-Schaal2 Sarah Kirstein2 Oscar Kuipers1 Bas Teusink1 Maria Jonsson1 Vitor Martins dos Santos1 David Rand1 David Wild1 Elizabeth Wellington1 Eriko Takano1 Gregory Challis1 Juan-Francisco Martin1 Kay Nieselt1 Lubbert Dijkhuizen1 Maggie Smith1 Nigel Burroughs1 Preben Krabben1 Rainer Breitling1 Wolfgang Wohlleben1 Bettina Siebers1 Walid Omara1 Carole Goble1 M. Tauqeer Alam1 William Gaze1 Brent Kiernan1 Roxane Legaie1 Anthony Palathingal1 R Jansen1 Jens Reuther1 Antonio Rodríguez-García1 Louise Thomas1 Leif Steil1 Sebastian Henkel1 Ibrahim Mehmeti1 Susanne Gerber1 Clara Navarrete1 Jan Maarten van Dijl1 Morris Swertz1 Maria Elena Merlo1 Colin Harwood1 Maike Bartholomae1 joseph newman1 Priyanka Nannapaneni1 Wouter Kuit1 Fiona Achcar1 Antje Sieg1 Ruben Mars1 Eduard Kerkhoven1 John Raedts1 Wayne Aubrey1 Klaas Hellingwerf1 Ron Henkel1 Katharina Kruse1 Rostyslav Kuzyakiv1 Dagmar Waltemath1 Irina Medvedeva1 Lars Snipen1 Dominic Nanton1 Vasundra Toure1 Andreas Albersmeier1 Roel Van Driel1 Jan Boren1 Adil Mardinoglu1 Jasper Koehorst1 Huseyin Tas1 Jan Hasenauer1 Vânia Pobre1 Peter Schaap1 Kathrin Thedieck1 Tobias Anzeneder1 Mathias Ziegler1 Baudoin Delépine1 Janina Leyk1 Eileen Marie Hanna1 Angeles Hueso-Gil1 DAVID RODRIGUEZ ESPESO1 Hannah Kinmonth-Schultz1 Petra Engele1 Ghadeer Mobasher1 PoLiMeR_user Martines_data1 Alejandra Gilabert1 Ahmed Hemedan1 Hong Yang1 Birger Wolter1 Leonard Schmiester1 Emmalie Jager1 Johannes Darms1 Chris Wilson1 Sophie Klopfenstein1 Julia Koblitz1 Aaron Laier1 Shareefa AlGhamdi1 More...

Data6 Molecular property (general)1 Organism report1

PDB26 ZIP format23 Format (by type of data)3 xlsx2 Workflow format1

Experimental Assay Type1384 Model Analysis Type627 Gene Regulatory Network132 Transcriptomics56 Metabolic Network33 Metabolite Profiling29 Proteomics29 http://www.mygrid.org.uk/ontology/JERMOntology#metabolomics28 Metabolomics17 Organism or Strain Characteristics15 Gene Expression Profiling13 Enzymology12 Cultivation Experiment11 MicroRNA Profiling11 Protein Quantification11 Metabolism9 Enzymatic Assay8 Gene Expression7 Metabolite Concentration7 Transcriptional Profiling7 Genomics6 Protein Expression Profiling5 RNA-seq Profiling5 Genome Scale4 Discontinuous Enzymatic3 Extracellular Metabolite Concentration3 Glucose Pulse3 Protein Identification3 Interactomics2 Intracellular Metabolite Concentration2 Cell Count1 Cell Cycle1 Signal Induction1 More...

Technology Type1380 Next generation sequencing42 Mass Spectrometry33 http://www.mygrid.org.uk/ontology/JERMOntology#metabolomics28 Liquid Chromatography Mass Spectrometry23 Microarray19 Rna-seq17 Gas Chromatography Mass Spectrometry16 Custom Array10 Enzymatic Activity Measurements10 Liquid Chromatography-tandom Mass Spectrometry9 Imaging8 Tandem Mass Spectrometry8 HPLC7 NMR7 Orbitrap Velos7 qPCR7 qRT-PCR7 Microscopy5 Initial Rate Experiment4 Isotope Ratio Mass Spectrometry3 ChIP-on-chip2 Electrophoresis2 2D Gel Electrophoresis1 Chemostat Measurement1 Chromatography1 Gas Chromatography1 Gel Electrophoresis1 Ion Mobility Spectrometry Mass Spectrometry1 Molecule Labelling1 UPLC1 More...