Investigations
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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).
Submitter: Viviam Solangeli Bermúdez Paiva
Studies: C19DM - Macrophage logical model
Assays: No Assays
The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. In this investigation we compare cancer hallmark mapping strategies from different studies, based on Gene Ontology and biological pathway annotation. By analysing the semantic ...
Submitter: Katy Wolstencroft
Studies: Comparing Cancer Hallmark Descriptions, Evolution of Gene Ontology Terms, Prognostic and Hallmark Gene Networks
Assays: Analysing Changes to GO Biological Process, Annotation Consensus and GO Consensus, Hub genes of modules and enriched GO terms, Jaccard Index Prognostic Hallmark Genes, WGCNA Prognostic Hallmark Genes
The aim of this investigation is to understand molecular mechanisms of PUFA biosynthesis and regulation in order to enable the sustainable use of vegetable oils in aquafeeds as current sources of fish oils are unable to meet increasing demands for omega-3 PUFAs. By generating gene knockouts, we would like to study the genes that are crucial for multi-tissue synthesis of PUFA synthesis in vivo.
Multidisciplinary development of selective anti-parasitic multi-target inhibitors of PTR1/DHFR based on a pteridine scaffold.
Submitter: Ina Poehner
Studies: Docking to PTR1 and DHFR targets and off-targets, In silico property and correlation analysis
Assays: Compound library preparation, Correlation analysis between PTR1 and DHFR activities and anti-parasitic..., Correlation analysis between predicted ADMET properties and anti-parasit..., Docking receptor preparation, In silico ADMET data prediction, Induced-fit docking studies, PAINS filtering, Rigid-body docking studies
Present in many industrial effluents and as intermediate of lignin degradation, phenol is a widespread pollutant causing serious environmental problems, due to its toxicity to animals and humans. Removal of phenol from the environment by bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation in hostile environments. We combined metabolomics and transcriptomics together with metabolic modelling to elucidate the organism’s response to growth ...
Consortium website: https://covidclinical.net/
Slack: https://c19i2b2.slack.com/ Owner: Nils Gehlenborg (nils@hms.harvard.edu)
i2b2 tranSMART Foundation Call to Action: https://transmartfoundation.org/covid-19-call-to-action/
Submitter: Harald Kusch
Studies: General Information, Phase 1, Phase 1.1, Phase 2
Assays: Chats, Instructions, Websites
Objectives: Empowering smooth implementation and fruitful completion of all WPs and tasks. Implementation of a data management plan for efficient dissemination under F.A.I.R. principles.
Description of Work: The PI of the project with the heads of the collaborating groups will closely monitor the progress of the technical and administrative tasks and it will implement actions to correct any deviation from the established work-plan. The whole group will meet regularly every six months or more ...
Objectives: Establishment of the chemoenzymatic process with the best GO-ATA hybrid catalysts. Highlighting of the potential of the process in semi-preparative scale.
Description of Work: The best hybrid catalysts identified in WP3 will be investigated in coupled one-pot reactions selected in WP1, in batch and continuous flow reactors. The productivity of the system will be optimized with response surface methodology (RSM), for parameters such as temperature, duration, substrate concentration ...
Objectives: Development of efficient ATA immobilization approach. Production of a hybrid catalyst of high catalytic efficiency.
Description of Work: Τhe ATAs selected in WP2 will be expressed, purified and covalently and/or non-covalently immobilized on the GO selected in WP1. The catalytic behavior (in terms of catalytic activity, stability and reusability) and the structural implications of the immobilization will be investigated. For comparison purposes, the non-optimized ATAs (prior to the ...
Objectives: Identification of amine transaminases (ATAs) able to catalyze efficiently the amination of a desired set of ketones and aldehydes (expected products of GO oxidation). Optimization of the most potent biocatalysts, in terms of catalytic efficiency, stability, availability of functional groups for covalent immobilization.
Description of Work: ATAs from our construct selection (>30 wild-type and variants of both (R)- and (S)-enantioselectivity) with different substrate selectivity will ...
Objectives: Protocol identification and establishment for the synthesis of high-performing catalytic GO in the desired oxidation reactions under mild conditions. Characterization of the most prominent materials synthesized and comparison to commercially available material.
Description of Work: Several established chemical methods will be used for the synthesis of GO. Each batch will be characterized, for instance for its C/O ratio, surface area and conductivity. The catalytic profile of the ...
Submitter: Matthias Löbe
Studies: Entwicklung eines Tests zum Nachweis der Immunantwort bei Covid-19 (CoV2...
Assays: No Assays
Die Charité – Universitätsmedizin Berlin betreibt gemeinsam mit dem Berlin Institute of Health Clinical Study Center (BIH-CSC) eine zentrale Registerstudie ("Pa-COVID-19") und Phänotypisierungs- plattform für alle an der Charité behandelten Patienten mit COVID-19. Pa-COVID-19 dient der harmonisierten und standardisierten klinischen und molekularen Phänotypisierung von COVID-19 Patienten. Übergeordnetes Ziel ist die schnelle und umfassende Charakterisierung von COVID-19 zur Identifikation von ...
Governments and policymakers take different measures vis-à-vis the COVID-19 crisis, ranging from advice to reduce social activities, to a complete lock down of society and economy. To support them with tools that enable them to fulfill their tasks we constructed a differential equation model for the COVID-19 epidemics using systems biology methodologies.
Collection of cross-links to other sites that gather COVID-19 information
Submitter: Harald Kusch
Studies: University Medical Center Göttingen, ZB MED – Informationszentrum Lebenswissenschaften
Assays: COVI-19 Übersicht
Submitter: Jurgen Haanstra
Studies: Inhibition with Sulfasalazine (SSZ), Measurements of metabolism of HepG2 cells at 0 mM, 6 mM or 22 mM externa..., protein per cell for HepG2 cells
Assays: Cell counts and BCA Protein, Cell counts and metabolite levels, Inhibition experiment for the effect of SSZ on HepG2 metabolism
The raw data generated in the scope of the SysMetEx project for RNAseq, proteomics, and imaging analysis. The data was generated on single and mixed species cultures of A. Caldus, L.ferriphilum, and/or S.thermosulfidooxidans. Raw RNA data is combined in an ENA umbrella study summarising all short read data generated in the project. Raw proteomics data is provided for distinct conditions at the pride repository. Imaging data is provided for distinct conditions at a zenodo repository.
Submitter: Malte Herold
Studies: Biofilms on chalcopyrite grains, Continuous cultures, Planktonic cells, Supplemental Files
Assays: Links to code repositories, Microscopy imaging, Proteomics rawdata, Proteomics rawdata, Proteomics rawdata, RNAseq rawdata, RNAseq rawdata, RNAseq rawdata, Supplemental Files
The oxidative Weimberg pathway for the five-step pentose degradation to α ketoglutarate from Caulobacter crescentus is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. Here, we developed a novel iterative approach involving initial rate kinetics, progress curves, and enzyme cascades, with high resolution NMR analysis of intermediate dynamics, and multiple cycles of kinetic modelling analyses to construct and validate a quantitative model ...
Submitter: Jacky Snoep
Studies: Cell free extract, Initial rate kinetics, One pot cascade, Progress curves
Assays: Cell free extract, with Mn and NAD recycling, Cell free extract, with Mn, no NAD recycling, Cell free extract, without added Mn, with NAD recycling, KDXD, KGSADH, One pot cascade 10, One pot cascade 12, One pot cascade 13, One pot cascade 16, Progress curve KDXD, Progress curve KGSADH, Progress curve XAD, Progress curve XDH, Progress curve XLA, Progress curves combined, Steady state cell free extract, with Mn and NAD recycling, XAD, XDH, XLA
Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: F2014.1 - PLM_1030, PLM_67v3withTempPulse - PLM_81
Assays: F2014.1 - PLM_1030, version 1, PLM_67v3withTempPulse - PLM_81, version 1
Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes
RELATED ...
Submitter: Maja Zagorscak
Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: Supplementary Information, _A_01_GC_content-count, _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_02_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
- To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae
- To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M. hyopneumoniae for vaccine optimization
- To deploy the metabolic model(s) to: 1) the rational design and optimization of the vaccine chassis; 2) aid the development of a higher-growth rate chassis; 3) assist the development of a nutrient optimized a serum-free growth medium and; 4) assess, at genome scale, the metabolic ...
Submitter: Niels Zondervan
Studies: Core Model predictions, Core Model training, Core model predicting combined mutations and perturbations, Genome-scale, constraint-based metabolic modeling of M. hyopneumonia, Metabolomics measurements, Proteomics analysis, Transcriptomics of M. pneumoniae at different times of growth
Assays: 40 samples data analysis - metabolite correlation, 40 samples, OE mutants of glycolysis and pyruvate metabolism enzymes com..., All samples data, Comparison of Kcat values from the model and values from literature, Construction and training of the core model, Construction of a Genome Scale Metabolitic model of M. hyopneumoniae, Dynamic model simmulation pipeline, Metabolic control analysis (local and global), Metabolomics external metabolites measurements, Metabolomics internal metabolites, time series measurements, Proteomics assay, Transcriptomics assay of M. pneumoniae at diferent times of growth, Validation by simulating independent mutant and perturbation samples
Project to test effects of temperature cycles on expression of Arabidopsis florigen gene FT, and whether these are mediated by temperature-dependent leaf development or temperature-specific FT expression, or both. Re-used and extended Arabidopsis Framework Model v1 to address this question. Led by Hannah Kinmonth-Schultz in Kim and Imaizumi labs, collaborating with Millar lab.
Submitter: Andrew Millar
This is a collection of deep eutectic solvent (DES) experimental and simulation data that is stored in CML format and analysed using gradient boosting decision trees.
Collection of models submitted to PLaSMo by Yin Hoon and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Chew_et_al_2012_Photothermal_Model - PLM_73, Chew_et_al_2014_Framework_Model - PLM_76, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75, Salazar Photoperiodism Model with T6P - PLM_82, Salazar_et_al_2009_Photoperiodism_Model - PLM_74
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1, Chew_et_al_2014_Framework_Model - PLM_76, version 1, Part_of_Christophe_et_al_2008_Functional_Structural_Plant_Model - PLM_75..., Salazar Photoperiodism Model with T6P - PLM_82, version 1, Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: Arabidopsis clock model P2011, graphical diagram - PLM_1045, Arabidopsis clock model P2011.3.1 - PLM_1041, Arabidopsis clock model P2011.4.1 - PLM_1042, Arabidopsis clock model P2011.5.1 - PLM_1043, Arabidopsis clock model P2011.6.1 - PLM_1044, Arabidopsis clock models P2011.1.2 and P2011.2.1 - PLM_71, Arabidopsis_clock_P2011 - PLM_64, Arabidopsis_clock_P2012 - PLM_70, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, AuxSim - PLM_27, AuxSim full - PLM_30, DomijanTS_AtClock2011 - PLM_50, Locke2005_CircadianClock_tanh - PLM_8, Locke2006_CircadianClock_tanh - PLM_10, OK MEP pathway 2013 - PLM_72, P2012_AJMv2_NoABA - PLM_69, Salazar2009_FloweringPhotoperiod - PLM_9, Sorokina2011_Ostreo_starch - PLM_44, Wilczek photothermal Science - PLM_48
Assays: Arabidopsis clock model P2011, graphical diagram - PLM_1045, version 1, Arabidopsis clock model P2011.1.2 - PLM_71, version 1, Arabidopsis clock model P2011.2.1 - PLM_71, version 2, Arabidopsis clock model P2011.3.1 - PLM_1041, version 1, Arabidopsis clock model P2011.4.1 - PLM_1042, version 1, Arabidopsis clock model P2011.5.1 - PLM_1043, version 1, Arabidopsis clock model P2011.6.1 - PLM_1044, version 1, Arabidopsis_clock_P2011 - PLM_64, version 1, Arabidopsis_clock_P2011 - PLM_64, version 2, Arabidopsis_clock_P2011 - PLM_64, version 3, Arabidopsis_clock_P2011 - PLM_64, version 4, Arabidopsis_clock_P2012 - PLM_70, version 1, Arabidopsis_clock_P2012 - PLM_70, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 1, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 2, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 3, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 4, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 5, At_Pokh2011_LD_degr_Op1Ap3.xml - PLM_67, version 6, At_Pokh2011v6_plasmo_ltdParams.xml - PLM_68, version 1, AuxSim - PLM_27, version 1, AuxSim full - PLM_30, version 1, DomijanTS_AtClock2011 - PLM_50, version 1, DomijanTS_AtClock2011 - PLM_50, version 2, Locke2005_CircadianClock_tanh - PLM_8, version 1, Locke2006_CircadianClock_tanh - PLM_10, version 1, OK MEP pathway 2013 - PLM_72, version 1, P2012_AJMv2_NoABA - PLM_69, version 1, P2012_AJMv2_NoABA - PLM_69, version 2, Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2, Sorokina2011_Ostreo_starch - PLM_44, version 1, Wilczek photothermal Science - PLM_48, version 1, Wilczek photothermal Science - PLM_48, version 2
Project to test effects of natural compared to growth chamber 16:8 LD cycles, on expression of Arabidopsis flowering-time genes, and to define the genetic mechanisms and environmental triggers involved. Led by Young-Hun Song and Akane Kubota in the Imaizumi lab, with collaborators testing plants in parallel in Zurich and Edinburgh.
Supplementary files for the submission: Reverse Engineering Directed Gene Regulatory Networks from Transcriptomics and Proteomics Data of Biomining Bacterial Communities with Approximate Bayesian Computation and Steady-State Signalling Simulations
Submitter: Malte Herold
Studies: Supplementary files
Assays: Proteome data, RNA data, Simulations for network engineering
