Studies
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In this study, we integrate COVID19 Disease Maps curated regulatory information in a macrophage logical model. This allows logical simulations of the effects of acute inflammation caused by the SARS-CoV-2 virus, both in general and in a cell-specific perspective. Moreover, understanding the regulatory network behavior of macrophages following infection opens new ways to test and predict drug and drug combination effects, as a first step towards the development of new treatments.
Submitter: Viviam Solangeli Bermúdez Paiva
Investigation: Macrophage logical modeling
Assays: No Assays
Validation Validated against original code running under GNU FORTRAN 95. Comments on numerical integration No integration needed. Comments on running the (Simile) model The variable "num errors" accumulates the number of times the ribulose bis-phosphate limited photosynthesis rate cannot be calculated. See the documentation dialogue for the Simile variable "jl_electron transport" for details.Additional AttributesOriginal Model: Language: FORTRAN 95 Author:Daniel P. Rasse File name of original ...
Submitter: BioData SynthSys
Investigation: Davey, Chris
Assays: C3 photosynthesis (Farquhar, von Caemmerer, Berry) model - PLM_1, version 1
This study involves all data gathered from the Kollevåg study - studying environmental pollution at a capped waste disposal site in Kollevåg, Askøy.
Cod were caged in Kollevåg (Stations 1, 2 and 3 - from inner to outer parts) and at a reference location (Ref station) for a period of six weeks, from 2nd September 2016, to 17-18th October 2016.
Submitter: Karina Dale
Investigation: 1 hidden item
Assays: Chemical analyses, Enzyme activity assays, Enzyme immunoassay, Fish Biometrics, Gene expression, TBARS: Oxidative stress, Vitellogenin in blood plasma, Western blot - protein expression
Carbon loss due to instability of gluconeogenic pathway intermediates (BPG, GAP, DHAP) at high temperature in S. solfataricus
HSD11B1 was inhibited by CBX and the effect of the inhibition on Cortisone and 11KA4 conversion by HSD11B1/AKR1C3 incubations were measured.
Caylin G. Winchell, Sarah K. Nyquist, Michael C. Chao, Pauline Maiello, Amy J. Myers, Forrest Hopkins, Michael Chase, Hannah P. Gideon, Kush V. Patel, Joshua D. Bromley, Andrew W. Simonson, Roisin Floyd-O’Sullivan, Marc Wadsworth, Jacob M. Rosenberg, Rockib Uddin, Travis Hughes, Ryan J. Kelly, Josephine Griffo, Jaime Tomko, Edwin Klein, Bonnie Berger, Charles A. Scanga, Joshua Mattila, Sarah M. Fortune, Alex K. Shalek, Philana Ling Lin, JoAnne L. Flynn; CD8+ lymphocytes are critical for early ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Extraction - Metadata, DNA Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Attached, Immunohistochemistry - Data Linked, PET/CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Cell free extract - pathway analysis for Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, and Mn2+ on Xylose to aKG conversion is studied.
Cell survival was determined under different benzoic acid concentrations
This is the representation of major parts of the central metabolism in monocotyledon plants. The information has been derived from the MetaCrop [2] database, a manually curated repository of high quality information concerning the metabolism of crop plants. This includes pathways, reactions, locations, transport processes, and moreOriginally submitted to PLaSMo on 2012-03-05 11:52:18
Submitter: BioData SynthSys
Investigation: Beaton, Martin
"The CENTURY model is a general model of plant-soil nutrient cycling which is being used to simulate carbon and nutrient dynamics for different types of ecosystems including grasslands, agricultural lands, forests and savannas. CENTURY is composed of a soil organic matter/ decomposition submodel, a water budget model, a grassland/crop submodel, a forest production submodel, and management and events scheduling functions. It computes the flow of carbon, nitrogen, phosphorus, and sulfur through ...
Submitter: BioData SynthSys
Investigation: Muetzelfeldt, Robert
Mutant strains in which one or more of the potential glucose uptake systems was deleted have been analyzed in aerobic and anaerobic batch cultures, as well as aerobic chemostat cultures.
Submitter: Sonja Steinsiek
Investigation: Analysis of the glucose transport in Escherichi...
Assays: Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Characterization of MG1655 and mutant strains under conditions of glucos..., TFinfer2
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Originally submitted to PLaSMo on 2015-09-02 18:27:55
Submitter: BioData SynthSys
Investigation: Zielinski, Tomasz
Chemical named entity recognition (NER) is a significant pre-processing task in natural language processing. Identification and extraction of chemical entities from biomedical literature and entities linking to the knowledge base are essential steps for the chemical text-mining pipeline. However, the identification of chemical entities in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we ...
This is a photothermal model for Arabidopsis that predicts flowering time, published in Chew et al (2012). It is an improved version of the model in Wilczek et al (Science 2009). A Simile version of the model is attached. Instructions to run the Photothermal Model in Simile 1. Download the Simile file attached or import the XML into Simile: a. File > Import > XML Model Description 2. To run the model: a. Model > Run or click on the ‘Play’ ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Chew_et_al_2012_Photothermal_Model - PLM_73, version 1
This is the Framework Model (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111) that links the following: 1. Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - Carbon Dynamic Model 2. Part of the Christophe et al 2008 Functional-Structural Plant Model 3. Chew et al 2012 Photothermal Model 4. Salazar et al 2009 Photoperiodism Model To run the model in Simile, please download the Evaluation Edition of the software from http://www.simulistics.com/products/simile.php ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
This is a collection of data involving choline chloride:glycerol:water mixtures stored in CML.
Here we develop a set of new tools for S. pneumoniae and as a case study we show that S. pneumoniaea SMC is recruited to oriC by ParB and promotes chromosome segregation.
Submitter: Jan-Willem Veening
Investigation: Wetlab approach to transcription fidelity
Assays: ParB-GFP ChIP on chip
Jing Ge, Le P. Ngo, Simran Kaushal, Ian J. Tay, Elina Thadhani, Jennifer E. Kay, Patrizia Mazzucato, Danielle N. Chow, Jessica L. Fessler, David M. Weingeist, Robert W. Sobol, Leona D. Samson, Scott R. Floyd, Bevin P. Engelward,*
Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439179/
DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have ...
The two lactic acid bacteria L. lactis and S. pyogenes were studied with respect to the concentration of intracellular metabolites involved in glycolysis in time upon a glucose pulse. Models that describe this behavior are also constructed
Submitter: Martijn Bekker
Investigation: Investigation of glycolysis and pyruvate branch...
Assays: Global sensitivity analysis, Glucose pulsed L. lactis, Glucose pulsed S. pyogenes, Kinetics of L-lactate dehydrogenase from L. lactis, Model of L. lactis glycolysis, Regulation of the activity of lactate dehydrogenases from four lactic ac...
Multiple studies have devised mapping schemes to associate cancer hallmarks with Gene Ontology terms and biological pathway. This study compares the similarities and differences between them, in order to establish consensus knowledge.
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Submitter: Theresa Kouril
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Assays: Cell free extract activity measurements: L-fuc/d-glc, Metabolic model of Sulfolobus solfataricus, Proteome analysis: d-fuc / l-glu, RNA sequencing:l-fuc/d-glu, intracellular metabolome analysis: l-fucose vs d-glucose
To investigate phenol degradation in Saccharolobus solfataricus transcriptome and metabolome analyses were performed with cells grown on phenol as sole carbon source. Cells grown on D-glucose served as reference. Metabolic modelling was used to compare efficiency of phenol utilization in terms of oxygen demand and energy yield with the reference condition.
Submitter: Jacqueline Wolf
Investigation: Phenol degradation in Saccharolobus solfataricu...
Assays: Metabolome analysis: phenol vs D-glucose, RNA Sequencing: phenol vs D-glucose
To investigate amino acid degradation pathways in Sulfolobus solfataricus transcriptome, proteome and metabolome analyses were performed on cells grown on caseinhydrolysate as carbon source. Cells grown with glucose served as reference condition. Metabolic modelling was used to compare the efficiency of different degradation routes.
Submitter: Jacqueline Wolf
Investigation: Amino acid degradation in Sulfolobus solfataric...
Assays: Metabolic modelling of S. solfataricus during growth on casaminoacids, Metabolome analysis: Casaminoacids versus D-Glc, Proteome analysis: Casaminoacids versus D-Glc, RNA sequencing: Casaminoacids vs D-glc
Surface plots showing the computational analysis of combined HSD11B1/AKR1C3 ratios and HSD11B1 inhibition.
Submitter: Jacky Snoep
Investigation: Effect of 11BHSD inhibition on 11-ketotestoster...
Assays: Model for computational analysis of HSD11B1/AKR1C3 ratio variation and H...
Sequence and electrostatic potential analyses to identify sites in tubulins that differ between dinitroaniline-sensitive and dinitroaniline-resistant species.
The FMv1 was constructed from 4 existing models, with Matlab and Simile versions.
Submitter: Andrew Millar
Investigation: Arabidopsis Framework Model v1, predicting rose...
Assays: Arabidopsis Framework Model v1, Matlab and Simile version
Modelling and experiments for FMv2 components.
Assays for model composition here, in order to share model files; potentially training and validation data in other Studies.
Submitter: Andrew Millar
Investigation: Temperature effects on Arabidopsis floral induc...
Submitter: Malte Herold
Investigation: SysMetEx - Dataset collection
Assays: Proteomics rawdata, RNAseq rawdata
In this kind of studies sigmaB stress response is induced by the addition of artificial inducers of sigmaB. For example simgaB is downstream of a Pspac promoter and induced by the addition of IPTG. A ctc::lacZ reporter gene is used to monitor sigmaB activity.
Submitter: Ulf Liebal
Investigation: The transition from growing to non-growing Baci...
Assays: IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Stressosome activation dynamics
Predictions made using the core model for combinatorial perturbations to the model simulating combined effects from OE, KO mutants, perturbations and time series concentrations.
Submitter: Niels Zondervan
Investigation: Modelling of M. pneumoniae metabolism
Assays: 40 samples, OE mutants of glycolysis and pyruvate metabolism enzymes com...
Validation of the core model of glycolysis, pyruvate metabolism and ATPase reaction using OE, KO mutant samples and perturbation samples
Training of the core model, parameter estimation using Evolutionary Programming using metabolomics, proteomics and some flux data. The core model contains reactions in glycolysis, pyruvate metabolism and ATPase
These templates can be used for a selection of metabolomics data types. There is a MASTER template for general use and adaptation as well as several more specific templates for particular types of experiment (e.g. HPLC), or specific assay types (e.g glucose pulse)
Submitter: Olga Krebs
Investigation: Creating data sheet template for 'omics data
Assays: Metabolomics Master Template, Standard-based Excel template for metabolomics data
Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources
Submitter: Katy Wolstencroft
Investigation: Creating data sheet template for 'omics data
Assays: Proteomics Template (gel electrophoresis), Proteomics Templates (Mass spectrometry)
Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.
How does the current mediated by Trk1,2 depend on external and internal ion concentrations? How is the membrane potential shifted by the concentrations of various ions, especially ammonium?
How does the current mediated by Trk1,2 depend on external and internal ion concentrations? How is the membrane potential shifted by the concentrations of various ions, especially ammonium?