Absolute quantification of proteins using heavy labeled QconCAT as an internal standard and quantifying the native proteins in the complex sample via scheduled Multiple Reaction Monitoring(MRM) .

Testing the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Generates Fig. 2 C and D in the associated publication. Data from Aoyama et al. (1995).

Downoad and unzip "Model_notebooks.rar" and run "6, Fig2C+D-ACAD-partitioning-validation-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb".

Further fluxes (ammonium, chloride, calcium) will be measured dependent on the capacities of the MIFE/FLISE technique.

Antibody-Dependent Functional Profiling (ADFP) is a multiplexed systems serology approach that quantifies the capacity of antigen-specific antibodies to engage Fc receptors and activate diverse innate immune effector functions. The assay simultaneously measures multiple antibody-dependent activities — including phagocytosis (ADCP, ADNP), complement deposition (ADCD), and NK cell activation (ADNKA) — providing a comprehensive functional fingerprint of the humoral immune response. Antigen-coupled ...

Glucose transporter mutants were analyzed under aerobic and aerobic conditions in batch cultures with glucose as substrate. Acetate formation rates and glucose consumption rates were measured, as well as extracellular cAMP concentrations.

MG1655 and mutant strains with defects in glucose transport systems were analyzed in aerobic and anaerobic batch cultures.

Some examples of transcriptomics templates for Affymetrix data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

Penman Evaporation over water ( mm/day ). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).

Related Publications
Porter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82..

Originally submitted to PLaSMo on 2011-02-04 15:17:42

Number of days between 2 Julian days allowing for change of year and leap years. Assumptions : The gap between the two dates is less than 1 year also JDAY1 is before JDAY2. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).  Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82.. Originally submitted to PLaSMo on 2011-02-04 15:24:25 ...

Transform Calendar day to Julian Day. Converts day, month, year into the equivalent Julian Day allowing for leap years. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen. . Eur. J. Agron. 2(2): 69-82.. Originally submitted to PLaSMo on 2011-02-04 15:30:45

To calculate leaf and sheath dimensions for main stems and tillers given the emergence length of their leaves and empirical relationships linking leaf number to maximum laminar length. All sizes are in mm. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box.Related ...

To calculate today's daylength and photoperiod. Daylength is calculated following the treatment of Sellers, Physical Climatology,pp 15-16 and Appendix 2. Daylength is calculated with a correction for atmospheric refraction equivalent to 50 minutes of a degree. Photoperiod is calculated assuming that light is perceived until the centre of the sun is 6 degrees below the horizon. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and ...

To return daily thermal time with base TBASE. Thermal time for a day is calculated by splitting the 24 hour period into 8 * 3 hour periods whose relative contribution to thermal time for the day is based on a cosinusoidal variation in temperature between observed maximum and minimum values. See Weir,A.H. et al.,(1984).J.Agric.Sci.,Camb.,102,371-382. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).     All variables and parameters that are inputs ...

To return Vapour pressure calculated from Wet and Dry Bulb Temperatures. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly).

Related Publications
Porter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to Water and Nitrogen.. Eur. J. Agron. 2(2): 69-82..

Originally submitted to PLaSMo on 2011-02-04 15:55:57

To return today's vernalising effect (see Weir,A.H. et al.,(1984).J.Agric.Sci.,Camb.,102,371-382). This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box.Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of Wheat Incorporating Responses to ...

This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). Reads and processes todays weather data. Calculates Penman evaporation and converts day/month/year to Julian day (allowing for year change and leap years). We acknowledge Mikhail Semenov for kindly allowing us to supply this Rothamsted weather data set with this model. Euler integration with 1 day time steps.Related PublicationsPorter J (1993). AFRCWHEAT2: A Model of the Growth and Development of ...

To calculate the phenological stage of the crop. Note the following definition: phase = the period between two phenological stages, ie. the phase sowing to emergence. This is a submodel of AFRC Wheat 2 model in Simile notation (the XML version will follow shortly). All variables and parameters that are inputs to the submodel are in the "inputs " submodel box, all variables changed by the submodel are outputted via the "outputs" submodel box. Euler integration with 1 day time steps.Related ...

Originally submitted to PLaSMo on 2010-12-20 14:54:15

Kinetic characterisation en mathematical modelling of ALD.

Simple overview of all samples used for training, internal validation by copasi en external validation. Overview of samples metadata, mean metabolite concentration and enzyme concentrations used in the model. Only metabolites present in the model are shown.

Based on Hess et al. (2006) ammonium is suspected to be transported via Trk1,2 under potassium shortage. The ammonium concentration in the medium will be determined for several time points under the conditions of Navarrete et al. (2010).

This document describes by-product formation rates measured in MG1655 at steady-state conditions in Infors-Multifors-Bioreactors.

Analysis of Control Strains Neurospora crassa

Description

Purpose

Compare different siblings of the parental/control strains in the global screening of transcription factors capable to affect the circadian oscilator

Comments

Python workflow for the analysis of ITC-BIND, ITC-MIM and ITC-(r)SIM experiments. Organized in a *.zip folder. Requires the following directory structure:

./ITC_analysis.py ./input/BINDING/.apj ./input/BINDING/.csv ./input/KINETICS/.apj ./input/KINETICS/.csv ./scripts/binding_neu.py ./scripts/kinetics_neu.py

And can be executed by running python ITC_analysis.py in the directory. Filenames for the input *.apj and *.csv files are defined in ITC_analysis.py. The output directory is written by ...

Python workflow for the analysis of ITC-BIND, ITC-MIM and ITC-(r)SIM experiments. Organized in a *.zip folder. Requires the following directory structure:

./ITC_analysis.py ./input/BINDING/.apj ./input/BINDING/.csv ./input/KINETICS/.apj ./input/KINETICS/.csv ./scripts/binding_neu.py ./scripts/kinetics_neu.py

And can be executed by running python ITC_analysis.py in the directory. Filenames for the input *.apj and *.csv files are defined in ITC_analysis.py. The output directory is written by ...

This assay describes how to analyze gene expression rates via RT-PCR.

This is the analysis part of the Simulation Foundry, Version 1.5.

Download and unpack the zip file and the .sh bash script. Copy them into a folder which has a meaningful name. Launch the bash script, following the instructions in the manual.

Make sure you followed the instructions in "Preparation" before running this.

An antibody dependent complement deposition assay measures complement activation following antibody binding. The process detects deposition of complement proteins as an indicator of antibody-mediated immune function. Input: Antibody-treated target cells or particles Output: Complement deposition data file or fluorescence readout.

Antibody Dependent Functional Profiling* and Analysis Represents:

ADMP: Macrophage Phagocytosis

ADNP: Neutrophil Phagocytosis

ADDCP: Dendritic Cell Phagocytosis

An antibody titer assay determines the concentration of antibodies in a sample through serial dilution and detection. The process measures the dilution at which a detectable signal is maintained to assess immune strength. Input: Serum or antibody-containing sample Output: Quantitative antibody titer value.

Antibody titer analysis interprets and visualizes quantitative results from antibody titration assays. It calculates endpoint values and generates comparative summaries across samples or timepoints. Input: Raw antibody titer data Output: Processed antibody concentration results and summary plots.

Antibody-dependent cellular phagocytosis measures immune cell uptake of antibody-coated targets. The assay quantifies phagocytic activity as an indicator of antibody function and cellular response. Input: Antibody-treated target cells and effector cells Output: Phagocytosis data file (e.g., fluorescence or imaging-based readouts).

Antibody-dependent cellular phagocytosis measures immune cell uptake of antibody-coated targets. The assay quantifies phagocytic activity as an indicator of antibody function and cellular response. Input: Antibody-treated target cells and effector cells Output: Phagocytosis data file (e.g., fluorescence or imaging-based readouts).

Antibody-dependent cellular phagocytosis measures immune cell uptake of antibody-coated targets. The assay quantifies phagocytic activity as an indicator of antibody function and cellular response. Input: Antibody-treated target cells and effector cells Output: Phagocytosis data file (e.g., fluorescence or imaging-based readouts).

Antibody-dependent cellular phagocytosis analysis processes raw uptake data to quantify immune cell activity. It calculates phagocytic scores, normalizes results, and generates comparative summaries. Input: Raw phagocytosis data Output: Processed activity metrics and visualized response profiles.

Antibody-dependent complement deposition measures complement protein binding following antibody interaction. The assay detects complement activation as an indicator of antibody-mediated immune function. Input: Antibody-coated target cells Output: Complement deposition measurement or fluorescence data file.

Antibody-dependent neutrophil phagocytosis evaluates antibody-mediated uptake of targets by neutrophils. It measures fluorescence or imaging-based signals to assess innate immune activity. Input: Antibody-labeled target cells and neutrophils Output: Phagocytosis data file indicating neutrophil uptake efficiency.

Antibody-dependent neutrophil phagocytosis evaluates antibody-mediated uptake of targets by neutrophils. It measures fluorescence or imaging-based signals to assess innate immune activity. Input: Antibody-labeled target cells and neutrophils Output: Phagocytosis data file indicating neutrophil uptake efficiency.

Antibody-dependent neutrophil phagocytosis evaluates antibody-mediated uptake of targets by neutrophils. It measures fluorescence or imaging-based signals to assess innate immune activity. Input: Antibody-labeled target cells and neutrophils Output: Phagocytosis data file indicating neutrophil uptake efficiency.

This assay quantifies the ability of antibodies to mediate neutrophil-driven phagocytosis of target antigens (such as viral particles, bacteria, or opsonized beads), serving as a functional measure of antibody-mediated innate immune effector activity. Primary human neutrophils or neutrophil-like cell lines are incubated with fluorescently labeled antigen-antibody complexes, and phagocytic uptake is assessed by flow cytometry to determine the proportion of neutrophils that have internalized the ...

Antibody-dependent NK cell activation measures natural killer (NK) cell responses triggered by antibody-coated targets. The assay detects cytokine release or surface marker expression as indicators of immune activation. Input: Antibody-treated target cells and NK effector cells Output: Cytometric or fluorescence data representing NK activation levels.

Antibody-dependent NK cell activation measures natural killer (NK) cell responses triggered by antibody-coated targets. The assay detects cytokine release or surface marker expression as indicators of immune activation. Input: Antibody-treated target cells and NK effector cells Output: Cytometric or fluorescence data representing NK activation levels.

Antibody-dependent NK cell activation analysis processes activation readouts to quantify NK cell responses. It compiles signal intensities or cytokine levels to compare antibody-mediated activation across conditions. Input: Raw NK cell activation data Output: Processed activation summaries and response metrics.