Taverna services for Systems Biology

If you have any questions, comments or seek help with our WS or any other resource, please contact us via tav4sb discussion group or directly at tav4sb@mimuw.edu.pl.

This is a probabilistic model checking experiment for the
stochastic version of the enzymatic
reaction model (SBML). The The reward-based
CSL formula, which is being checked, asks
the model about **how many times, on average, the enzyme-substrate
complex association reaction have to occur before amount of the product
reaches 50% of its maximum?** This is motivated by the half maximal
effective concentration (EC50 coefficient). Question is asked for different
enzyme initial amount to find its optimal efficiency. As the PMC is time
consuming, the experiment is divided into "compute" and
"plot" workflows, mainly because plotting usually requires many
runs to fine-tune the plot parameters.

To run this experiment choose *File > Open workflow location...*
and copy-paste the link to the
"compute" workflow file. Then *File > Run workflow...*,
wait for results and from the *Results* perspective choose *Save
all values > Save in single XML document*. This workflow has no inputs
and all parameters to play around with are embedded in string constants
(`modelUrl`

, `constName`

, `varName`

,
`rewardsUrl`

, `propertiesUrl`

,
`initValues`

). Next, open and run
the "plot" workflow file.
This time Taverna will ask for filling in the input values, so in the input
values dialog choose *Load previous values* and point to previously
saved "compute" values. The `p_MAX`

PRISM model
parameter wont be interesting to plot, it is constant in our experiment.
Delete it from `constantNameList`

input values. Fill in the plot
options list; Taverna requires at least one input value, so if you don't
know what to put in, put at least `PlotLabel -> ""`

.
Now you're all set to run the plotting workflow.

As a result you have the `<results>`

XML element from
the computational part and an image of calculated formula values from the
plotting part. To obtain the following plot:

we used the following plot options:

AxesLabel -> { "E(0)", "Formula value" } PlotLegend -> None ColorFunction -> "TemperatureMap" PlotRange -> {{0., 20.}, {6., 13.}} MarkerColor -> Black

Note: for description of plotting options check `mathPlot`

WS operation
wrapper docs on
`optionList`

input at myExperiment or
input docs at
BioCatalogue.

The plot can be read as: if E(0) is equal to 1, then, on average, before product reaches half of its maximum, each enzyme has to convert slightly more than 6 substrates. To no surprise, when E(0) is equal to 12 (the initial amount of substrate), each enzyme has to convert at most one substrate. The total, parallel enzymatic reaction system's efficiency doesn't improve significantly from that point as not much more than 12 complex formation reactions r1 are needed to achieve half of the maximum product amount.

Taverna 2 workflow files: