BatchKi Reference Manual

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Concentrations

The concentration of enzymes, inhibitors, and substrates dispensed on each plate is given in the <Concentration>...</Concentration> section of the BatchKi data file. It contains three subsections corresponding to the enzyme(s), substrate(s), and inhibitor(s) on each plate.

  <Concentration>
    <ConcEnzyme identical="[yes|no]"
                unit="[M|mM|uM|nM|pM]"
                external="no">
...
    </ConcEnzyme>
    <ConcSubstrate identical="[yes|no]"
                   unit="[M|mM|uM|nM|pM]"
                   external="no">
...
    </ConcSubstrate>
    <ConcInhibitor identical="[yes|no]"
                   unit="[M|mM|uM|nM|pM]"
                   external="no">
...
    </ConcInhibitor>
  </Concentration>

The identical attribute

This attribute can have one of two allowable values:

• identical="yes"
• identical="no"

If the identical attribute is set to `yes', the particular XML element (<ConcEnzyme>, <ConcSubstrate>, or <ConcInhibitor>) may contain only one concentration that will be applied to all wells on the given plate.

Example 1 - Identical concentrations

    <Enzyme identical="yes" unit="nM">
1.23
    </Enzyme>
    <Substrate identical="yes" unit="uM">
123
    </Substrate>

If the identical attribute is set to `no', the particular element must contain a tab-delimited table or spreadsheet with the number or rows and columns that is specified in the <Plate...> element above.

Example 2 - Non identical concentrations

<Plate rows="8" columns="3" id="...">
...
  <Substance>
...
    <Inhibitor identical="no" unit="nM">
0     1     1
0     3     3
0     9     9
0     27    27
0     81    81
0     243   243
0     729   729
0     2187  2187
    </Inhibitor>
...
  </Substance>
</Plate>

Concentration values can be input in the scientific format using either uppercase `E' or lower case `e' followed by the plus or minus sign to represent decimal exponents. For example, 1.23e-6 (or .123e-005, or 12.3E-07) all represent the value $1.23 \times 10^{-6}$.

The unit attribute

This attribute can have one of six allowable values:

• unit="M"
• unit="mM"
• unit="uM"
• unit="nM"
• unit="pM"
• unit="fM"

The attribute values correspond to the usual scientific notation, where `M' represents moles per liter as a unit of concentration, `mM' represents millimoles per liter, etc. Note that the Greek letter $\mu$ for micromolar concentrations is represented by the lower case `u' in `uM'.

The external attribute

The external attribute must have only one possible values:

• external = "no"

This attribute determines whether the concentration information is embedded in the BatchKi XML data file, or whether the concentration information is contained in a separate text file. See section 5.4.2 for details.

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Petr Kuzmic | Jul 12 2008