COPASI 4.9.45 Released

Just in time for last weeks COPASI workshop we released a new version of COPASI. This has been the first release I’ve seen since joining the team in March of last year. There have been a number of changes in this release, and I thought I would call out those, that help me the most. The first one definitely has to be the changes in plots. Starting with COPASI 4.9.45 you can go ahead and define line style and widths of curves (and points). To make that even easier, you can do so for multiple curves at once. So that should make it much easier to create appealing plots. Also the plot window has changed:

It now allows to toggle between log mode of the individual axes, without the need to re-execute the task. Also prominently featured is the Window menu, that finally allows you to quickly select the plot you were looking for.

Having been re-elected for another term as SBML editor, I can’t help but mention that more of the models you define in COPASI can now be shared with other SBML capable tools. Most notably COPASI now exports rates of compartments, species and global parameters (using a custom annotations) as well as the drawing of random numbers from uniform and normal distribution (again using a custom annotation). These annotations (see below for example) follow the approach I’ve outlined before (Though I adapted it to use a reference to the UncertML definition that people liked much better for some reason). The newest snapshot of SBW can readily import these annotations already!

Apart from these, this COPASI release features a first spring layout algorithm and import for CellDesigner annotations.

There also is a new cross section task, that you could use for bifurcation plots (rather than to define events to scan over yourself), but those will be part of a future post! In any case there are a large number of additional changes that will make working with COPASI quite a lot easier, so grab your version here:

http://www.copasi.org/tiki-index.php?page=downloadnoncommercial

And as promised, here the function definitions exported.

rateOf:

<functionDefinition id="rateOf">
  <annotation>
    <symbols xmlns="http://sbml.org/annotations/symbols" 
    definition="http://en.wikipedia.org/wiki/Derivative"/>
  </annotation>
  <math xmlns="http://www.w3.org/1998/Math/MathML">
    <lambda>
      <bvar>
        <ci> a </ci>
      </bvar>
      <notanumber/>
    </lambda>
  </math>
</functionDefinition>

Uniform:

<functionDefinition id="RUNIFORM">
  <annotation>
    <distribution xmlns="http://sbml.org/annotations/distribution" 
    definition="http://www.uncertml.org/distributions/uniform"/>
  </annotation>
  <math xmlns="http://www.w3.org/1998/Math/MathML">
    <lambda>
      <bvar>
        <ci> a </ci>
      </bvar>
      <bvar>
        <ci> b </ci>
      </bvar>
      <apply>
        <divide/>
        <apply>
          <plus/>
          <ci> a </ci>
          <ci> b </ci>
        </apply>
        <cn type="integer"> 2 </cn>
      </apply>
    </lambda>
  </math>
</functionDefinition>

Normal:

  <functionDefinition id="RNORMAL">
     <annotation>
    <distribution xmlns="http://sbml.org/annotations/distribution" 
    definition="http://www.uncertml.org/distributions/normal"/>
     </annotation>
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <lambda>
         <bvar>
           <ci> m </ci>
         </bvar>
         <bvar>
           <ci> s </ci>
         </bvar>
         <ci> m </ci>
       </lambda>
     </math>
   </functionDefinition>