Add terms for terms of UniformTimeCourse

[luciansmith]

I have put the following into the SED-ML specification, so it would be nice if they could be created for real. I could do it, but I feel like I messed up a few things last time? Anyway:

KISAO:0000840: start time KISAO:0000841: max end time KISAO:0000842: observed step size

[luciansmith]

I also put in this, since I think it'll take too long to come up with something 'proper':

<listOfSimulations>
    <analysis id="non_uniform_time_course">
        <algorithm kisaoID="KISAO:0000xxx" name="Reachability analysis">
            <algorithmParameter kisaoID="KISAO:0000xxx" value="0" name="something_relevant"/>
        </algorithm>
    </analysis >
</listOfSimulations>

but if you think you can add something for these too, I'll stick those in.

(Also, I'm happy to change things before we submit.)

[jonrkarr]

Go ahead and add the additional terms. The unit tests will check whether the ids are consistent (they should match ^KISAO_\d{7,7}$). At Matthias' suggestion, I adopted the convention for names and synonyms that they should start with lowercase letters, except for proper names such as "DNA".

There's no term for reachability analysis yet. There is a term for identifying trap spaces of regulatory networks (KISAO_0000662).

This has a parameter (KISAO_0000216) to indicate whether the computation should be done on a reduced model.

[matthiaskoenig]

I think I figured out how to do the KISAO updates (@jonrkarr thanks for the great documentation). @luciansmith If you provide the term definitions, I can add these terms: The actual KISAO terms will be different, because the ids are already used (KISAO_0000840, KISAO_0000841, KISAO_0000842).

• [ ] KISAO:0000XXX: start time
• [ ] KISAO:0000XXX: max end time
• [ ] KISAO:0000XXX: observed step size
• [ ] KISAO:0000XXX: reachibility analysis

[jonrkarr]

I'd like to see parameters analogous to the attributes of UniformTimeCourse. This can be a way to document the meaning of those attributes within KiSAO and unify the existing types of simulations with the new Analysis class.

• Initial time
• Output start time
• Output end time
• Number of steps

I'd also like to see parameters that enable non-uniform time courses. We can outline some parameters now. Since there are many ways to do this, simulation tools can propose more KiSAO terms as needed.

• List of points to record
• Whether or not to record at events in addition to uniformly-distributed time points (default behavior of PySCeS)

As simulation tools start to use these new terms, it will be important for tools to broadcast the terms they recognize since most tools will likely only support a subset of all terms and simulation tools will expect terms to be used in specific combinations.

I suggest we wait on reachibility analysis for input from the CoLoMoto community. I'm working with them on organizing simulation methods and tools. They have strong opinions about how to organize methods for logical modeling.