Agenda for Today

[Oliver Ruebenacker]

Hello All,

What would you like to see on the agenda today?

Suggestions:

- Planning for 2009
- Cellular chemical reactions on the pool level of granularity
- Relationships between measurements, models and reality

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org

[JSL913]

Hi and Happy New Year!

In the planning for 2009, I'd like to focus on evaluation -

How can we evaluate what we build (or have built) so that we can
demonstrate it's utility (and re-use capability) to our community?

Maybe this is what you meant by bullet number 3.

I may be in by skype (or email/chat).

Joanne

[Oliver Ruebenacker]

Hello Joanne, All,

Happy New your to you, too.

I think that's a great idea.

One way of evaluation would be to present software that accomplishes
something. For example, I am working on software turning BioPAX into
SBML, and my interest in improving BioPAX is to make this easier, or
possible in cases where it was not possible before.

Take care
Oliver

[JSL913]

Great.

What would be helpful then is articulate some specific examples of

some BioPAX code and some SBML that represents it

What are some examples of why it is hard - what makes it hard or not
possible. What are the cases?

Also, can you think about some metrics for measuring? Will it be
simply comparing an expected output with an actual output? Is there
some other way (queries?) that the results of the transformation be
tested? Are there some inferences that can be checked?

Joanne