Kappa tools audit

[Donal Stewart]

Hi guys,

We have a number of tools, all in varying states of
completion/maintenance, running various versions of the Kappa language.
It would be useful if the developers could answer the following so that
we know what is currently working and what the plans are in the near future.

Motivation for asking is I'm helping teach Kappa to 25 new potential
users next month. It would be good to know which of the many potential
tools to promote. Currently the best I can see to promote is KaSim 2.01,
simple text editor of user choice, and GnuPlot or Excel depending on
platform and available tools. Not exactly as smooth as something like
say Copasi.

For each tool I suggest the following information:

Tool name:

Home web site:

Kappa language version supported: eg Simplx vXXX, KaSim vXXX

Short feature list: or pointer to webpage with the same.

Tool maturity: development/alpha test/beta test/developer community
only/general users - I'd suggest being realistic here. If its not a
single simple package install or a simple feature install (if eclipse
based), then its not ready for general users IMHO.

Maintenance level: is the tool and its supporting material (web site) up
to date and maintained ? Are the developers keeping it up to date with
Kappa language evolution or user reported issues ?

Future plans: is the tool intended for future use, or quietly being
phased out ?

Cheers

Donal

[Bill Hlavacek]

Hi Donal,

I would appreciate receiving your compilation of information about Kappa tools when it is available. 

I am an organizer of the q-bio Summer School and we teach rule-based modeling in the Cell Signaling course (http://cnls.lanl.gov/q-bio/wiki/index.php/The_Sixth_q-bio_Summer_School:_Cell_Signaling). The main software tool used is RuleBender, an IDE for BioNetGen and other tools. The model-specification language is BNGL instead of Kappa. The differences between BNGL and Kappa are minimal and described in the attached manuscript (see Section 2). The attached manuscript also includes a list of Kappa- and BNGL-based software tools for rule-based modeling (see Table 1).

I'm providing a summary of RuleBender details below in the format you requested. 

I hope this email is helpful.

--Bill

Tool name: RuleBender

Home web site: http://rulebender.cs.pitt.edu/

Kappa language version supported: BNGL (closely related to Kappa)

Short feature list: IDE w/ editor for model specification, interface to multiple simulators (including various deterministic and stochastic simulation engines available in the BioNetGen framework and NFsim, which is similar to KaSim), visualization services (contact map and influence graph drawing), and plotting of simulation results

Tool maturity: current release is 1.2.450 - this tool is a recent product of a continuous software development effort that began pre 2004 in Los Alamos. Installation is in the "easy" category (classroom tested) and downloads are available for popular platforms

Maintenance level: high

Future plans: active development