ChemChains 1.0 Release Update

[heli...@gmail.com]

OK,
After lots of code fine tuning, the manuscript discussing ChemChains
has been finally submitted to the BMC Systems Biology journal.
While most of the changes and prep work for the release have been
finished, I want to continue the new-feature development freeze on
source code in trunk until we know the paper has been actually
accepted for publication. The reason for that is that in the case the
reviewers suggest that we make changes/revisions to the submitted
code, we still have the same version of ChemChains we submitted.

On the other hand, Jay has mentioned he had some cool framework he was
working on for ChemChains (sorry about the delay on being able to
submit stuff), so I created a branch called CC1_0-rc1 (available in
branches/CC1_0-rc1) that can be used for new development. Once the
paper is published, the code in trunk will be tagged as version 1.0
and all new revisions in the above mentioned branch will be merged
with trunk which then can return in the heavy devel phase.

Please let me know if you have any questions.

Tom

[Jay Hannah]

On Aug 6, 2008, at 1:03 PM, heli...@gmail.com wrote:
> On the other hand, Jay has mentioned he had some cool framework he was
> working on for ChemChains

Uh, threatening to work on. I haven't done anything yet. :)

http://testanything.org/

These files disappeared again? They don't seem to be in trunk nor
branches/CC1_0-rc1 now.

cpp/inFiles/CChain/logic/logic9_clean.txt
cpp/inFiles/CChain/specs/specs.txt

Thanks,

j

[Tomas Helikar]

Sorry about the delayed response - I'm still out of country.

The files have been removed from the official version of ChemChains. I will make them available on MathBio home page. I can email them to you in the mean time, if you'd like.

Tom

[Jay Hannah]

On Aug 19, 2008, at 4:47 PM, Tomas Helikar wrote:
> Sorry about the delayed response - I'm still out of country.

No worries. :)

> The files have been removed from the official version of
> ChemChains. I will make them available on MathBio home page. I can
> email them to you in the mean time, if you'd like.

Well, of course they're still in the repo, I just have to

svn up -r{20080702}

and poof! There they are. :)

I suppose I'll add them to TAP/ (http://testanything.org/) if you're
not planning on having them in cpp/ anywhere...? That's where I was
going to start throwing test harnesses for regression/cross-language
testing...

Ponder,

j
http://jays.net/wiki/ChemChains_sandbox

[Tomas Helikar]

That's fine. Although, I think we might want to do testing on smaller, toy networks. It would make our lives easier for any debugging purposes.

My 2c

Tom

On Tue, Aug 19, 2008 at 5:05 PM, Jay Hannah <j...@jays.net> wrote:

On Aug 19, 2008, at 4:47 PM, Tomas Helikar wrote:
> Sorry about the delayed response - I'm still out of country.

No worries.  :)

> The files have been removed from the official version of
> ChemChains. I will make them available on MathBio home page. I can
> email them to you in the mean time, if you'd like.

li

[Jay Hannah]

On Aug 19, 2008, at 5:10 PM, Tomas Helikar wrote:
> That's fine. Although, I think we might want to do testing on
> smaller, toy networks. It would make our lives easier for any
> debugging purposes.

I was thinking T 0..100 of logic9_clean.txt + specs.txt + a known set
of inputs + no chaos would do a really good job of flushing out
corner cases?

I did my early devel on a little 3 node network (fake.txt), but I'm
sure I don't know enough to flush out a toy network that covers
everything that should be verified.

j