ceqea-interest — This is the general CEqEA interest mailing list

[CEqEA] CEqEA w/systems diagrams

[Rene V. <ve...@ja...>]

I have just uploaded CEqEA v2.1.131 to http://ceqea.sourceforge.net/

The main new feature is the ability to produce systems diagrams:
* causation diagrams are algorithmic accounts of modeled systems
* in most cases the algorithm is distributed
* a systems diagram, in turn, is a sequentialized form (approximated)

In other words, for single-celled organisms, a systems-diagram view of 
the organism's regulatory mechanisms will amount to a life-cycle prediction.

Cheers,
Rene

Re: [CEqEA] MIG grammars

[Rene V. <ve...@ja...>]

Hi,

The permanent home of the MIG specification language is

	http://ceqea.sourceforge.net/MIG/

A proper index page will be set up soon, along with more information 
about the project itself. For now, there's just the files I discussed in 
my previous emails.

Speaking of which, sorry for all the emails in rapid succession about 
this: I didn't expect the layout issue to be resolved quite that fast.

Cheers,
Rene

Re: [CEqEA] MIG grammars

[Rene V. <ve...@ja...>]

Hi, again,

I've added a graphical presentation of the individual rules to the 
earlier linked grammars. If you open one of the .html files at

	ftp://ftp.jaist.ac.jp/pub/sourceforge/c/project/ce/ceqea

you should be able to click the rule names and have the graphical 
version displayed. The graphical version is probably better for 
understanding single rules while the full .html version is likely to be 
better for understanding a whole grammar.

I will migrate these files to a more permanent home soon. Any comments 
would be welcome.

Cheers,
Rene

[CEqEA] CEqEA v2.1.116

[Rene V. <ve...@ja...>]

Hello,

CEqEA v2.1.116 has just been uploaded to 
https://sourceforge.net/projects/ceqea/files/

Bug reports would be most welcome for this and any other versions in the 
next month or so.

Cheers,
Rene

[CEqEA] MIG grammars

[Rene V. <ve...@ja...>]

Hi,

I've made BNF-style grammars of the MIG specification language available 
as .html-files at https://sourceforge.net/projects/ceqea/files/

They can also be found at
- ftp://ftp.jaist.ac.jp/pub/sourceforge/c/project/ce/ceqea/symbols.html
- ftp://ftp.jaist.ac.jp/pub/sourceforge/c/project/ce/ceqea/syntax.html
- ftp://ftp.jaist.ac.jp/pub/sourceforge/c/project/ce/ceqea/modalities.html

The first of these defines how characters are combined into tokens, 
i.e., the words of the language. The second file defines the main 
syntax, based on the tokens in the first file; this amounts to the 
sentences of the language. The third file defines the modality-specific 
syntax, which is glossed over in the second file in order to separate 
concerns. The second file defines where modality-specific tokens may 
appear in the main syntax, while the third files defines exactly how 
modalities may be written.

The grammars are written as BNFs enriched with regulation-expression 
operators. For example

RuleName
   : option1*
   | (option2a | option2b)+
   | option3a? option3b
   ;

defines RuleName to be
- either 0, 1, or more occurrences of option1-syntax (defined elsewhere)
- or 1 or more occurrences of option2a and/or option2b
- or 0 or 1 occurrences of option3a followed by an option3b.


Please let me know whether this way of presenting the language is 
helpful. The presentation is precise and is intended for reference 
purposes, rather than for learning the language from scratch.

Cheers,
Rene

Re: [CEqEA] Edge ids

[Rene V. <ve...@ja...>]

Dear all,

I should probably have made it clear that this is new functionality for 
the plugin to ZGRViewer, i.e., it is functionality for the windows that 
pop up and show graphs after pressing the analyze button in CEqEA.

For any newcomers, let me also note that CEqEA is cross-platform and 
almost entirely self-contained. To run CEqEA, simply download the .zip 
file from sourceforge, extract the content, and double-click 
<ceqea_macos.command> on Mac OS, <ceqea_windows.bat> on Windows, and 
<ceqea.sh> on pretty much everything else. The one exception is that

* you need Graphviz (2.26.3, or higher !) installed, see 
www.graphviz.org --- the website has been unstable lately, but I've got 
installers for Mac OS and Windows, for anyone who wants it. Most Linux 
distributions have Graphviz in their repositories.

Cheers,
Rene

On 04/07/2011 11:08 AM, Rene Vestergaard wrote:
> Dear all,
>
> There's a new release of CEqEA at
> https://sourceforge.net/projects/ceqea/files/ --- v2.1.69.
>
> The main new functionality is the ability to show edge ids by
> (temporarily) displaying edges as texts. The two main edge ids are
>
> - press and hold CTRL+SHIFT+i --- text shown is the number of the
> originating influence in the MIG specification
>
> - press and hold CTRL+SHIFT+d --- as above plus domain info(*)
>
> (To animate all edges, press CTRL+SHIFT+<enter>.)
>
>
> No new functionality is planned for the foreseeable future. Please
> report bugs, annoyances, etc.
>
> Cheers,
> Rene
>
>
> --
>
>
> (*)
>
> All influences have exactly one _covariant_ domain; the (possibly-empty)
> set of edges that pertain to the specified polarity. If the influence
> has + polarity, the covariant edges will increase states; for -, they
> will decrease states.
>
> An influence may also have 0, 1, or more _contravariant_ domains: those
> edges that are induced by the use of strong inhibition: A |-- !B. If the
> polarity of an influence is listed as +, all contravariant edges will
> decrease states.
>
> Domains are visualized in edges-as-texts as either '.', for the
> covariant domain, or with letters, with 'a' used for the first
> contravariant domain, and so on.
>
> The contravariant letters can also be found on some inhibitors annotated
> to edges, e.g., as -Obj.state/a. When such an inhibitor is activated
> (CTRL+SHIFT+<left click>, choose inhibitor in pop-up list), CEqEA will
> animate the edges that belong to the annotated (contravariant) domain.
>
>
> NB! When animating, CEqEA will consistently use blue for covariant edges
> and magenta for contravariant edges.
>
> ------------------------------------------------------------------------------
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> It's a major breakthrough. An authentic gaming
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> _______________________________________________
> CEqEA-interest mailing list
> CEq...@li...
> https://lists.sourceforge.net/lists/listinfo/ceqea-interest

[CEqEA] Edge ids

[Rene V. <ve...@ja...>]

Dear all,

There's a new release of CEqEA at 
https://sourceforge.net/projects/ceqea/files/ --- v2.1.69.

The main new functionality is the ability to show edge ids by 
(temporarily) displaying edges as texts. The two main edge ids are

- press and hold CTRL+SHIFT+i --- text shown is the number of the 
originating influence in the MIG specification

- press and hold CTRL+SHIFT+d --- as above plus domain info(*)

(To animate all edges, press CTRL+SHIFT+<enter>.)


No new functionality is planned for the foreseeable future. Please 
report bugs, annoyances, etc.

Cheers,
Rene


--


(*)

All influences have exactly one _covariant_ domain; the (possibly-empty) 
set of edges that pertain to the specified polarity. If the influence 
has + polarity, the covariant edges will increase states; for -, they 
will decrease states.

An influence may also have 0, 1, or more _contravariant_ domains: those 
edges that are induced by the use of strong inhibition: A |-- !B. If the 
polarity of an influence is listed as +, all contravariant edges will 
decrease states.

Domains are visualized in edges-as-texts as either '.', for the 
covariant domain, or with letters, with 'a' used for the first 
contravariant domain, and so on.

The contravariant letters can also be found on some inhibitors annotated 
to edges, e.g., as -Obj.state/a. When such an inhibitor is activated 
(CTRL+SHIFT+<left click>, choose inhibitor in pop-up list), CEqEA will 
animate the edges that belong to the annotated (contravariant) domain.


NB! When animating, CEqEA will consistently use blue for covariant edges 
and magenta for contravariant edges.

[CEqEA] Consolidation

[Rene V. <ve...@ja...>]

Hello,

On the advice of Emmanuel Pietriga, who's experienced in 
sourceforge-hosted projects, I've consolidated the CEqEA and the 
CEqEA_ZGRViewer projects into just one, CEqEA.

SOURCE CODE
* the CEqEA svn repository now holds all files, and has been 
correspondingly reorganized

DOWNLOADS
* the main executable is now only tri-numbered 2.1.x; it can be found at 
the location I announced earlier 
https://sourceforge.net/projects/ceqea/files/

ONLINE
* http://ceqea.sourceforge.net will remain in place
* http://ceqeazgrviewer.sourceforge.net will hopefully fluctuate back 
out of existence soon

Nothing else should change.

Cheers,
Rene