syntax

[Nausheen Fatima]

Hi!

I was looking at a previous model and it has some species in reactions in quotation marks. Does that signify anything? Also what does a colon indicate in a reaction?

Thank you!

[Frank Bergmann]

The Quotes in Names denote that you used characters like spaces in a species name, and are just there to demarcate where a species name starts and stops: 

"species 1" -> "species 4"

for example. The semicolon denotes, that the reaction has activators or inhibitors influencing the reactions that are not substrates or products. 

A -> B; D

here we had a process transforming A to B, resulting in A most likely decreasing and B increasing, influenced by a species D (which might not change). 

best

Frank

[Nausheen Fatima]

Thank you Frank. I know about the semicolon, but I see some reactions in a model that use “colon” in a reaction. Here’s an example:

IKK[P]:IkBe:NFkB -> IKK[P] + NFkB

Nausheen.

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[Pedro Mendes]

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Hi Nausheen,

colons are part of the species name. Often they are used to show that
the molecule is the result of two other molecules binding, as for example:

A + B -> A:B

A:B is a new species and this notation makes it explicit what are the
composing moieties. However this is not a COPASI notation, this is used
by modelers

Pedro

On 5/4/24 23:14, 'Nausheen Fatima' via COPASI User Forum wrote:
> Thank you Frank. I know about the semicolon, but I see some reactions in
> a model that use “colon” in a reaction. Here’s an example:
>
> IKK[P]:IkBe:NFkB -> IKK[P] + NFkB
>
> Nausheen.
>
>
>
>
>
> On Sat, May 4, 2024 at 2:17 AM Frank Bergmann
> <frank.thom...@gmail.com

> <mailto:frank.thom...@gmail.com>> wrote:
>
> The Quotes in Names denote that you used characters like spaces in a
> species name, and are just there to demarcate where a species name
> starts and stops:
>
> "species 1" -> "species 4"
>
> for example. The semicolon denotes, that the reaction has activators
> or inhibitors influencing the reactions that are not substrates or
> products.
>
> A -> B; D
>
> here we had a process transforming A to B, resulting in A most
> likely decreasing and B increasing, influenced by a species D (which
> might not change).
>
> best
> Frank
>
>
> On Friday, May 3, 2024 at 11:08:11 PM UTC+2 nfat...@binghamton.edu

> <mailto:nfat...@binghamton.edu> wrote:
>
> Hi!
>
> I was looking at a previous model and it has some species in
> reactions in quotation marks. Does that signify anything? Also
> what does a colon indicate in a reaction?
>
> Thank you!
>
> --
> You received this message because you are subscribed to the Google
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> To unsubscribe from this group and stop receiving emails from it,
> send an email to copasi-user-fo...@googlegroups.com

> <mailto:copasi-user-fo...@googlegroups.com>.

> To view this discussion on the web visit

> https://groups.google.com/d/msgid/copasi-user-forum/665b8213-e976-4560-be1c-558f5e760f2en%40googlegroups.com <https://groups.google.com/d/msgid/copasi-user-forum/665b8213-e976-4560-be1c-558f5e760f2en%40googlegroups.com?utm_medium=email&utm_source=footer>.

>
> --
> You received this message because you are subscribed to the Google
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> To view this discussion on the web visit

> https://groups.google.com/d/msgid/copasi-user-forum/CAF_8nBFQ%3DyQaqncBCi045y4tzPFmC2Vf-wX-M8CDnLtKBvNHpg%40mail.gmail.com <https://groups.google.com/d/msgid/copasi-user-forum/CAF_8nBFQ%3DyQaqncBCi045y4tzPFmC2Vf-wX-M8CDnLtKBvNHpg%40mail.gmail.com?utm_medium=email&utm_source=footer>.

--
Pedro Mendes, PhD
Professor and Director
Richard D. Berlin Center for Cell Analysis and Modeling
University of Connecticut School of Medicine
group website: http://www.comp-sys-bio.org

[Nausheen Fatima]

Thank you for this clarification. It’s making more sense now. 

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