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Hector Medina
Mar 17
Contact Map rendering
Hi folks, I've added some advanced contact map rendering support to my tool suite, KaSaAn. While
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Contact Map rendering
Hi folks, I've added some advanced contact map rendering support to my tool suite, KaSaAn. While
Mar 17
Hector Medina
Mar 17
Notepad++ syntax highlighting
Hi folks, I maintain a Notepad++ language definition for the Kappa language, focused on syntax
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Notepad++ syntax highlighting
Hi folks, I maintain a Notepad++ language definition for the Kappa language, focused on syntax
Mar 17
Gordon
2
11/2/21
Kappalanguage.org site is unreachable
UPDATE: Walter informed me that there's something going on with the Harvard servers in which the
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Kappalanguage.org site is unreachable
UPDATE: Walter informed me that there's something going on with the Harvard servers in which the
11/2/21
Octave Hazard
,
Héctor F
2
9/22/21
Taking distance into account in unimolecular reactions?
Hi Octave! Yes, this is implemented and works as expected. The manual maintainers will someday update
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Taking distance into account in unimolecular reactions?
Hi Octave! Yes, this is implemented and works as expected. The manual maintainers will someday update
9/22/21
William Waites
,
Walter Fontana
2
5/28/21
tools.kappalanguage.org SSL certificate...
Thanks for pointing this out. It should be fixed now. (The certificate was renewed a while back, but
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tools.kappalanguage.org SSL certificate...
Thanks for pointing this out. It should be fixed now. (The certificate was renewed a while back, but
5/28/21
Matheus Gimenez Fernandes
5/7/21
Is it possible to add a diffusion term in the simulation alongside the already present binding term?
Hello, I think Kappa models rules using binding terms like this: Rule/Reaction Differential Equations
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Is it possible to add a diffusion term in the simulation alongside the already present binding term?
Hello, I think Kappa models rules using binding terms like this: Rule/Reaction Differential Equations
5/7/21
William Waites
, …
Ricardo Honorato Z
7
3/22/21
Observable for rule activity
Sorry for the lag in responding… > I believe the activity of a rule could, in the past, be
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Observable for rule activity
Sorry for the lag in responding… > I believe the activity of a rule could, in the past, be
3/22/21
Matheus Gimenez Fernandes
,
Héctor F
2
3/1/21
Highlighter for Notepad++
Hi Matheus, It's here -> https://github.com/Kappa-Dev/Kappa-Dev.github.io/tree/master/
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Highlighter for Notepad++
Hi Matheus, It's here -> https://github.com/Kappa-Dev/Kappa-Dev.github.io/tree/master/
3/1/21
Matheus Gimenez Fernandes
,
William Waites
2
2/24/21
How to bound 3 or more agents?
Matheus Gimenez Fernandes <mgimenez...@gmail.com> writes: > I'm new to Kappa
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How to bound 3 or more agents?
Matheus Gimenez Fernandes <mgimenez...@gmail.com> writes: > I'm new to Kappa
2/24/21
Luciana Renata de Oliveira
, …
yarde...@gmail.com
3
2/3/21
Time step for simulations
The stochastic simulation has no time step, as Walter noted, but KaSim does have a time step setting
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Time step for simulations
The stochastic simulation has no time step, as Walter noted, but KaSim does have a time step setting
2/3/21
Ryan Krueger
, …
Pierre Boutillier
5
4/29/20
Kappy broken on python 3.8
So, Why `make agents` not part of `make all`? Because agents have more OCaml dependencies than the
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Kappy broken on python 3.8
So, Why `make agents` not part of `make all`? Because agents have more OCaml dependencies than the
4/29/20
Ryan Krueger
4/20/20
Kappapp on Ubuntu
I am running Ubuntu 19 and can't get the GUI to work. The executables in resources work fine (eg,
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Kappapp on Ubuntu
I am running Ubuntu 19 and can't get the GUI to work. The executables in resources work fine (eg,
4/20/20
Jan Meyer
, …
Pierre Boutillier
9
2/15/20
feasibility questions
Hi all, Extremely late reply indeed, Sorry. - Dealing with heat is indeed doable with tokens. Despite
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feasibility questions
Hi all, Extremely late reply indeed, Sorry. - Dealing with heat is indeed doable with tokens. Despite
2/15/20
Yarden Katz
,
Héctor F
3
8/15/19
feature wishlist/proposal: a database representation for collections of snapshots
On 8/15/19 5:41 PM, Héctor F wrote: My understanding of graph databases like Google's
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feature wishlist/proposal: a database representation for collections of snapshots
On 8/15/19 5:41 PM, Héctor F wrote: My understanding of graph databases like Google's
8/15/19
Sakrapee Paisalnun
,
Yarden Katz
2
8/15/19
How to obtain variable values from Python API
You can get this information from the "variables" entry in the object returned by "
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How to obtain variable values from Python API
You can get this information from the "variables" entry in the object returned by "
8/15/19
n4323
,
Ricardo Honorato Z
3
5/9/19
Replicate an agent including internal state
hi ricardo, thanks for the suggestion. in the meantime i started an issue on the kappasim github, and
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Replicate an agent including internal state
hi ricardo, thanks for the suggestion. in the meantime i started an issue on the kappasim github, and
5/9/19
Héctor F
2
5/7/19
Pygments Highlighting for Kappa
Hi all, The pull request has been submitted to the Pygments package. However, it seems development
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Pygments Highlighting for Kappa
Hi all, The pull request has been submitted to the Pygments package. However, it seems development
5/7/19
Sébastien Légaré
,
Jonathan Laurent
6
2/25/19
Print all events of a trace with Kappa-TQL
Ok thanks for the example. I see that it could cause trouble. In that case, the transition { S(x{u/p}
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Print all events of a trace with Kappa-TQL
Ok thanks for the example. I see that it could cause trouble. In that case, the transition { S(x{u/p}
2/25/19
wwa...@ieee.org
,
Jean Krivine
4
2/6/19
kcomp, kgen, tools for combining biological parts
Yes please I would love to have a look at the manuscript if that's ok with you. Thanks! On Wed,
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kcomp, kgen, tools for combining biological parts
Yes please I would love to have a look at the manuscript if that's ok with you. Thanks! On Wed,
2/6/19
Valentin Z
, …
Sébastien Légaré
5
1/22/19
Introducing Topkappy: a Kappy wrapper for easier Python model building and results analysis
Hi Valentin, Thank you for Topkappy. I tried it for a new project and so far it works great. I was
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Introducing Topkappy: a Kappy wrapper for easier Python model building and results analysis
Hi Valentin, Thank you for Topkappy. I tried it for a new project and so far it works great. I was
1/22/19
David C Sterratt
,
Bill Hlavacek
2
1/18/19
Tau-leap for kappa?
BioNetGen implements a partitioned leaping algorithm (a variation of tau leaping): https://www.ncbi.
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Tau-leap for kappa?
BioNetGen implements a partitioned leaping algorithm (a variation of tau leaping): https://www.ncbi.
1/18/19
Alex
11/27/18
Generating .ka from kappy after parse_project
Hi there, Before I write my own and/or create a pull request, I was wondering if there is a
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Generating .ka from kappy after parse_project
Hi there, Before I write my own and/or create a pull request, I was wondering if there is a
11/27/18
debdaspaul
, …
Jérôme
3
11/19/18
Convergence of sample paths produced by Kappa
Exactly, Jérôme Le lundi 19 novembre 2018 12:23:06 UTC+1, David Sterratt a écrit : I think the
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Convergence of sample paths produced by Kappa
Exactly, Jérôme Le lundi 19 novembre 2018 12:23:06 UTC+1, David Sterratt a écrit : I think the
11/19/18
debdaspaul
,
Pierre Boutillier
2
11/16/18
Running Kappa script in GPU
Hi, There is no known way! I'm not sure it would even do the speedup you expect: - GPU cores have
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Running Kappa script in GPU
Hi, There is no known way! I'm not sure it would even do the speedup you expect: - GPU cores have
11/16/18
Miran Bozicevic
,
Walter Fontana
2
10/13/18
Ancient string sets
Miran, I'll get back to you outside the kappa-users group, since your question is not directly
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Ancient string sets
Miran, I'll get back to you outside the kappa-users group, since your question is not directly
10/13/18
Sandro Stucki
, …
Jérôme
8
9/26/18
How to run the Kappa web UI locally
Thanks Pierre for the instructions. That worked perfectly for me as well. Combining Pierre and
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How to run the Kappa web UI locally
Thanks Pierre for the instructions. That worked perfectly for me as well. Combining Pierre and
9/26/18
debdaspaul
,
Jérôme
3
7/27/18
Kappa rule for the following statements
Many thanks, Jérôme! On Friday, July 27, 2018 at 5:23:05 PM UTC+2, Jérôme wrote: Le vendredi 27
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Kappa rule for the following statements
Many thanks, Jérôme! On Friday, July 27, 2018 at 5:23:05 PM UTC+2, Jérôme wrote: Le vendredi 27
7/27/18
shader j
6/10/18
Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع
YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea
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Fwd: Us congress hearing of maan alsaan Money laundry قضية الكونغجرس لغسيل الأموال للمليادير معن الصانع
YouTube videos of US Congress money laundering hearing of Saudi Billionaire " Maan Al sanea
6/10/18
Gordon
, …
Pierre Boutillier
3
4/18/18
The Kappa App Influence Map
> Le 19 févr. 2018 à 16:09, Gordon Webster <gdwe...@gmail.com> a écrit : > I also have
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The Kappa App Influence Map
> Le 19 févr. 2018 à 16:09, Gordon Webster <gdwe...@gmail.com> a écrit : > I also have
4/18/18
Gordon
, …
Héctor F
5
4/3/18
Maintaining an agent at steady state levels
Hi Gordon, Hopefully this email doesn't get deleted en route to the forum... One way you can
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Maintaining an agent at steady state levels
Hi Gordon, Hopefully this email doesn't get deleted en route to the forum... One way you can
4/3/18