Re: [stem-dev] Optional parameters for pajek graph

["James Kaufman" <jhkauf@xxxxxxxxxx>]

Thank you Emily, it looks great :-)

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:      
 Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
To:      
 James Kaufman <jhkauf@xxxxxxxxxx>
Cc:      
 "Ahmad.Swaid@xxxxxxxxxxx"
<Ahmad.Swaid@xxxxxxxxxxx>, Judy Douglas <judyvdouglas@xxxxxxxxxxx>,
"Marcel.Fuhrmann@xxxxxxxxxxx" <Marcel.Fuhrmann@xxxxxxxxxxx>,
'Matthias Filter' <Matthias.Filter@xxxxxxxxxxx>, "sedlund@xxxxxxxxxx"
<sedlund@xxxxxxxxxx>, 'Taras Guenther' <Taras.Guenther@xxxxxxxxxxx>
Date:      
 10/18/2018 01:30 AM
Subject:    
   Re: Optional
parameters for pajek graph

---

Hi Jamie,

Thanks for that. I've uploaded all the
images now. 

Best wishes,

Emily

Emily Nixon
PhD Student

Demonstrator


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

---

From: James Kaufman <jhkauf@xxxxxxxxxx>
Sent: 17 October 2018 18:31:16
To: Emily Nixon
Cc: Ahmad.Swaid@xxxxxxxxxxx; Judy Douglas; Marcel.Fuhrmann@xxxxxxxxxxx;
'Matthias Filter'; sedlund@xxxxxxxxxx; 'Taras Guenther'
Subject: Re: Optional parameters for pajek graph
 
Hi Emily,
Here are some steps for imges
i) Log into the wik
ii) Navigate to the page you want to edit
iii) Click Edit
iv) On the LHS click "Upload a File"
v) Select the image you want to use from your laptop, give it a name. Probably
put STEM in the name so other Eclipse wiki pages don't accidentally use
it.
vi) After it uploads look at the name. Sometimes letter case changes in
the Eclipse Naming (ie it might become upper case)
vii) In your wiki markdown language, add some thing like the following
at the spot you want the image to appear
[[Image:STEM_YOURIMAGENAME.png|600px]]

where STEM_YOURIMAGENAME.png is your image file (uploaded)

If you want to right justify  you simply time
[[Image:STEM_YOURIMAGENAME.png|right|600px]]

you can make 600px smaller or larger to control size.


Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        Emily
Nixon <emily.nixon@xxxxxxxxxxxxx>
To:        Judy
Douglas <judyvdouglas@xxxxxxxxxxx>, 'James Kaufman' <jhkauf@xxxxxxxxxx>
Cc:        "Ahmad.Swaid@xxxxxxxxxxx"
<Ahmad.Swaid@xxxxxxxxxxx>, "'Christian Thöns'" <christian.thoens@xxxxxxxxx>,
"Marcel.Fuhrmann@xxxxxxxxxxx" <Marcel.Fuhrmann@xxxxxxxxxxx>,
'Matthias Filter' <Matthias.Filter@xxxxxxxxxxx>, "sedlund@xxxxxxxxxx"
<sedlund@xxxxxxxxxx>, 'Taras Guenther' <Taras.Guenther@xxxxxxxxxxx>
Date:        10/17/2018
09:25 AM
Subject:        Re:
Optional parameters for pajek graph

---

Hi Judy,

I have made changes to the wiki page https://wiki.eclipse.org/Importing_a_Pajek_Graph

I would like to add some updated images, but I'm not sure how to do this?

Best wishes,

Emily 
Emily Nixon
PhD Student

Demonstrator 


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

---

From: Judy Douglas <judyvdouglas@xxxxxxxxxxx>
Sent: 15 October 2018 21:09:38
To: 'James Kaufman'; Emily Nixon
Cc: Ahmad.Swaid@xxxxxxxxxxx; 'Christian Thöns'; Marcel.Fuhrmann@xxxxxxxxxxx;
'Matthias Filter'; sedlund@xxxxxxxxxx; 'Taras Guenther'
Subject: RE: Optional parameters for pajek graph
 
Emil, 
Let me know once it’s up, and send me a link. Thanks!
 
From: James Kaufman [mailto:jhkauf@xxxxxxxxxx]
Sent: Monday, October 15, 2018 10:10 AM
To: Emily Nixon
Cc: Ahmad.Swaid@xxxxxxxxxxx; Christian Thöns; Judith Douglas; Marcel.Fuhrmann@xxxxxxxxxxx;
Matthias Filter; sedlund@xxxxxxxxxx; Taras Guenther
Subject: Re: Optional parameters for pajek graph
 
Hi Emily,
Please definitely go ahead and update the doc. The wiki does versioning
so go ahead and make the changes (with comments when you save) but please
let Judy know so she can serve as editor for your new content.
Also, in the future, we should all be using stem-dev@xxxxxxxxxxx as the
email for these discussions so they get logged in the developers forum.
Thank you very much for helping with that!

Sincerely,

Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        Emily
Nixon <emily.nixon@xxxxxxxxxxxxx>
To:        James Kaufman
<jhkauf@xxxxxxxxxx>, "Christian Thöns" <christian.thoens@xxxxxxxxx>
Cc:        "Ahmad.Swaid@xxxxxxxxxxx"
<Ahmad.Swaid@xxxxxxxxxxx>, Judith Douglas <judyvdouglas@xxxxxxxxxxx>,
"Marcel.Fuhrmann@xxxxxxxxxxx" <Marcel.Fuhrmann@xxxxxxxxxxx>,
Matthias Filter <Matthias.Filter@xxxxxxxxxxx>, "sedlund@xxxxxxxxxx"
<sedlund@xxxxxxxxxx>, Taras Guenther <Taras.Guenther@xxxxxxxxxxx>
Date:        10/15/2018
09:19 AM
Subject:        Re:
Optional parameters for pajek graph

---

Hi all,

Thanks very much Chris for taking a look. It's nice that it isn't actually
a problem, although embarrassing that I didn't notice that associated predicates
and triggers are also made when you import the pajek graph!  I've
now found these and got them to work by dragging them into my scenario.
 I would like to update the wiki page  https://wiki.eclipse.org/Importing_a_Pajek_Graphso
that this is mentioned here. I think there are also a few other things
on the page that could be updated, for example, when importing the pajek
graph you can specify whether or not to use absolute migration rates, but
this isn't mentioned in the "Using the dialog" section. 

Shall I send my suggestions for edit just to Jamie, Judy and Stefan, or
would anyone else like to be included on that email thread?

With regards to what I am trying to achieve with 122 parameters per edge,
I am happy to collaborate with Jamie on this once he is more available.
I think I've worked out a simpler (albeit less accurate) way I can do what
I would like to do for now. 

Best wishes,

Emily   
Emily Nixon
PhD Student

Demonstrator 


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

---

From: James Kaufman <jhkauf@xxxxxxxxxx>
Sent: 12 October 2018 18:53
To: Christian Thöns
Cc: Ahmad.Swaid@xxxxxxxxxxx; Emily Nixon; Judith Douglas; Marcel.Fuhrmann@xxxxxxxxxxx;
Matthias Filter; sedlund@xxxxxxxxxx; Taras Guenther
Subject: Re: Optional parameters for pajek graph

Chris, thank you very much! You are still awesome :-)

Emily, I'm still testing the e4 branch with Ahmad and have not yet tested
predicates and triggers (but they should work). I'll let you know as soon
as I can confirm that.
I have not had a chance to look at your scenario in detail but rather than
specify 122 parameters per edge we may be able to handle the changes you
want programmatically either with predicates or with rule in a custom model.
How urgently do you need this? Ideally I'd like to get the e4 branch tested
and merged back. Then it will be easier to collaborate on your model....

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        "Christian
Thöns" <christian.thoens@xxxxxxxxx>
To:        emily.nixon@xxxxxxxxxxxxx
Cc:        James Kaufman
<jhkauf@xxxxxxxxxx>, Ahmad.Swaid@xxxxxxxxxxx, Judith Douglas <judyvdouglas@xxxxxxxxxxx>,
Marcel.Fuhrmann@xxxxxxxxxxx, Matthias Filter <Matthias.Filter@xxxxxxxxxxx>,
sedlund@xxxxxxxxxx, Taras Guenther <Taras.Guenther@xxxxxxxxxxx>
Date:        10/12/2018
10:14 AM
Subject:        Re:
Optional parameters for pajek graph

---

Hi Emily,

I tested the importer with the attached Pajek file using the STEM4 branch
. It creates a graph with 2 edges and the default rates defined in the
file (1.0 and 0.2). Specifying the optional parameters does not change
anything in the graph itself, but a list of predicates with triggers is
created based on it (see attached result.png). This works as expected.

I don't know if these predicates and trigger are applied correctly in a
STEM simulation (it was working when I used it more than 5 years ago).
If that's not working, I cannot fix it anyway since it's quite complex
and I haven't worked on STEM for several years.

Regarding your question on a limit on the number of optional parameters:
I did not set a limit, using 122 should work fine unless your graph has
too many edges. Then you might hit some other limits I don't know of.

Cheers,
Chris

Am Do., 11. Okt. 2018 um 17:49 Uhr schrieb Emily Nixon <emily.nixon@xxxxxxxxxxxxx>:
Hi Chris,

Just wondering whether once the optional parameters are up and running
on the pajek graph, whether there used to be a limit on how many optional
parameters you could specify per edge?

I'm asking because I would like an optional parameter, rate, to be in place
for longer than one day (122 days!) and so once it is up and running, I
will need to specify this optional parameter 122 times for each edge involved.
(The rest of the days in the year, it will then go back to the normal rate
that is specified). 

In future, I may put in a feature request for having the option to specify
a time period that a rate is applied for, rather than just one date, as
this would be easier in some situations like mine.  However, I don't
mind specifying it for each day at the moment, as long as you think this
will work?

Thanks again for your help.

Best wishes,

Emily




Emily Nixon
PhD Student

Demonstrator 


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ
Tel +44 (0)117 394 1389

---

From: James Kaufman <jhkauf@xxxxxxxxxx>
Sent: 05 October 2018 22:04:35
To: Christian Thöns
Cc: Ahmad.Swaid@xxxxxxxxxxx;
Emily Nixon; judyvdouglas@xxxxxxxxxxx;
Marcel.Fuhrmann@xxxxxxxxxxx;
Matthias Filter; sedlund@xxxxxxxxxx;
Taras Guenther
Subject: Re: Optional parameters for pajek graph

Hi Chris,
STEM is branched right now since we are working to upgrade to e4. The best
thing to do would be to get the e4 branch and then send Ahmad Swaid a patch
so he can push any changes to git (he has done all the new creative work
on that branch :-)

Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





From:        "Christian
Thöns" <christian.thoens@xxxxxxxxx>
To:        emily.nixon@xxxxxxxxxxxxx
Cc:        Taras Guenther
<Taras.Guenther@xxxxxxxxxxx>,
Matthias Filter <Matthias.Filter@xxxxxxxxxxx>,
Ahmad.Swaid@xxxxxxxxxxx,
Marcel.Fuhrmann@xxxxxxxxxxx,
James Kaufman <jhkauf@xxxxxxxxxx>,
sedlund@xxxxxxxxxx,
judyvdouglas@xxxxxxxxxxx
Date:        10/05/2018
12:38 PM
Subject:        Re:
Optional parameters for pajek graph

---

Hi Emily,

Sorry for the issues you have with the pajek importer. I will have a look
at it, but i won't make it before end of next week.

@All: I cannot push to the STEM repo, since I'm not an Eclipse committer
anymore. Who can I send the code to, if I fix it?

Cheers,
Chris

Am Fr., 5. Okt. 2018 um 18:47 Uhr schrieb Emily Nixon <emily.nixon@xxxxxxxxxxxxx>:
Hi Chris,

Sorry to disturb you about a STEM issue when I know you are no longer working
at BFR or on STEM. 

I was hoping that you wouldn’t mind just giving some advice to us.

We have found that the optional parameters for the pajek graph (additional
dates and rates) no longer seem to be implemented in STEM.

Do you have any idea why this might be? Or how we could fix this? 

Hope you are enjoying wherever you are working now. 

Best wishes,
Emily 

[attachment "result.png" deleted by James Kaufman/Almaden/IBM]
[attachment "dialog.png" deleted by James Kaufman/Almaden/IBM]
[attachment "test.net" deleted by James Kaufman/Almaden/IBM]