Sample models

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We will need some sample models (both l2 & l3) checked in to the sources and to 
be distributed with the installers. Pass it on to Merve if you like.

Original issue reported on code.google.com by ugurdogr...@gmail.com on 19 Sep 2012 at 10:40

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I am passing this on to Merve. We can use the same l2 models (or a subset) 
which are still in the sourceforge project. 

Original comment by ozgunba...@gmail.com on 19 Sep 2012 at 6:58

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Samples are now added to the source. I have chosen a subset of the previous 
samples for L2 models and queried PC to generate L3 sample models.

Original comment by mervecak...@gmail.com on 25 Sep 2012 at 2:56

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please review/verify

Original comment by ugurdogr...@gmail.com on 25 Sep 2012 at 4:32

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Sample models are not laid-out. Do you think we should work on pretty layouts 
for sample models (as before) or can we depend on the auto-layout? Currently, 
auto-layout generates incomprehensible geometry for some of the sample models.

Original comment by ozgunba...@gmail.com on 26 Sep 2012 at 7:15

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I think we should try for a good layout a number of times. If it doesn't look 
very hopeful, we should do some manual improvements to the layout and save the 
sample models.

Original comment by ugurdogr...@gmail.com on 27 Sep 2012 at 7:16

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I noticed that IDs of molecules in L3 sample models are different than the ones 
in the current Pathway Commons. These should have changed in PC after creation 
of sample models. This breaks querying from pop-up menu.

Let's not update sample models yet. IDs may still change. But we should do it 
prior to the release.

Original comment by ozgunba...@gmail.com on 10 Oct 2012 at 6:48

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Level 3 sample models are now updated. I have performed new PC queries to 
generate models. I have also done some minor manual improvements on the layouts 
if automatic layout fails to generate a good result. 

However, I did not update Level 2 samples. I have tried improving the layout 
and saving the models, but when I loaded these models, ChiBE automatically 
performed layout and did not use the saved layouts. This was not the case for 
L3 models. What should I do with L2 models? 

Original comment by mervecak...@gmail.com on 3 Dec 2012 at 3:39

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That shouldn't be the case, right Ozgun? Could you take a look please?

Original comment by ugurdogr...@gmail.com on 5 Dec 2012 at 8:38

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We didn't save layouts in L2 sample models previously. They were laying out 
each time we load. We can save them layed out this time for the sake of 
consistency.

Original comment by ozgunba...@gmail.com on 5 Dec 2012 at 6:38

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Is this easy to implement Ozgun? Can you do it or can you let Merve how to do 
it? Please let me know when done, so I can have Cagdas prepare the installers.

Original comment by ugurdogr...@gmail.com on 6 Dec 2012 at 12:58

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Done.

Original comment by ozgunba...@gmail.com on 6 Dec 2012 at 8:55

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Merve, please beautify the layout of l2 samples now and let me know.

Original comment by ugurdogr...@gmail.com on 10 Dec 2012 at 11:52

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I have updated the layout of Level 2 samples. I have replaced some models which 
would require extensive manipulation to reach a good layout. 

Original comment by mervecak...@gmail.com on 20 Dec 2012 at 1:02

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Original comment by ugurdogr...@gmail.com on 28 Dec 2012 at 9:17

• Changed state: Verified