gsoc project timeline - goal 11

Hi Jan

in:

http://informatics.nescent.org/wiki/PhyloSoC:_Extending_Jalview_support_for_handling_RNA

I noticed that you have goal 11 - extend goal 7 with new JABAWS services. Should that be 'extend goal 8' rather than 7 ?

I was also wondering how the datamodel investigation is going, and the progress with the goal 2.5 (which might actually be goal 3, since there is curently no goal 3!). Perhaps you'd consider switching goal 2.5 and 2 - because its pretty easy to set up a test case to check if the annotation IO preserves secondary structure patterns.

One final thought - if all goes well with VARNA, your likely to be completing all the goals with time to spare. However, your bonus goals involve generating a couple of new file formats (stockholm files and covariance matrices) from annotated alignments. When you have some non-coding time, you should take a close look at these goals and add in some of this additional detail, to get a clearer idea of how much work is really involved in achieving the goal.

Jim.

ps. will email later about the continuous build... just thinking how best to structure it - I think you should probably have a personal build branch (called something like 'jans build') that you can use to test your code integrations.

Hi Jim, Peter and everybody interested in RNA structure,

I investigated last week the differences in the RNA data model between
Jalview and VARNA.
In Jalview the RNA-class mainly consists of an array of SequenceFeatures
that represents the base pairs. Every SequenceFeature has a begin and an
end value that are the opening and closing part of the base pair.
Additionally there is a class that determines for each base pair to
which helix it belongs.

The VARNA (Visualization Applet for RNA) RNA-class contains a base list
and a lot of drawing algorithm stuff. The base list seems quite similar
to the one in Jalview. It's main part is a ArrayList of ModelBase's. The
VARNA ModelBase has a variable called _elementStructure which is -1, if
the position is unpaired. Otherwise it's value is the index of the
corresponding base.

We discussed to change the Jalview data model because there are some
problems with the RNA display at the moment. I created a new issue
(JAL-836) for them. I'm investigating at the moment what is the origin
of this problems. Maybe it's just a incomplete usage of ActionListeners,
instead of a general problem with the data model but I'm not sure about
this so far.
Anyway it should be quite easy to call a VARNA application even with
different data models since there is a constructor that just requires
the sequence and structure as strings.

This is mainly to keep my mentors up to date but if anybody has helpful
comments feel free to take part in our discussion.

Jan

ยทยทยท

On 05/25/11 22:43, Jim Procter wrote:

Hi Jan

in:

http://informatics.nescent.org/wiki/PhyloSoC:_Extending_Jalview_support_for_handling_RNA

I noticed that you have goal 11 - extend goal 7 with new JABAWS
services. Should that be 'extend goal 8' rather than 7 ?

I was also wondering how the datamodel investigation is going, and the
progress with the goal 2.5 (which might actually be goal 3, since there
is curently no goal 3!). Perhaps you'd consider switching goal 2.5 and 2
- because its pretty easy to set up a test case to check if the
annotation IO preserves secondary structure patterns.

One final thought - if all goes well with VARNA, your likely to be
completing all the goals with time to spare. However, your bonus goals
involve generating a couple of new file formats (stockholm files and
covariance matrices) from annotated alignments. When you have some
non-coding time, you should take a close look at these goals and add in
some of this additional detail, to get a clearer idea of how much work
is really involved in achieving the goal.

Jim.

ps. will email later about the continuous build... just thinking how
best to structure it - I think you should probably have a personal build
branch (called something like 'jans build') that you can use to test
your code integrations.
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