Hi all,
I've taking a look at JAL-1375
<http://issues.jalview.org/browse/JAL-1375>and also googling I've some
examples of using Cytoscape 3, in fact, you can
find some at (). However at JAL-1375 there is a reference to
JAL-1260<http://issues.jalview.org/browse/JAL-1260>which says that we
need a GenBank file parser first. I've found that
BioJava has this kind of parsing done. However, I don't know if LPGL 2.1 is
compatible with Jalview license or if there is any other constraint and we
do have to develop our own parser. If this is the case, I'll be glad to
start from here, just reassign me the jira ticket and I'll ask the
resolution to Santa. ;-)
Cheers,
David
2013/12/9 Jim Procter <[email protected]>
> Hi David.
>
> Thanks for the request - I'm a little busy preparing for the Jalview &
> JABA workshop this week, but I'll communicate on the issue tracker
> regarding these bugs.
>
> With regard to genomic databases - we should start on this seriously in
> 2014 when we have our new developer in place. Until then, one useful
> feature that is somewhat straightforward is to implement a Genbank record
> parser and emitter. That would allow people to import data from a wider
> number of databases. You could also take a look at the database fetcher
> infrastructure under jalview.ws.dbfetcher - there are a series of proxies
> that Jalview uses to retrieve sequence database records, and we've had a
> request for an NCBI retrieval client here:
>
> http://issues.jalview.org/browse/JAL-1375
>
> I also started a new branch with some code from Cytoscape 3 that should do
> the job - it just needs to be hooked up. Take a look at the additional code
> in the branch called JAL-1375_ncbiclient and let me know how you get on !
> Jim
>
>
> On 06/12/2013 17:23, David Roldán Martínez wrote:
>
> Hi all,
>
> I would like to increase my contributions but don't know where to start
> from. As I'm expert on i18n issues, I've thought that it could be a good
> idea to start reviewing once again i18n
> (JAL-1355<http://issues.jalview.org/browse/JAL-1355>)
> and then work on JAL-998 <http://issues.jalview.org/browse/JAL-998>and
> JAL-1390 <http://issues.jalview.org/browse/JAL-1390> (for this one I
> would need some help). I'm also interested at loading and querying genomic
> databases.
>
> Just let me know who you think I can help.
>
> Cheers,
> David
>
>
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