Willing to increase my contributions

Jalview Developers
1

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) and then work on JAL-998 and 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

2

Hi all,

···

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:

3

Hi,

OK. Remember my offer to talk about i18n. I’ll be available on Thu from 17 pm (Spanish time). Just ping me through Skype. It will be a pleasure for me. :wink:

Cheers,

David

···

2013/12/9 Jim Procter <jprocter@compbio.dundee.ac.uk>

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) and then work on JAL-998 and 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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4

Hi all,

I’ve taking a look at 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 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. :wink:

Cheers,

David

···

2013/12/9 Jim Procter <jprocter@compbio.dundee.ac.uk>

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) and then work on JAL-998 and 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

_______________________________________________
Jalview-dev mailing list
[Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)

Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev