Re: [basedb-devel] Mage-Tab export plugin

[Gildas Le C. <lec...@sb...>]

Bonjour,

This is good news if you can develope this plugin and I have enought 
datas on Base2 to test it :P

My contribution on the former plugin Tab2Mage was to add a feature to 
manage pooling of samples (or extracts) and the possibility to have 
several "Files[raw]" per RawBioAssay (ex : one cy3 and one cy5) because 
we used nimblegen multi-color arrays.
Are you plan to manage that feature ?

Gildas


Le 01/09/2011 14:43, Pawel Sztromwasser a écrit :
> Hallo,
>
> I haven't been to the milestones page for a while, and I didn't know 
> that work on BASE 3 was in such an advanced state. Great job guys! 
> Support for sequencing data is excellent news for us.
> Anyway, before it is released and before we are ready to migrate, we 
> will certainly have experiments to export. We could keep using the 
> Tab2Mage exporter this year, and the conversion script later, but I 
> think I'd prefer to start working on the plugin now when we have time, 
> develop against BASE 2 where we would have immediate use for it, and 
> port to BASE 3 later after we migrate. It will not be a big change I 
> hope.
>
> Gildas, I have actually started developing the plugin. If you're 
> willing to contribute, I could send you the jar/code when it is 
> more-or-less ready for testing, so we could debug it on our sites 
> simultanously and make it bullet-proof;)
>
> Helen, IMO it is better with one format than two, so I think removing 
> support for Tab2Mage (and providing conversion tools) is a move 
> forward. One thing I was wondering, if there are any plans for an 
> XML-based format for description of MA experiments? MAGE-ML is a bit 
> too complex I guess, but an XML Schema equivalent to the current 
> MageTab format would be favored by programmers and for programmatic 
> access, in comparison with the tab-delimited files.
>
> Best wishes,
> Pawel
>
> Nicklas Nordborg wrote:
>> On 2011-09-01 09:15, Gildas Le Corguillé wrote:
>>> Hello,
>>>
>>> Our group still interesting in this kind of exporter. It was the main
>>> reason why we decided to use Base. We are in a public lab so we like to
>>> share :P
>>> Last year, I repaired the existing Tab2Mage-exporter module for Base.
>>> So if you need help, I can spend some time on that. But I'm not
>>> necessarily a good developer ^^'
>>
>> I think that a Mage-Tab exporter has to be developed by the BASE 
>> community. We can provide space and user accounts on our 
>> subversion+trac (baseplugins.thep.lu.se) if someone is interested to 
>> start on this. Unfortunately we have no time to help with the actual 
>> development. Of course, we'll try to answer questions and provide the 
>> information that is necessary.
>>
>> As a starting point, we try to collect and document the major API 
>> changes in http://base.thep.lu.se/ticket/1603
>>
>> My guess is that #1153 and #1597 are the major changes that cause 
>> problems for the current Tab2Mage exporter.
>>
>> /Nicklas
>>
>>
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>
>
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