[Biodevelopers] Regarding microarray database development

[Wiepert, Mathieu]

Hi,

Did you take a look at MAGE object model http://www.mged.org/Workgroups/MAGE/mage.html?  That should take you a far ways down the path...

See www.mged.org for more information.  Good luck,


-mat

> -----Original Message-----
> From: biodevelopers-admin at bioinformatics.org
> [mailto:biodevelopers-admin at bioinformatics.org]On Behalf Of kaustubh
> shinde
> Sent: Monday, March 29, 2004 9:46 AM
> To: biodevelopers at bioinformatics.org
> Subject: [Biodevelopers] Regarding microarray database development
> 
> 
> Hi,
> I am computer science masters graduate and new to the field of 
> bioinformatics. My objective is to set up a system that will download 
> microarray data from public databases like NCBI, EBI etc 
> which in turn I 
> want to use for data mining. I would like to develop a 
> relational database 
> in mysql on linux.
> 
> I have spent last 2-3 weeks reading about the NCBI toolkit, 
> Arrayexpress, 
> and Miamexpress tools and also about Biojava.
> While NCBI toolkit is specific to the NCBI, Arrayexpress and 
> Miamexpress are 
> data submission tools and would not allow me to download data 
> directly from 
> the servers. Biojava seems pretty useful but I am not sure if 
> and how I 
> could save the data in MAGE-ML format.
> 
> Keeping the objective - to make a system to download and 
> analyse microarray 
> data from VARIOUS public databases - in mind, what steps 
> should I take? I 
> understand that this question might sound utterly stupid to 
> you. But I hope 
> you understand the difficulties of a computer guy having very little 
> background in biology or bioinformatics. Having said that, I 
> have done quite 
> a lot of reading on biology, microarrays and DNA, chromosomes related 
> matter.
> 
> If you could show me the right direction that will be a great 
> help. Right 
> now I am lost and don't know how exactly I should proceed.
> 
> Thanks for you time. I am hoping for a positive reply.
> Thank you,
> Kaustubh
> 
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