Importation on windows

[roald...@student.uclouvain.be]

Hi,

I'm in my last year at UCL (catholic university of Louvain-la-Neuve) and my master thesis is: "Design of an in-memory biochemical database for assisted drug design". Thanks to that, i'm really intersted in your project Bio4j.

I want to import a few module of Bio4j (Gene Ontology, Expasy Enzyme, UniprotKB and Protein interactions). 

I've a few questions:

Is that possible to import Bio4j on windows OS? 

Is it possible to import theses modules just for the human species?

Can i add my own module like MetaCyc to analyse the links between the proteins, their regulations and the metabolic pathways they may affect.

Sorry for my bad english.

Best regards,

Roald Targé

[roald...@student.uclouvain.be]

I found the answer of my first question in older topics and it's yes :). But when i try to download executionsBio4j.xml, batchInserter.properties, uniprotData.xml I've an Error 404. Can you help me?

Thank you,

Roald Targé

[Pablo Pareja Tobes]

Hi Roald,

Great to hear about your interest in Bio4j project ;)

Regarding your questions:

> Is that possible to import Bio4j on windows OS? 

Of course, Bio4j is a cross-platform database. Thus, the only requirement to import Bio4j is having a fully ready JVM installed so that you can run the importing programs.

> Is it possible to import theses modules just for the human species?

Well yes and no. In the case of both Gene Ontology and Enzyme DB it won't make sense to partially import them mainly because they're quite small in terms of size so they shouldn't be a problem at all for virtually any machine specifications.

Regarding Uniprot KB you could build yourself an XML file holding the specific entries you're interested in but I wouldn't advise it, I'd go for importing the whole thing. In fact, the requirements for having the complete version of Uniprot KB module wouldn't be hard to meet and that way you'd have everything in the case where later you may decide to expand the amount of data you want to traverse.

> Can i add my own module like MetaCyc to analyse the links between the proteins, their regulations and the metabolic pathways they may affect.

I'm not 100% sure to understand what you mean but if what you're asking is whether it's possible to add new data to Bio4j the answer is yes! Keep in mind that in the end what you have is just a graph so you can add your own new nodes/relationships at any time making the best out of your own scenario.

About your second e-mail, please check the answer I just posted in this other message here (last couple of messages):

https://groups.google.com/forum/#!topic/bio4j-user/EcFVvzefM80

Anyways don't hesitate to contact us for any other questions you may have.

Cheers,

Pablo

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[roald...@student.uclouvain.be]

Thank you for this quick answer.

Best regards, 

Roald Targé

[roald...@student.uclouvain.be]

I still have the error 404 when i try to download  executionsBio4j.xml, batchInserter.properties, uniprotData.xml . I was wondering if it was normal!

Thank you,

Roald 

Le mardi 11 février 2014 16:56:52 UTC+1, Pablo Pareja Tobes a écrit :

[Pablo Pareja Tobes]

Hi Roald,

I apologize for the inconveniences but we're carrying out a major reorganization of Bio4j platform (including repository changes, documentation updates, code refactoring, a more robust release system, and much more...)

Bio4j is growing quite fast and we needed to do all this before everything got out of hand.

Unfortunately all this is taking us a bit longer than we expected but as soon as things are sorted out (it shouldn't take more than a week) I will let you all know.

Please bear with us till then. 

Cheers ;)

Pablo

[roald...@student.uclouvain.be]

Hi Pablo,

Thanks for this message. 

Any news about if it's ok right now?

Best regards,

Roald