User talk:Dan

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Yo

Just made you an admin. I'll have to look into those other problems later tonight. Have fun. =]

Cheers dude! --Dan 11:27, 23 July 2009 (UTC)

Nice work! and thoughts on discussions...

This is pretty amazing what you've been doing here. I'm totally focused on getting up to speed on MW, SMW, and SF...so you have my blessing to continue as you see fit.

You will be better than me in no time! I guarantee it! --Dan 11:29, 23 July 2009 (UTC)

To address one point re: discussions...I'm thinking about the best way to handle this, both for discussions about the wiki project itself, and a way to conveniently house and organize the relevant conversations that will definitely take place re: each package (troubleshooting, benchmarking, etc). One option is to house these entirely on the package's talk page...but "talk" discussions are pretty hard to follow. Another would be to refer each talk page back to a dedicated thread on the forum (ideally isolated in a Software subforum).

Still thinking about it! Opinions welcome.

I put some comments on your talk page so you would get 'pinged' ... the MW 'discussion' system is seriously flawed. I think your idea to replace talk pages with (sub)forum threads is really excellent. --Dan 11:29, 23 July 2009 (UTC)

Fixed all of those problems....

...Semantic bundle was hosing things up...as it brought along another (different yet the same version) SemanticMediaWiki and also include()'d it (explains the two Browse Properties links).

The Special:Browse problem was solved by reinstalling everything, and NOT using the SMW version that comes bundled in bundle.

Who knows...seems to work now. :D

Awesome! As I said, I don't actually use Semantic Bundle, but I know that installing > 10 extensions can be a real pain, so I though I'd suggest that rather than the individual extensions. I'll make a 'configuration' page somewhere so we can keep track of these things... how bout SEQwiki:Configuration?

No problem

Thanks for the kind words. It feels good to give something back to the broader bioinformatics community. Plus, it makes SEQAnswers my universally findable personal notebook on NGS software :-)

Dan:

Glad I can contribute.

I think the main thing I would like to do, but it is tedious to do one-by-one, is to tighten up the keywords a bit. I think the "bioinformatics domain" vs "application domain" is a useful concept but the border has been a bit fuzzy. Probably can't make it totally sharp, but in my head "application domain" should be the place for concepts biologists would recognize whereas "bioinformatics domain" is going to have more things a computer scientist would recognize (classes of algorithms & such).

I've also been slowly lumping together keywords which I feel are the same thing or nearly so -- i.e. "ABI Solid" vs. "Solid". One small request:

Just let me know if I ever go overboard!

Keith

Hyperlinking classifications in the software entries

Is there any easy way to have the keywords in places like "Principal Bioinformatics Methods" in the software entries be hyperlinked? I.e., if I'm looking at one program & see a category of interest, make it quick to see the other programs in that category

K

I must not quite have the syntax right -- I was trying to put wiki links in the short descriptions for programs (e.g. Crossbow) & it seems to cause some of the hidden tags to be printed

program classification

Hey Dan - I finally registered after wondering who it was writing about setting up an SMW representation for bioinformatics apps. Given that wikipedia doesnt have the SMW yet, perhaps this is the best place to host the reduct of the programs reviewed for VizBi ?

Geneious Pro and Geneious Server

Hi Dan,

Geneious Pro is a package that does de novo and reference assembly as well as a myriad of other sequence analyses. http://www.geneious.com. Geneious Server is the workstation solution designed to integrate with Geneious Pro to simplify Next Gen requirements. http://www.geneious.com/default,1251,geneious.sm

Would it be possible to please list these as part of the wiki?

Disclaimer: I am the Market Development Manager at Biomatters, the company that creates Geneious.

Regards, Peter

Reply

Hey Peter (Springbok28 - who has chosen not to receive private messages on the forum!),

SEQwiki is totally 'open free' for anyone to use in any way that they see fit, be that commercial, non-commercial, profit or non-profit.

For this reason, it would definitely be possible to list Geneious Pro and Geneious Server as part of the wiki, irrespective of weather you are the CEO or just an average user :-)

At SEQwiki we aren't evangelical Wikipedians ;-)

To get started, here is a link that will allow you to create a page called 'Geneious':

http://seqanswers.com/wiki/Special:AddData/Bioinformatics_application/Geneious

To create (or edit) a page with a different name, just fill in the "Add a new bioinformatics application to the wiki" form, here:

http://seqanswers.com/wiki/Software

If you find SEQwiki useful, tell your friends :-D

It's a shame there isn't a forum on SEQanswers to discuss the wiki (i.e. for discussions like this one). I keep bugging ECO, but all I hear back is vague promises and excuses ;-) (Only kidding Eric!, but a forum for the wiki would rock).

All the best, Dan.

PM page counter

Could you point me to more information about Template:Bioinformatics_application/Popular and what populates the PM page counter variable? Cariaso 06:15, 15 March 2010 (UTC)