User talk:Krobison

Hi --Dan 07:55, 18 September 2009 (UTC)

Krobison++

Thanks for all your contributions to SEQwiki! --Dan 16:08, 24 October 2009 (UTC)

Hey K

Thanks again for your efforts on the wiki Kris.

Can I ask, do you have any feedback about the site? What would you most like to see improved next? i.e. it's easy to add new fields or new forms to the site. Similarly the 'Browse Software' page can be extended easily... Do you know any other site editors? Would you like a forum on SeqAnswers for the wiki? (this talk page system of communication is quite painful compared to the forum).

About the site, I'm pretty embarrassed about the state of the 'references' section of the wiki currently, but I think fixing that 'properly' will take quite some work. I'm thinking to add some 'query forms' to the site, to allow people to query for applications using fields of the forms. Also, I'd like to add a section on sequencing centres to show off the maps feature of SMW, and to absorb the other 'data heavy' thread on SeqAnswers.

Let me know what you think. Cheers, --Dan 00:17, 9 December 2009 (UTC)

Hi Keith,

You said:

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).

Yeah, I totally agree on this point. I didn't think out the categories clearly when I designed the form, and now we are somewhat 'stuck' with a less than optimal categorization. I think the best thing to do is to (perhaps) rename the keyword classes to something better, and provide documentation and better examples in the form. i.e. we could list the most common tags in each class, to help users get a flavour of what the tags are for. If you have some specific changes that you would like to make on many pages, I can write a script to automate that process.

I've also been slowly lumping together keywords which I feel are the same thing or nearly so -- i.e. "ABI Solid" vs. "Solid". Just let me know if I ever go overboard!

No I think that is a good idea. The perils of user input ;-) We can actually constrain the input to a combo box, making it harder (but not impossible) for users to define new terms. Let me know which fields you think that would benefit from such a change. Again, if anything is wrong in more than say 10 pages, I can write a script to fix it. I'll post the scripts back to the wiki, so you can start to develop 'batch jobs' yourself.

One small request: 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

Yeah, I know what you mean. Typically there are several clicks to find progs with that keyword (via Browse software), or it just isn't possible (apparently). There is a slightly convoluted method you can use to get what you want though. On the page of interest, click 'Browse properties'. e.g.:

• http://seqanswers.com/wiki/BSMAP ->
• http://seqanswers.com/wiki/Special:Browse/BSMAP

And then click the little magnifying glass next to the property value of interest. e.g. the 'Mapping' value of the 'Bioinformatics method' property:

• http://seqanswers.com/wiki/Special:SearchByProperty/Bioinformatics-20method/Mapping

I could try to construct URLs like the above as you suggested. However, where would you like the link to appear? On the term itself? Or perhaps on a little magnifying glass next to the term?

Thanks for the feedback, it's good to know that we were thinking broadly along the same lines ;-). All the best --Dan 18:10, 22 December 2009 (UTC)

Links in fields

Right, you can't put wiki syntax in any of the 'database fields' for a software package. It's kind of a pain, but it makes sense in a way. i.e. short descriptions should only be text. The full text description can contain wiki syntax...

Let me know if (and why) you think the short description should carry wiki syntax, and I can try to work on a solution.

HTH, --Dan 09:20, 5 January 2010 (UTC)

Editing pages just now?

I'm about to make some edits...

--Dan 18:10, 22 May 2010 (UTC)