[BioSQL-l] questions

[Tamas Hegedus]

Hilmar Lapp wrote:
> On Thursday, January 27, 2005, at 01:25  PM, Tamas Hegedus wrote:
>> -----------------------------
>> DOCUMENTATION; WHYs; packing
>> -----------------------------
>> However, I know that BioSQL is under development, but it is not a 
>> 'theoretical' projects, intend to be used by users.
>> More users, more feedback, more development, happier programmer.
>> But at this moment very difficult to recognize its advantages:
>> => Why is BioSQL (RDBMS) better than other solution (e.g. flat files); 
>> why should I use it for my project?
> I summarized the most popular use cases at BOSC03. You may want to check 
> out
> http://www.open-bio.org/bosc2003/slides/Persistent_Bioperl_BOSC03.pdf
Thanks. But my problem was that it is pretty difficult to find on the 
web. If somebody is looking for solutions on the web, he will not stop 
at your site, will not strugle to find out if BioSQL is OK for him or not.

>> => What to download, from where to download? (In my opinion CVS is 
>> definitely for programmers not for biologist.)
>> => What programs can I use to access the data? Only scripting? No! I 
>> can  use it e.g. with GBrowse, exactly what I need...
> There is an adaptor that bridges biosql to be used by gbrowse, there's 
> just been a thread on this on the gbrowse mailing list. There's possibly 
> some wrinkles though that need to be worked out so that Gbrowse finds 
> the features it is supposed to find. Check out the last week in the 
> gbrowse mailing list archive.
Sorry. I was very theoretical in my posting. I do not need gbrowse. I 
just wanted to picture that it would be great for visitors to see what 
type of 'client'/ready-to-use program package (like gbrowse) can be used 
with BioSQL.

>> => Is there any convinient way to query the database? I do not really 
>> want to learn SQL. How to perform and link queries/returned entries to 
>> 'conventional' analysis tools (like pattern search)?
> Bioperl-db provides you with an interface (object-relational mapper) 
> that lets you interact with the database through bioperl and query 
> objects, not SQL. When you run a search ($adaptor->find_by_XXX) you'll 
> get bioperl objects returned.
> Note though that ultimately SQL is always going to be so much more 
> powerful.
This means that only/mainly programmers with SQL and perl (java) 
experience are able to use the features of this RDBMS system.
I may be impatient: I would like to have everything now, although the 
BioSQL project is not at the final stage of development.

>> For developers: if you work on BioSQL constantly (from the beginning), 
>> you will know what column is for what (like 'Rank'), what are the role 
>> in a specific relation; but you can find  out these things, if you 
>> populate the database, and dig into it: so much energy needed that the 
>> developer find out an easier way to solve his problem.
> Have you checked out the doc directory in the repository? There is a 
> schema overview and an ERD. Those two will still leave many questions 
> open, like 'rank', but it could be a start nonetheless.
I checked. But it is so frustrating for me, that I always stop and start 
again after 2 months. But this could be because of my stupidity :-(

>> I know that it is a huge work to create (and keep uptodate) a website. 
>> Personally I really do not like (hate) creating web-pages. But I think 
>> a web-site for BioSQL would greatly accelerate the BioSQL project.
> Unfortunately, almost all developers have the same enthusiasm for 
> creating web-pages as you have. Volunteering web-page authors is what 
> the OBF needs most desperately. I have no doubt that informative, 
> well-organized, and most importantly regularly updated web pages would 
> help the biosql project, but this is also the area where people could 
> volunteer most easily.
> Biosql like all other OBF (and generally open-source) projects is a 
> project built by people who volunteer their time ...
I know. I really appreciate.

And thanks for all answers,
Tamas

-- 
Tamas Hegedus, Research Fellow | phone: (1) 480-301-6041
Mayo Clinic Scottsdale         | fax:   (1) 480-301-7017
13000 E. Shea Blvd             | mailto:hegedus at mayo.edu
Scottsdale, AZ, 85259          | http://hegedus.brumart.org