[Biophp-dev] gone for two weeks

S Clark biophp-dev@bioinformatics.org
Fri, 1 Aug 2003 10:23:17 -0600

That's quite alright...and even if it wasn't, I'd be in no position
to berate you, as I've been shamefully procrastinating the next two
parts of the project I've got queued up to work on (Sequence EFetch and
an alternate seq object implementation) just because I've got
so much going on at the moment (job search, college application and
search for funding to finally finish my degree and move on, a couple
of volunteer cooking projects [now finished, thankfully], and so on) and
the next couple of parts appear to be more tedious than anything else
(Sequence EFetch isn't really DIFFICULT, but there are a large number
of fields to handle and 'map' onto a seq object), though I really will be
getting to these very soon.  After those, though, I'd be willing to look into

Come to think of it, perhaps it'd be worth me looking into it sooner - the
layout and intent of the BioSQL tables could influence how I lay out the
alternative seq object (and in turn affect the 'mapping' of the sequence
EFetch data...)

Thanks for the update!  In addition to contributions of code, you're
obviously welcome to just pop in with comments, suggestions, and
opinions as well.

I'll be posting another small update of things on my side of development
as well sometime in the next day or two.

Good luck!


On Thursday 31 July 2003 09:36 pm, Nico Stuurman wrote:
> As you can see I really took some time off!  That was great.  It also
> made me realize that I simply do not have enough time to fully engage in
> this project.  I'll still try to do something now and then, but don't
> expect too much.
> I made a start with the BioSQL scripts.  The script to generate the
> BioSQL tables using adodb works (but is a little futile since there are
> already scripts to generate these tables for MySQL and Postgres).  Oh
> well.  I also started working on a function that writes a seq object to
> a BioSQL database. Hmm.  It seems that almost every field in BioSQL has
> the attribute 'NOT NULL'.  That makes it virtually impossible just to
> write a simple sequence with a name to it.  I am afraid that it will
> takes some time to fully grasp what people are doing with BioSQL and how
> they fill those tables.  If someone else feels like trying, that would
> be great!