[Bio-software] Re: GCG non-support

Steve Thompson via bio-soft%40net.bio.net (by stevet from bio.fsu.edu)
Fri Aug 3 13:55:28 EST 2007


On Fri, 3 Aug 2007, Peter Rice wrote (in part):

> [Re. SeqLab custom extensions availablity] In this case, sharing may be 
> possible. I can ask anyway.

Yes, that would be great, especially if we get Accelrys to release 
SeqLab's code.  I was quite pessimistic a couple of weeks ago, but have 
some [small] hope now.  But I do realize not to 'hold my breath.'

> Can you make a quick list of the additional functionality you would like 
> to see [in GDE]?  I seem to recall "rich sequence format" was one of 
> GCG's major extensions.

Yes, some have already been mentioned in this thread; I think these two 
are the most important:

1) The ability to directly load sequence data from output sequence lists 
from other programs such as BLAST, FastA, and a reference searching 
program (in GCG that is the SRS derivative LookUp) with the option of 
trimming that data to the length id'ed by a similarity search.  As Nick 
mentioned this ability to handle "ad-hoc" databases can be very powerful.

2) The ability to display FEATURE information from database entries in 
colored and graphical representations.  This is especially helpful for 
homology inference of active sites and secondary structure.

> [Re. Accelrys' "perpetual license" plan] Interesting. I see it mentions 
> Pipeline Pilot. EMBOSS is an ISV partner and committed to interfacing 
> EMBOSS applications as Pipeline Pilot components.

Pipeline Pilot is exciting and incredibly powerful from all I can tell, 
but also incredibly expensive - well beyond the budget of most university 
departments and/or research institutes, especially these days.

> I hope there is some source code release. We had the source code at Sanger 
> not just for EGCG - but also because the sequencers needed more than the 
> 350kb limit on sequence length.
>
> But I see no quick way to decide on possible source code licensing. Too 
> many authors, too many companies/institutes. I am not surprised that 
> nothing is promised at this stage.
>
> Hang on to your licences though ... one (legally speaking) relatively easy 
> possibility would be a cheap source license for existing licensees.

Oh yes, I don't plan on letting anything that we already own get lost.

> [Re. getting SRS5 code under SeqLab or GDE] That would be difficult ... 
> and I am not too confident of the status of SRS5 code anyway. But there 
> are some alternatives around.

Too bad, but I'm glad there are alternatives.  Perhaps some variation of 
NCBI's stand alone Entrez, but it is designed for ASN.1 data . . . . .

> [Re. my old days at WSU's VADMS Center] Hah! Not the one I meant (VADMS 
> had an alpha binary release). The beta test was at HGMP/RFCGR in Hinxton 
> - where the EMBOSS development team was and it was their closure that 
> threw EMBOSS into crisis mode.

Yes, that was another terrible shame of funding drying up.

> An early version of MSE was used by GCG for several of their editing 
> applications, so at least that and GDE 2.3 are currently available with 
> source code. EMBOSS's MSE is under GPL. I will try to figure out what GDE's 
> licence really means.

A clarification of GDE's license would help a lot.  Thanks!

                              Cheers - Steve
                                                 Steven M. Thompson
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