SEQUENCHER FOR UNIX? WHY?

Gabriel Gabriel
Tue Oct 8 17:38:34 EST 1996


Howard Cash wrote:

>Don Gilbert posted a query on the AUTOMATED-SEQUENCING group soliciting
>opinions on different software packages for DNA sequencing and assembly.
>He summarized responses on the net at
>   http://www.bio.net/hypermail/AUTOMATED-SEQUENCING/9608/0047.html
>There were subsequent postings on the subject
>  http://www.bio.net/hypermail/AUTOMATED-SEQUENCING/9609/0007.html
>> The unanimous favorite software was Sequencher. However only two
>> respondents expressed experience with the Unix programs (Phrap &
>> Staden),
>> so this does not offer as clear an answer as I had hoped. ...


>Without challenging that premise, what do people think is the main value
>of having sequence assembly software on a UNIX platform?

Sheer speed.


>If Sequencher
>is already such a favorite on the Mac, is there something to be gained by
>going to the trouble to develope a UNIX version?

More choices. Yet, we would only consider Sequencher on UNIX if we could
access it through a true MacOS client interface (as PerkinElmer did with
INHERIT). For us, MacOS means productivity. A Unix box might be too
powerful, yet we have not the time or resources to train people on UNIX
complexities... even under the XWindow GUI. And we have tried Unix
alternatives.

>As an engineer, I like UNIX for software development, but I am biased
>towards the Macintosh for delivering ready-to-use analysis tools.  Larger
>research groups with existing UNIX-based data-management systems ask us
>about porting to that platform, but is there a compelling reason for us
>to develop Sequencher for Unix?  What would the advantage be in the
>average lab, other than the undeniable freedom to work in front of the
>computer of one's choosing?

I guess Sequencher on Unix would be interesting for large corporations or
University Central Services with many concurrent users than to individual
labs which would likely stick with the MacOS version (more below).

>hearing your opinions on the value that you or your immediate colleagues
>would get from a UNIX version. What operating system characteristics
>would you want us to take advantage of that might not be available on a
>Mac.  Keep in mind that, in the real world of finite resources, the
>effort that we would put into porting all or part of Sequencher to a new
>platform would come at the expense of our ability to quickly add features
>to the program if it is only on the Mac.

If you had the resources, I would say, go for Unix with MacOS client
interface. Yet, with the new MacOS 8 (Copland) due for June 1997 (I think
the SDK is in beta now) and nPOWER multiprocessing already running 
(DayStar
GenesisMP) and due to become popular now that Apple, Umax, PowerComputing
and others have embraced it, I guess it would be much more productive to
make Sequencher nPOWER multiprocessing savvy (symmetric MP with Copland)
and port it to MacOS 8.

Those are my opinions.
Hope it helps,

Gabriel Dorado
bb1dopeg at uco.es






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