Next Grant

Dr J.C. Ison jison at
Wed May 21 10:31:38 UTC 2003

Hi Jose

On a related note there is now a course for would-be EMBOSS developers:

"Bioinformatics Software Development using EMBOSS"

I promoted that course to encourage EMBOSS developers outside the
EMBOSS "Inner Core" : )   All dates are booked for this year, but we've
just arranged new dates for 2004.

So if y'all know anyone who's interested, please forward the the link.



"José R. Valverde" wrote:

> We were discussing about how to facilitate/encourage people participation
> in EMBOSS development and why there are so few code submissions.
> On Tue, 20 May 2003 10:21:58 +0100
> Peter Rice <pmr at> wrote:
> >
> > So you always tell them how to contribute, right?
> >
> Half as well as I'd like. And that is less than half they deserve.
> All I can tell them is to contact Alan.
> Look, I'm on your side, I know, you know, _we all_ know.
> What you fail to understand is that you are at _Hinxton_. Developers
> outside tend to look with awe to Hinxton, where the elite dwells and
> performs amazin magic. Honest.
> It is very common for people outside to be shy about their work.
> And everybody is told not to use a list to post a single question that
> is probably a FAQ. So they don't go to emboss-dev.
> Picture it another way: which looks less intimidating, an FTP server
> with an "incoming" directory or one with no evident way to upload
> software to? A shared disk or another guy's PC?
> Or put another way: why does Jemboss ship with EMBOSS while wEMBOSS,
> W2H, EMBOSS-GUI didn't? What is outsiders' perception?
> Don't tell *me*. I'm on your side. I know. You know. But _they_ don't
> know.
> When the TMPC addressed the core team, what we asked was for a
> visible documentation of the submission process: how does one go
> around it? Whom do they send their code? What is needed for code
> to be accepted? If accepted, how do they gain access to the CVS
> tree to maintain it?
> It's no help that when we see a few guys once a year we encourage them
> to go to the web site if they don't _feel_ a warm welcome there.
> So, please, don't repeat what we all know. Just tell everybody what
> the exact procedure is and provide an example in the website that
> makes it look like "Whoa man, that was easy!! wasn't it?".
> Something along the lines of "choosing a project/getting access
> to a part of the CVS tree/using CVS to maintain your code/notifying
> the 'core' team when it is done/getting universal recognition and a
> free beer next time we see you..." You get the idea.
> And let's move this to emboss-dev from now on.
>                                 j
> --
> P.S.: since you ask, I've been trying to make an Embassy for MD package
> TINKER for over two years now. I work on my scarce spare time and must
> reverse engineer obscure physicists-written FORTRAN code, and it takes
> me time to write front-ends for over 50 programs changing over various
> releases. If I ever happen to catch-up, we'll have free MD/MM code in
> EMBOSS. But it's all on my own spare time, which is a real rarity, I'm
> not expected to do development at work, I'm supposed to be a service
> guy.
> P.P.S.: on the same line, BEN developed interfaces for blast/fasta. Why,
> they were shy to offer working, but localised code. I've been working on
> making it generic (again on my spare time) and feel confident they should
> work, sort of, but am looking for another piece of my spare time to test
> my changes (amazing, isn't it?) before submitting it. You must be aware
> that I need to find some time at work after I finish work and when I have
> nothing else pending to simply run the test. And I'm heavily overloaded.
> P.P.P.S.: AR and us are putting up a proposal to the TMPC to add LIMS
> facilities to EMBOSS. *WE* care. *WE* are on your side.

Jon C. Ison, PhD
Bioinformatics Applications Group
UK MRC Human Genome Mapping Project Resource Centre
Hinxton, Cambridge, CB10 1SB, UK
E-mail : jison at
Tel    : 01223 49-4548

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