Reorganisation of EMBOSS

[Gary Williams, Tel 01223 494522]

Sorry - I'm guilty of imprecise terminology here.

When I said "A program should have a function", I meant that a program
should have a single biological job to do, not that a program should
only have one call to a single function in the code libraries, (which I
agree is very silly.)

Gary

Tim Carver wrote:
> 
> I agree with Lisa......  because this is the sort of feedback that comes from the courses! It does
> not look impressive having so many programs that do a single function.
> 
> Surely a function is what the libraries are for and a program can then call a number of these
> functions. You still have modular libraries that the enthusiast can cobble together to do what
> they want, but combine highly reletated programs and then just add flags!
> 
> If you expect them to wade through the groups to get to the program that they are looking for then
> the groups maybe could do with a re-think.
> 
> Tim
> 
> "Gary Williams, Tel 01223 494522" wrote:
> 
> > Which programs were you proposing to amalgamate?
> >
> > Surely it is the job of an interface to group programs and to guide the
> > user to the appropriate function?
> >
> > A program should have a function.
> >
> > A program should not have several functions.
> >
> > Perhaps a good rule is:
> > If the function cannot be simply expressed in one line of description,
> > then the program is too complex and should be split. If two programs can
> > be described together in one line then they complement or overlap in
> > function and should be merged.
> >
> > Gary
> >
> > Lisa Mullan wrote:
> > >
> > > Here is the eagerly awaited ppt file!
> > >
> > > I don't seem to have BeeJay's address, or anyone else from theEBI, but
> > > trust it will be shared.
> > >
> > > To continue the conversation we were having at the meeting regarding the
> > > splitting, or amalgamating of programs, I think we should look for a
> > > consensus on  one thing or the other.
> > >
> > > For my part, I think it is rather silly that bench biologists (who are the
> > > main users of these tools) have to wade through hundreds of programs often
> > > with names that bear little or no relation to what they do (although we
> > > find them funny!)
> > >
> > > On the side of people that are developing their own softwre using EMBOSS
> > > applications, I feel that it would be possible to switch off the functions
> > > they don't need by using the option flags.
> > >
> > > I cannot see an argument for so many tiny programs, apart from the
> > > author's own convenience, which should perhaps be lower down the priority
> > > list?
> > >
> > > Lisa
> > >
> > > Lisa Mullan
> > > HGMP Resource Centre
> > > Hinxton,
> > > Cambridge, CB10 1SB
> > > Tel: 01223 494526
> > > Email: lmullan at hgmp.mrc.ac.uk
> > >
> > >   ------------------------------------------------------------------------
> > >                               Name: emboss_coordination.ppt
> > >    emboss_coordination.ppt    Type: Microsoft PowerPoint Show (application/vnd.ms-powerpoint)
> > >                           Encoding: BASE64
> >
> > --
> > Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
> > mailto:G.Williams at hgmp.mrc.ac.uk           http://www.hgmp.mrc.ac.uk/
> > Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK