Reorganisation of EMBOSS

Claude Beazley cbeazley at
Mon Oct 14 10:09:30 UTC 2002

However, having said that, UNIX does not have 15 different "ls" commands (one 
ls for listing the files, another for listing the files with file sizes, a 
third one for sorting and listing the files... etc) it does have one "ls" 
command with switches for sorting, stats etc. 

So if that is the sort of integration that Lisa is thinking of, then it should 
be carefully considered.


>On Monday 14 Oct 2002 10:48 am, Claude Beazley wrote:
> The UNIX design philsophy (which has served us well for nearly 40 years) is
> KISS (Keep It Simple Stupid). i.e. Create lots of small well designed tools
> each of which serve a very specific function. These tools can be then
> linked together (through piping, redirection or simple file
> writing/reading) to perform very complex tasks.  It keeps  debugging sane
> and allows
> users/developers to utilise the tools in ways that the original developers
> may not have thought of.  This allows the biologists the  high degree of
> creativity which is important for research. OK. so they have to learn
> stuff, but that is nothing new for Biologists. If they really have problems
> developing new tools, then they can approach us or get their IT dept to
> develop in-house solutions.
> Also from a distributed programming perception, monolithic code structures
> would be an absolute nightmare to deal with.
> This modular approach also largely negates the problem of reinventing the
> wheel for each app. It also means that bench-biologists don't have the
> problem of massive code-bloat when they want to run a simple app. Many
> researchers (for example in third world countries) have old and
> underpowered PCs (people still use 486s would you believe). Keeping EMBOSS
> modular allows them to still use these machines whereas the total
> integrated approach would force them to enter the hardware upgrade
> treadmill. This is a  prohibitive path which would  keep  them from using
> EMBOSS. (One of the reasons that GNU/Linux is so successful is that it can
> run pretty much on anything, due to this approach.)
> KISS keeps stuff running efficiently, cleanly and with sanity.
> >On Monday 14 Oct 2002 10:15 am, 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
> -------------------------------------------------------

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