Reorganisation of EMBOSS

Claude Beazley cbeazley at
Mon Oct 14 09:48:08 UTC 2002

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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