Bioperl: Joining up...

Ewan Birney
Mon, 25 Jan 1999 19:15:23 +0000 (GMT)

Having talked to some people around hinxton (Sanger Centre, EBI and HGMP)
I realised that some people like bioperl in concept but don't feel happy
about contributing to it or 'joining' it. In this email I hope to remove
those fears...

We aren't scary computer scientists -

The main people at bioperl are not computer scientists but self taught
biologists who learnt perl and programming generally because they had
problems that they wanted to solve. Some of us have gotten deeper into the
CS side (to the point of being indistinguishable from them?), but all of
us are here because we use Perl to solve biological problems and that is
still our aim.

We don't mind 'bad' code -

Some people are very embarrassed about showing their code to others for
fear of being told that there is a better way of doing it. It is fine
to have kludges and make hacks - at least if they work - and bioperl has
a number of wince-making or obtuse bits of code. Eventually someone takes
them out and (hopefully) fixes it. Nearly all of us have made some real
howlers in our time (I know I have) so we've all been there.

We aren't a little tight group

We honestly don't mind who does what - the people who have done the
backbone of the work has changed over time and will continue to change.
you can quite easily (if you wanted to) become one of the key members
of bioperl by contributing alot. I wasn't a founder member at all
for example.

We don't have some pseudo-legal heirarchy

We are a very open source, anarchistic group. The only person who is
different from anyone else is Steve Chervitz who does the official
announcing of releases. Otherwise we just let people actually do whatever
they like (it is better if you discuss things first of course), and take
decisions by informal consensus. I guess that if there was a real bust up
in bioperl we would have to ask steve to figure it out. But it hasn't
happened yet (cross fingers).

It is easy to join...

	- in some senses you have already by being on this list.

	- if people want to hear what the real internal people
are discussing, subscribe to the guts list. (at the moment steve is
getting ready to make a new maintaince release for example). 

	From here on in, you've just been passive. Now to become more
active these are the things you can do

	- contribute to the discussions on this list (I know a number
have and it makes for great reading).

	- post bug reports or suggestions for the modules through the
bug interface (I know there are a number of bugs that have been noticed
but not reported. Please report them! It is great stuff to find a bug.
We want to hear about them. Honestly).

	- get an account on by emailing (anyone involved in the project can get one).

	- learn how to use cvs to edit the web site (for documentation)
or the code (for... the code!)

	- Contribute actively!

To learn me about who we actually are, go to

though I notice that not everyone who does use and contribute to bioperl
is on that (if people can send chris with their little four liners that
would be great).

there are lots of things to do in bioinformatics, and re-coding some
arcane format parsing or data structure layout should not be one of the
main things we do. Ask yourself what you spend most of your time doing...

Bioperl is all about being able to do interesting things and sharing the
ability to get through the tedium of bioinformatics.

Ewan Birney

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