Questions about OSS projects.

[bio_enthusiast]

I was wondering how to go about starting an open source project for
doing routine biological problems? There is a plethora of scripts and
a fairly large biopython project to back up anyone who tried, these
however cater to the bioinformatics community and it loses the vast
majority of the wet-lab scientists. How can someone who is used to
writing small scripts and doing wet-lab work contribute to the open
source community? Starting software projects seems to be the domain of
people with much more experience and skill but there are some serious
needs by people who do not have the skills to upkeep any software
based project.

 

[Grant Edwards]

I was wondering how to go about starting an open source
project for doing routine biological problems?

Generally you either start writing code to fulfill a need of
yours, or you pay somebody else to write it for you.

There is a plethora of scripts and a fairly large biopython
project to back up anyone who tried, these however cater to
the bioinformatics community and it loses the vast majority of
the wet-lab scientists. How can someone who is used to writing
small scripts and doing wet-lab work contribute to the open
source community?

For existing projects, you can help a lot by submitting good
bug reports, documentation enhancements or translations,
patches, etc.

Starting software projects seems to be the domain of people
with much more experience and skill but there are some serious
needs by people who do not have the skills to upkeep any
software based project.

That's what money is for. People with no need for (or interest
in) program X (and indeed don't even know about the need)
aren't going to write program X unless you pay them to. You
could try to recruit some SW types to write the code for free,
but they're probably already busy working on OSS projects that
they need/want.

There are sites where you can offer "bounties" as incentives
for people to work on the OSS you want them to work on.

 

[Daniel Dittmar]

I was wondering how to go about starting an open source project for
doing routine biological problems? There is a plethora of scripts and
a fairly large biopython project to back up anyone who tried, these
however cater to the bioinformatics community and it loses the vast
majority of the wet-lab scientists. How can someone who is used to
writing small scripts and doing wet-lab work contribute to the open
source community? Starting software projects seems to be the domain of
people with much more experience and skill but there are some serious
needs by people who do not have the skills to upkeep any software
based project.

If you've written a few small scripts that might be of use to others and
that you assume that there are others who do the same, you might start
with a wiki or something like the Python Cookbook
(http://aspn.activestate.com/ASPN/Python/Cookbook/), but geared toward
labs and biology.

If this gains any traction (that is if you get additional code snippets,
people are commenting etc.), after a while, it might be useful to look
at the material and see if there is enough code that warrants a library.
This does not mean to simply package all the scripts into one package,
but to see if there are any common tasks among the scripts to 'refactor'
them into a library.

Daniel

 

[Paul McGuire]

If you've written a few small scripts that might be of use to others and
that you assume that there are others who do the same, you might start
with a wiki or something like the Python Cookbook
(http://aspn.activestate.com/ASPN/Python/Cookbook/), but geared toward
labs and biology.

I would suggest going the wiki route - wikispaces.com makes this very easy,
and free if you don't mind ads on your wikipages. Could be a
low-cost/low-effort way to get started.

-- Paul

 

[Terry Hancock]

I would suggest going the wiki route - wikispaces.com makes this very
easy, and free if you don't mind ads on your wikipages. Could be a
low-cost/low-effort way to get started.

Specifically, I would recommend that you build up a links list and/or
repository of scripts that you find relevant. Eventually, if there's
enough accumulation, somebody might express interest in creating
a more integrated tool based on them. Maybe there's somebody who'd
be willing to do that, but doesn't know where the material is.

Cheers,
Terry