BioForge, a SourceForge-like server for genome assemblies (Re: a GitHub of science)

[Dan Bolser]

Matthew Levitt came up with an interesting proposal based on GMOD
'Idea #9' [1], namely, to host genome assemblies on a 'SourceForge-
like' server, where they could be checked out, modified, checked in,
branched, tagged, merged, etc.

I think this is a great idea, not least because we're about to have
thousands of new genome assemblies on our hands in the next 3-5 years
[2].

I read an interesting article that reminded me of this idea, here:

http://marciovm.com/i-want-a-github-of-science


Just thought I'd pass it on.
Dan.

[1] http://gmod.org/wiki/GSoC#IDEA_9:_Develop_collaborative_genome_assembly_tools_and_databases
[2] http://genome10k.soe.ucsc.edu/

[॥ स्वक्ष ॥]

On Sun, Apr 10, 2011 at 17:30, Dan Bolser <dan.b...@gmail.com> wrote:
> Matthew Levitt came up with an interesting proposal based on GMOD
> 'Idea #9' [1], namely, to host genome assemblies on a 'SourceForge-
> like' server, where they could be checked out, modified, checked in,
> branched, tagged, merged, etc.

IIRC git was the original choice, so I'm curious why DVCS systems like
git, mercurial or even bazaar are not under consideration. I do have a
bias as I've used them more than svn but besides that there are many
features which, say, 'git' offers that subversion does not.

PS#0. This isnt intended to be a svn vs. git/other DVCS flamebait,
rather I'd trying to understand what are the merits/demerits between
svn and other DVCS.

PS#1. Dan since I've used my gmail ID, could you please unsub the
other ID. Google groups does not allow me to unsub my non-gmail id's.

Thanks,

--
peace,
vid || http://svaksha.com

[॥ स्वक्ष ॥]

Furthermore, I was thinking a bit about this and wanted to suggest
that a BioForge on the lines of Berlios[0] would be very interesting.
Unlike, say, github or bitbucket, it runs completely on free/libre
software and supports many DVCS (mercurial, git, cvs and svn)[1].

[0] http://en.wikipedia.org/wiki/BerliOS
[1] http://en.wikipedia.org/wiki/Comparison_of_open_source_software_hosting_facilities

What do you all think? Maybe we should have this interesting
discussion on the genome-informatics list too?

[Dan Bolser]

Hi Vid,

On Apr 11, 4:02 am, ॥ स्वक्ष ॥ <svak...@gmail.com> wrote:

> On Sun, Apr 10, 2011 at 17:30, Dan Bolser <dan.bol...@gmail.com> wrote:
> > Matthew Levitt came up with an interesting proposal based on GMOD
> > 'Idea #9' [1], namely, to host genome assemblies on a 'SourceForge-
> > like' server, where they could be checked out, modified, checked in,
> > branched, tagged, merged, etc.
>
> IIRC git was the original choice, so I'm curious why DVCS systems like
> git, mercurial or even bazaar are not under consideration. I do have a
> bias as I've used them more than svn but besides that there are many
> features which, say, 'git' offers that subversion does not.
>
> PS#0. This isnt intended to be a svn vs. git/other DVCS flamebait,
> rather I'd trying to understand what are the merits/demerits between
> svn and other DVCS.

I think it's as simple as the fact that 'SourceForge' -> 'BioForge' is
a good pun / name to encapsulate the idea. There is no requirement to
use a particular technology.

I'm afraid I don't know enough about the different technologies to
give a detailed answer here. Some of the concepts from git seem very
useful, however. For example, I was thinking that changes to the
genome assembly made by improvements in computational algorithms could
be separated from manual edits. Then when the computational algorithm
is improved, all manual edits could be rolled back, its edits reverted
and then reapplied, and then the manual edits merged back where
appropriate. It seems that git supports those kinds of usage pattern.

> PS#1. Dan since I've used my gmail ID, could you please unsub the
> other ID. Google groups does not allow me to unsub my non-gmail id's.

Done.

[Dan Bolser]

On Apr 11, 5:36 am, ॥ स्वक्ष ॥ <svak...@gmail.com> wrote:
> On Mon, Apr 11, 2011 at 03:02, ॥ स्वक्ष ॥ <svak...@gmail.com> wrote:

>
>
>
>
>
>
>
>
>
> > On Sun, Apr 10, 2011 at 17:30, Dan Bolser <dan.bol...@gmail.com> wrote:
> >> Matthew Levitt came up with an interesting proposal based on GMOD
> >> 'Idea #9' [1], namely, to host genome assemblies on a 'SourceForge-
> >> like' server, where they could be checked out, modified, checked in,
> >> branched, tagged, merged, etc.
>
> > IIRC git was the original choice, so I'm curious why DVCS systems like
> > git, mercurial or even bazaar are not under consideration. I do have a
> > bias as I've used them more than svn but besides that there are many
> > features which, say, 'git' offers that subversion does not.
>
> > PS#0. This isnt intended to be a svn vs. git/other DVCS flamebait,
> > rather I'd trying to understand what are the merits/demerits between
> > svn and other DVCS.
>
> > PS#1. Dan since I've used my gmail ID, could you please unsub the
> > other ID. Google groups does not allow me to unsub my non-gmail id's.
>
> Furthermore, I was thinking a bit about this and wanted to suggest
> that a BioForge on the lines of Berlios[0] would be very interesting.
> Unlike, say, github or bitbucket, it runs completely on free/libre
> software and supports many DVCS (mercurial, git, cvs and svn)[1].
>
> [0]http://en.wikipedia.org/wiki/BerliOS

> [1]http://en.wikipedia.org/wiki/Comparison_of_open_source_software_hosti...

>
> What do you all think? Maybe we should have this interesting
> discussion on the genome-informatics list too?

Sounds good!