Question: A Cvs-Ish System For Genome Annotation
7
gravatar for Jarretinha
8.8 years ago by
Jarretinha3.3k
São Paulo, Brazil
Jarretinha3.3k wrote:

Hi biostar people,

Kind of very busy these weeks. And I was wondering if there is some sort of concurrent versioning system for genome annotation. Most of my pals work from different timezones and places. Of course, it's always possible to use git or similar. But, explaning how such tool works (and why) to biologists can be rather cumbersome.

genome • 1.9k views
ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 8.8 years ago by Jarretinha3.3k

would something like Dropbox work? https://www.dropbox.com

ADD REPLYlink written 8.8 years ago by Istvan Albert ♦♦ 79k

Not really. It need to be concurrent for real, in the spirit of git. In such a way that we could test and commit versions of the annotated genome made with rather different pipelines.

ADD REPLYlink written 8.8 years ago by Jarretinha3.3k

I vaguely remember attending a seminar from an OBO/ChEBI curator who was explaining how do they were doing the annotation versioning. However, I can't find any link to this now... I am sorry, it was really a long time ago :-)

ADD REPLYlink written 8.8 years ago by Giovanni M Dall'Olio26k
6
gravatar for Neilfws
8.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

You'd think, wouldn't you, that version control and genome annotation go hand-in-hand. Yet a web search for those terms throws up very little.

One approach might be to use a wiki, e.g. the popular MediaWiki. Wikis feature version control, they often have plugins that allow extensive customisation and they have been used in other biological curation projects.

Some genome projects employ other tools for community annotation. A good example is the Paramecium project, which uses tools from GMOD. I'm unsure to what extent version control is employed.

The main web-based annotation software package that I know of is Manatee. It can store "old" annotations alongside "new", but I don't think it does true version control. It also requires quite a bit of administration to install (apache, mysql, multiple perl modules).

If you do want to go with just basic RCS, I think git could work. Subversion has a central repository, but anyone with rights could upload to it without notification. Using git, people could work in their own way then submit a pull request, which other members would approve before incorporation.

ADD COMMENTlink written 8.8 years ago by Neilfws48k

svn supports notifications via commit hooks (scripts can be set to run pre and post commit). Having a central repository can also be thought of as a benefit.

ADD REPLYlink written 8.8 years ago by Istvan Albert ♦♦ 79k

That's true - I don't recall svn so well since moving to git :-)

ADD REPLYlink written 8.8 years ago by Neilfws48k

One option might be 'gitit', which is MediaWiki-like in its interface, but which uses a VCS (git or darcs) underneath.

ADD REPLYlink written 7.9 years ago by Ketil3.9k
3
gravatar for Istvan Albert
8.8 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

I don't think there is simpler version control than what is already available.

I found that svn was easy to explain to nontechnical users, especially using it via TortoiseSVN. I would avoid distributed systems such as git or mercurial.

ADD COMMENTlink written 8.8 years ago by Istvan Albert ♦♦ 79k

It don't need to be simple. Biologists usually think of curation when doing version control. Curation can be rather cumbersome as well. In my imagination there is a system that is concurrent/distributed able to deal with tickets/milestones and community approval. Maybe just creating a "relational" layer on top of git to translate curation/annotation into versioning . . .

ADD REPLYlink written 8.8 years ago by Jarretinha3.3k

Why would you avoid a distributed system, since they are ideally suited to something like this? They might not be the right solution in this case, but would be better than SVN.

ADD REPLYlink written 8.8 years ago by Mndoci1.2k

centralized systems are easier to understand. And they would need a centralized main repository anyhow. I have learned to never underestimate complexity, one tool may be substantially more powerful than the other, but a tiny bit of extra complexity may make it far less usable - thus far less effective in the big picture.

ADD REPLYlink written 8.8 years ago by Istvan Albert ♦♦ 79k
3
gravatar for Sean Davis
8.8 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Questions like this often end up being answered with something like "You can use tool X". While that may be true, it is very important to define the use cases, work flows, and other requirements (web-based versus command-line, for example) before it is possible to evaluate answers. Spend some significant time planning and discussing some of these points with users/participants. Then, it will be clearer where to go next.

ADD COMMENTlink written 8.8 years ago by Sean Davis25k

In my mind I always imagine that people will come up with an application X and an example on how to use it. Of course, I consider that most participants here are computer science guys or similar. What I really want to know is if there is a git-like system for genomes and where I can find it.

ADD REPLYlink written 8.8 years ago by Jarretinha3.3k
2
gravatar for Science_Robot
8.8 years ago by
Science_Robot1.1k
Gainesville, FL
Science_Robot1.1k wrote:

I've seen git used.

http://github.com/michaelbarton/Pseudomonas-fluorescens-R124-genome

ADD COMMENTlink modified 5 months ago by RamRS20k • written 8.8 years ago by Science_Robot1.1k

Barton's repo isn't of much help. It's just like the ones I have locally. There's just me (him)! I would like to see a real repo with lots of people messing around, just to see how they thrive. . .

ADD REPLYlink written 8.8 years ago by Jarretinha3.3k
2
gravatar for Mndoci
8.8 years ago by
Mndoci1.2k
Issaquah, WA
Mndoci1.2k wrote:

While in principle a system similar to that used for Open Blogging should work, I am not sure that biologists can do this unless presented with simple templates on top of the platform. Personally, I'd use a wiki. Easier to use, understand and adopt (and that's hard enough). E. Coli Hub is a good example

ADD COMMENTlink written 8.8 years ago by Mndoci1.2k
2
gravatar for Hanif Khalak
8.8 years ago by
Hanif Khalak1.2k
Doha, QA
Hanif Khalak1.2k wrote:

Semantic MediaWiki is pretty straightforward to setup and seems like it has a lot of the features you're looking for.

I'd like to see an annotation interface like Google Wave with an integrated Google Maps style (i.e. non-Flash JavaScript) genome browser. Google Wave does versioning using XML-based operational tranformations.

ADD COMMENTlink written 8.8 years ago by Hanif Khalak1.2k
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