About the JBSM submission (thematic series)

[Andrea Splendiani]

Hi,

is it possible to have an extension for the JSBM submission whose deadline was May 7th ?
Artem (one of the co-authors) took the lead on the paper, but asked for... 5 weeks more.
Would this be ok ?

best,
Andrea

[Toshiaki Katayama]

Hi,

Well, I learnt from the journal editor that we are already able to submit to the series.
All we need is to indicate in the cover letter that the submission is for the BioHackathon thematic series.
When enough number of submissions are made, the series will be launched and published.

As far as I'm aware of, two other submissions are in preparation,
one is almost complete and the other will be finished by the end of May hopefully.

We still need to increase the number of submissions for quick and successful launch of the series,
so, Andrea, the answer to your inquiry is YES but please hurry up as much as possible! :)

Regards,
Toshiaki

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[Joachim Baran]

Hello,

First, let me share the photos that I have taken in Toyama last year: http://www.flickr.com/photos/25919479@N05/sets/72157632032676595/

Second:

On 2013-05-04, at 5:25 PM, Toshiaki Katayama <kt...@dbcls.jp> wrote:
> As far as I'm aware of, two other submissions are in preparation,
> one is almost complete and the other will be finished by the end of May hopefully.

We (Geraint, Jin-Dong, Kevin, Michel and me) are currently scrambling to get a short BioInterchange manuscript ready. I think we need until the end of the month to wrap up the writing though.

I have updated the BioInterchange web site and the documentation is almost complete now: http://www.biointerchange.org (minor glitch: GVF demo fails in the interactive web interface, rest of documentation will be copy/paste from the paper)

If you do not like to click through the web site, then you can get a quick glimpse of the documentation via the README in BioInterchange's repo: https://github.com/BioInterchange/BioInterchange

For GFF3/GVF RDFization, two ontologies have been developed: GFF3O and GVF1O (http://www.biointerchange.org/ontologies.html). Both of them support FALDO as one of two data description options. BioInterchange currently does not write out FALDO RDF yet, but I can hack that when I am on the plane to BH2013.

Third: opacmo's text mining pipeline also runs on Amazon's EC2 now. Well, that will not be that much interesting to most of you. It is just something I talked about last year and its done now.

Fourth: Amazon's Spot market and AWS outreach asked me to write a guest blog post for them and to generalize opacmo's pipeline. The guest post is currently being reviewed, but I have made the generalization of the pipeline available already: https://github.com/joejimbo/EC2Workflow That tool makes it much easier to run workflows/pipelines on EC2. Please have a look at the sequence diagram to see how the thing works. It may come in handy some day.

Joachim