nodalpoint.org - Source Code for Biology and Medicine - Comments

I would like mandatory source or proof of concept samples

lbbros — Mon, 30 Oct 2006 10:59:34 -0500

I like the concept behind this new journal. I think it's a sad state of affairs that a lot of algorithms and methods are published without source code, and some even without public implementations (search PubMed for CARAT and take a read on the relevant paper, you'll see). When one submits a paper detailing a new algorithm, I think it should be mandatory to have at least a proof of concept to enable everyone to reproduce its results. IMO sending snippets to referees only to have a paper published is counter productive.
This may also help the community in fixing bugs and introducing new features, as well.

No connection to a code repository

PedroBeltrao — Thu, 26 Oct 2006 05:52:17 -0400

(I am sure I did not notice the first issue:)

If the focus is on the code then it would make sense to put more emphasis on it somehow. It would have been nice if they had some connection with a code repository. Institutional pages are always changing and it would be nice to see a more standardized access to the code coming out of the journal, better access to the code from the journal's web page, etc.

only kidding :)

Neil — Wed, 25 Oct 2006 21:59:19 -0400

True, the original announcement was just that the journal was established, it now has some papers. I think it was covered on Pedro's blog too - all Blogger blogs are giving me a 500 server error as I write.

Yeah, you slept through that

Greg — Wed, 25 Oct 2006 03:19:41 -0400

Yeah, you slept through that one :)

Doh!

I could have sworn I saw that on Pedro's blog and not on nodalpoint. In my defense I posted this because papers had actually been published on the site, when I checked the original announcement they were only accepting papers.

source code in journals

Neil — Tue, 24 Oct 2006 22:57:18 -0400

While I wasn't watching...

Yeah, you slept through that one :)

I'm undecided as to the merits of a journal for code, but I suppose it's an opportunity when you're really desperate for a publication.

Source Code for Biology and Medicine

Greg — Tue, 24 Oct 2006 19:52:57 -0400

While I wasn't watching Source Code for Biology and Medicine, a new journal from Biomed Central, was released. The first volume is a little light, but I'm sure once everyone has tidied all those uncommented Perl modules we'll see submissions increase.

The cynic in me thinks that journals like this will allow authors to spin three papers per project, one for the the biology, one for the algorithm and one for the module that implements it. If anything it will hopefully decrease the number of parser papers published in regular journals.