This post originated from an RSS feed registered with Python Buzz by Titus Brown. Original Post: 18 Nov 2004 Feed Title: Advogato diary for titus Feed URL: http://advogato.org/person/titus/rss.xml Feed Description: Advogato diary for titus Latest Python Buzz Posts Latest Python Buzz Posts by Titus Brown Latest Posts From Advogato diary for titus

Academic publishing may not quite be ready for Open Source just yet...

When last we met our fearless hero, I'd talked about submitting an article on my software to BioTechniques. We got word back on Tuesday: editorial rejection prior to review. The reason? Lack of originality, because, to quote:

"As noted by the authors, the programs described in this manuscript are available online and already in wide use."

Silly me: I thought that having shown that the programs worked for a wide variety of biological systems was a good thing!

It seems that the logic-challenged people at BioTechniques only want unproven software published. If I convolute my own logic processor, I can understand this, sort of: why would anyone read an article about software that they're already using? Of course, the assumption going into that is that the sole purpose of publishing is to introduce people to completely novel results, not just something that most people won't have seen. It's certainly not like FRII is so widely used that Joe Developmental Biologist will have already seen it.

O well. On the advice of a friend more seasoned than I, I am re-submitting to BMC Bioinformatics, where I am told that functioning software is welcomed.

I do have to say that this little interaction has not raised my opinion of BioTechniques. The editors didn't bother sending it out for peer review, they simply slotted it into their narrow preconceptions of How Software Is Done and cut off the bits that didn't fit. At least I don't have to be upset with my peers; I can just call the BT editors "clueless" and move on!

There appear to be very few places to actually publish software. This is surprising, given how much biology is starting to depend on it in this new era of too much sequence. The standard technique is to do some moderately interesting bit of science using the software & then drop it into a moderately good journal like Genome Research. That's great -- if the software you're writing has some immediate scientific value that can be ascertained without experiments. If you need to do experiments, you're talking about a 6-12 mo wait before you can finish the experiments & then publish the software. Not exactly timely.

It's more troublesome that you can't expose your software to the Real World and publish it as novel once other people know about it. Next time I write a standalone piece of software I'll have to remember not to tell anyone else before publishing it...

Thursday morning miscellany

Johnny Bartlett, a fine member of this august site, asked me to pimp his book, although he acknowledges it's not a must-read for software architecture. The book is "Programming from the Ground Up"; not having read it, I am willing to pimp it not only by request but because Joel Spolsky recommends it. Go buy it.

A sinaesthetic friend sent me this fascinating article on tetrachromatic women. I think it's a very interesting philosophical exercise to contemplate what such people see & realize that we will never know. The article makes a big point of the adaptability of the human brain; I'm not that surprised, because it seems like the brain adapts to place people in their own political realities easily enough... ;) I guess that physical adaption on the level of new nerve pathways is moderately surprising, although not new: see this article, & search for "inverted".

Normally I hate reposting links without commentary, 'cause meme tracking has shown that everyone does it, so why should I waste my time? But sometimes you run across something so hilarious that you've just gotta share: sometimes you need a bigger tow truck than you originally thought. There was also a great story about crashing doorbells, but I won't repost that.

Support our troops (if you're from the US)

Last but not least, check out AnySoldier.com. Whether or not you believe in the war (I do think getting rid of Saddam was a good idea) or support our leader (are you kidding?), we should remember that the troops who are over there are generally good people who are in an uncertain combat environment fighting for their lives. It behooves us to support them, whatever you think of the people who sent them there.

A friend who is also a military nut said this about what units to contribute to:

On one hand, I'd suggest reserve/nat'l guard units - they being in a more protracted and stressful situation than they expected. On the other hand, reservists are more likely to have a better support structure from their families (more likely married). Active duty Army GIs and Marines are more likely to be single, 18-21 year olds. Obviously both have families, but, you know, direct support from a spouse and children in addition to the rest of the family is what I'm getting at.

So, send books & chocolate, and support 'em.

--titus

This diary entry dedicated to my synaesthetic friend Tamara.