Mailund on the Internet

Years back, when I was studying computer science, I took a course on virtual machine design by Lars Bak.  At the time he had just returned to Denmark but was still working at SUN and he managed to get a VP from SUN to give one of his lectures for him (I forget who it was, as I said it was many years ago).

That particular lecture wasn’t about building object oriented virtual machines but about building successful software companies.  (No snide remarks about someone from SUN talking about that, please).

This was during the .com bubble or just while it was bursting, and the advice he gave was: “when everyone is digging for gold, you get rich by selling shovels”.

If you build the basic infrastructure that everyone needs, it might not be as glamorous and if you are selling commodity products you won’t get rich over night, but if you are selling something that everyone needs, you won’t loose your market over night.

Personal genomics and medicine shovels, anyone?

I’m telling this story because I just read this post at Genetics Future. It concerns genetic testing and how it will soon change with complete re-sequencing which will be cost-effective Real Soon Now(tm).

The post ends:

There are ruthless economies of scale in the human disease genomics business, both in terms of sequencing infrastructure and the costs of assembling reliable knowledge bases for interpretation, so it will be increasingly difficult for smaller companies to stay competitive.

The personal genomics and genetic testing field is another gold rush (although one where small garage companies aren’t quite in on the game yet).  Right now there’s plenty of testing labs, but with resequencing we’ll probably only get a few large companies, at least until the price for resequencing drops significantly.

I don’t want to compete here.  I’m sure I’ll lose.  I would absolutely love to be selling shovels to the gold diggers!

What will all these companies need?

Of course they will need IT infrastructure to manage their data and statistical methods to correlated genotypes with phenotypes.

The question is, of course, whether it will be possible to sell bioinformatics to such companies, or whether they will want to build all their informatics in house.  Some, they want to, of course, as that will give them a competitive advantage, but surely there will be some commodity software they will want to buy somewhere else.

They won’t build their own OS or database system, but probably their own specialised statistical models. Somewhere in between, there is money to be made, if I can only figure out how…

Cool talks related to medicine…

I’ve just made a release of our association mapping tool, Blossoc.  The new release, nicknamed QBlossoc, adds full support for quantitative phenotypes.  We’ve had support for quantitative phenotypes for a while now, but this version is the “official” release for it, with tuned default options and such.

It is mainly the work of Søren Besenbacher, who’s been running simulation experiments for the last several months to figure out which scoring methods, and with which parameters, works best.

Although the quantitative traits method hasn’t been published yet — we only submitted the paper last week — it has already been used by Monica Ledur et al. to analyse the data set from the XII QTLMAS workshop in Uppsala.  There should be a paper coming out on that as well.  I don’t know its status, but Monica was kind enough to send the manuscript to me.

I just noticed that I’ve passed 10,000 hits since I restarted my blog!  10,429 right now, to be precise.  Cool.

Following up on the last post, and an older one, I’m going to rant a little bit about the reviews I’ve gotten on two papers recently.

I’m not complaining about the reviews I’ve gotten for the Bioinformatics paper I mentioned in the previous post.  Those are detailed, thoughtful, relevant and all reasonable.  There my only problem is that I have a page limit that keeps me from adressing all the comments.

What I am a bit miffed about is two papers submitted to BMC Bioinformatics.  Do not take it as a critisism of that journal, though, I have also gotten nice reviews there.  I have another paper submitted there, that is getting nice reviews (in the sense that there are lots of suggestions to consider, not that they are just positive). Not so for the last two papers.

First of all, the review reports are very short.  Maybe 15-20 sentences.  Secondly, there aren’t really any constructive criticism. Not surprising with less than 20 sentences, of course. Thirdly, and this is the most annoying, they haven’t made any decision!

The “positive” reviews are just summaries of the paper (essentially paraphrasing the abstract).  The “negative” reviews are saying things like: “I do not really like this / I do not find it interesting” or “other people are doing something similar”.

Of course reviewers are permitted to not like a paper and to not find it interesting.  They shouldn’t make their decision on this, but on whether the results are novel and sound.  If they think that the results are too small an increment on existing work — and there will always be similar work out there, if I submit it to BMC; it it was truly novel I would go for higher impact — in that case they should say so, justify it, and reject the paper!

Telling me that they do not find the results interesting, and then telling me to resubmit is just crazy! How can I make any improvements if that is all the criticism I get?

If I resubmit, the paper will end up with the same reviewers, and they still won’t like it.

The form letter from the editor just asks us to resubmit and include a cover letter “addressing the reviewer concerns”.  That is of no help at all!  “To make the paper more interesting, we have included a Dilbert strip and a picture of a clown.”  Is that going to work?  I doubt it.

This is really pissing me off.

If, as a reviewer, you do not have any constructive criticism — good or bad — just make your decision and let us get on with our lives.  If the paper is rejected, it would probably also be rejected after a resubmission, but now I know that so I can decide on whether to abandon the paper or try somewhere else.

It is not just the reviewers that are the problem here, though.  In a situation like this, I think the editor has a lot of the responsibility.  The final decision is his, so he should get involved at some point.  By now, he should a good idea about whether the papers will get accepted or rejected.  After all, there are no additional experiments or improvements suggested, so the content of the papers are not going to change.

As a side note, BMC isn’t that bad in this regard.  We once had a paper at European J of Hum Gen in review for more than a year, where each iteration consisted of very minor changes but the form letter kept telling us that no decision was made yet.

We all want our papers as good as we can get them, so if you have made your decision then let us know!  If it gets rejected, we wont waste any more time on it, and if it gets accepted we will still address reasonable comments to improve the final version.

You are no more “unable to make a decision” at this point than you will be after a resubmission, if the reviews do not ask for any actual additional work!

Grrr!