Mailund on the Internet

This is a typical situation for me: I submit a paper to a journal or conference that is just to  under the page limit.  I get review reports back, and each reviewer has a few reasonable suggestions to additional experiments or possible extensions or papers worth referencing.  I want to do the extra work — it is reasonable and I will learn something from it — but there just isn’t room in the paper to write about it!

Right now, I’m editing a paper for Bioinformatics, where the page limit is seven pages.  I’ve done all the work suggested by the reviewers but I’m practically putting it all in the cover letter instead of the paper.  The cover letter is now as long as the paper itself.

What do you do in a situation like this?

The reviewers’ decision is based on the submitted paper, so there is a limit to how much I can remove.  I cannot completely rewrite the paper, since the journal want me to mark up all changes (and I doubt that they will be happy with markups showing that I’ve changed everything).  So with the submitted manuscript being seven pages, I can only make very minor changes to the paper, and I still need to find a way to address all reviewer comments.

It is an impossible task!

I guess I should always leave a page or so for the second submission, but usually I find it hard to get down to the page limit in the first place…

My friends at CLC Bio has just released their Genomics Workbench.  When I talked to them last Friday, I couldn’t quite figure out what the marked for this software is, but Next Generation Sequencing is a hot topic right now, so there probably is one.

Anyway, I wish them luck with it!

Wednesday this week I’m giving a talk at the Danish Society for Computer Science. I was asked to give the keynote talk at this years general assembly before they hand out this year’s Best Thesis Award.

I’m tired of talking about my main project — association mapping — so I decided to give a talk on our CoalHMM work (although I am only working on that a small percentage of my time).

The slides file is too big to upload to slideshare, but if my flash hack works you should see them below:

You can also get it as a PDF file, a PowerPoint file or a Keynote file, if you want.

The last couple of presentations I’ve made I have been using the Keynote program on my Mac. I’m really happy with the program. It makes it very easy to put together pretty presentations (if I say so myself) with very little work. Especially its handling of graphics impresses me. Compared to using OpenOffice, as I usually did before getting the Mac, there’s essentially no work involved in including graphics. Automatic masking and alpha channels beats modifying images in Gimp any day!

I couldn’t really figure out how to put presentations on my homepage, though. Keynote files are really directories, so you cannot just copy them to the homepage directory. I found out, though, that if a Mac downloads a zip’ed Keynote file it will just open it in Keynote, so I guess that is the way to do that.

Reading through a page at Nature about metagenomics (probably requires subscription…) I saw this sentence:

“The biggest metagenomic project on Earth might be our Neanderthal genome project,” says Egholm. They are using 454 to sequence the complete genome of a Neanderthal, which Egholm says they hope to release by the end of the year. But 95–98% of the DNA in the Neanderthal sample comes from the environment rather than from a Neanderthal. This means that to get the 1 coverage, or roughly 3 billion base pairs, of the genome, the team must sequence somewhere between 70 billion to 100 billion base pairs of these environmental samples.

Sequencing the Neanderthal must be quite some challenge! Of course, contamination by bacteria should be fairly easy to discover and get rid of compared to contamination by the humans doing the sequences. We are just too closely related to the Neanderthal for that to be a simple task.

Of course, the Neanderthal specimens are handled carefully, but some contamination is unavoidable.  How much of a problem it is, I do not know, though.  I tried googling for it, but didn’t really find any consistent answers.

I look forward to getting my hands on the Neanderthal sequence, though.  I would love running it through our CoalHMM analysis!

With the music festival season coming up, I just have to share today’s Wulffmorgenthaler:

In case you are not familiar with this comic strip, I suggest you go read a few strips. Crazy humour at its best!

It’s a pair of Danish  comedians, Mikael Wulf and Anders Morgenthaler. Well, Mikael Wulf is a comedian, I guess Anders Morgenthaler is more all-round artist.  They had a few shows on Danish television.  The first was great, but after that the quality dropped.

Their comic strips are still very funny, though.