Dear Mom,

Our local Toys’R’Us store contains an overwhelming range of baby paraphernalia. Most of this makes me rather stressed (why are there so many types of bottles?), but one item caught my eye: It is the Tots Bots nappy!

It comes in 5 exciting colours (apart from the traditional white – which they can keep in my opinion), it is shaped, and it has a handy (and hopefully idiot-proof) strip of material to put the nappy liner onto.

It is perhaps telling that I am more pleased by the fact that baby Hap could wear coloured nappies than I am about sparing the environment, but I am sure that I will get a warm glowy feeling about making effort to minimise the volume of dirty disposables cluttering the landfill sites.

If you would like to watch me putting nappies on a teddy bear you can click on these links to youtube:

Tots-Bots nappy

Muslin cloth

I had added these to the comedy rather than to the educational section, as there is no doubt some subtle/major point that I have overlooked.

If you would like to know more about cloth nappies, The Nappy Lady is a good source of information.

Yours etc.

Bronwen

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Today, I was directed to an on-line resource that I think is potentially very useful.

It is called DigitalExpert

This is a quote from their “about” page:

“This tool helps authors, publishers, societies, and our companies to develop and process files that meet minimum requirements to be printed in an effective and quality manner. The objective of the system is to examine digital files and identify those with problems…”

Here is a list of file types that it can look at:
File Formats

Here is an example of a report that I received:
Example report

I have tried it now with quite a few images, and think that it is good for finding potential weaknesses in an image and the website overall seems to be a useful source of information regarding “how to prepare images of sufficiently high resolution for publication”.

Of course this website cannot tell you if your figures are meaningful or aesthetically pleasing. :)

For those of you who have never seen me, or have not seen me in a very long time: I have all-of-a-sudden become very fat!

This is my favourite of the profiles. It was taken at 16 weeks. I had another scan today, but unfortunately Hap-the-contortionist had fallen asleep folded up into a bundle of arms and legs that could not all be brought into focus.

One popular theme for questions on our Nature Protocols Discussion Forum is apoptosis.

The latest question is from Lisa Venticinque and relates to measuring late stage apoptosis.

She is interested in studying the mechanism of cell death in response to viral infection. It seems like forever since I have written in my blog, but this idea does seem to have a (well admittedly tenuous) connection to my last post.

Do any of you have an answer to this or any of the other questions on our forum?

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At the Biological Complexity: From Molecules to Systems meeting, Perdita Stevens gave an excellent talk on work that she is doing towards modelling viral infection. The two viruses that she spoke about were influenza and the Semliki Forest Virus – the latter spends part of its life-cycle in mosquitos.

Simulating the intracellular behaviour of the virus is ever so complicated – the process is made up of many equations each requiring that you input numbers: How many viruses should enter the cell? What is the rate of binding of the viral nucleic acid to the relevant polymerase? What are the rates of all the steps towards making the capsid proteins and then assembling these around the nucleic acid? What is the cell doing about stopping the virus from doing all this?

In many cases, the numbers are not actually known and either experiments need to be done to get the “real numbers” or you need to take a guess and see what happens (whether the model behaves in a way similar to “reality”).

This problem, reminded me of a game that we used to play at university called WA-TOR. It looked like this:

and simulated the dynamics of shark and fish populations that had the specifications that you plugged in.

It has since evolved somewhat (as things do) and now looks like this:

(green = fish, red = sharks, blue = water)

Anyway, Prof. Stevens is using DIZZY (an open source tool developed by Stephen Ramsey) for the virus simulations. I don’t pretend to understand such things, but the quote below from the user manual seems to imply that it is useful to think of the system-to-simulate in terms of a series of “chemical equations”. This pleases me!

“Dizzy is a chemical kinetics simulation software package implemented in Java. It provides a model definition environment and various simulation engines for evolving a dynamical model from specified initial data. ... A model consists of a system of interacting chemical species, and the reactions through which they interact. The software can then be used to simulate the reaction kinetics of the system of interacting species.”

Other things from the talk that were pleasing (and that I want to find out more about) were:

• that there seems to be something different about cell death in mosquitos in comparison to mammals
• mosquitos seem to only have an “innate” immune system, and RNAi plays an important part in it
• the wild-type variant of the Semlicki Forest Virus is gone by day 16 after infection and is replaced by a small-plaque, attenuated variant.

Every two years, the Protein Structure Prediction Center organises a community-wide experiment (CASP) to compare the programs and methods for predicting protein structure. The eighth one is this year and the results will be discussed in a meeting in early December!

Some high flyers from the last experiment are:

I-TASSER
Rosetta
Protein Structure Prediction by Global Optimization

For a list of the results talks, click here.

I think that there should also be a special prize for the cutest acronym. My current vote in the protein modeling field is 3D-GARDEN – which is a system for modelling protein-protein complexes.

On Thursday and Friday last week I had the privelage of attending Biological Complexity: From Molecules to Systems. There were many very interesting talks from members of the Weizmann Institute as well as by researchers at UCL and other UK institutions.

The experience underlined the idea that there are people modelling just about everything; and over the next few blog posts I will give you some examples that I thought were elegant (or that pleased me for some other reason).

Today, though I would like draw your attention to the special online collection of articles at Science entitled Forests in Flux mentioned in the keynote talk given by Stephen Emmott from Microsoft Research, Cambridge.

There are also two videos of Drew Purves talking about modelling forest dynamics that you might find interesting.

Link to the Climate Feedback blog.

I have just had one of those stunned moments which I thought I would share with you.

On the 25th of June, Alain and I are planning to take the train from Plymouth back home to Woking, so I wanted to investigate how much this would cost. I went to The Trainline and plugged in the necessary details. This is what I got:

After trying in vain to find a time when the prices would be cheaper, I absent-mindedly typed Plymouth to London. And this is what I got:

London to Woking:

(from Paddinton to Waterloo will cost 3 pounds using our oyster cards)

Present

Memorable theme-tune
Snakes
Scorpions
Impaling implements
Army ants (hungry)
Miscellaneous cute wildlife
Savages with masks
Nuclear explosion
Knife fight
Sword fight
Fist fight
Gun fight
Love interest
Soviet army-types (with accents)
Magical bullets that cannot hit Indy
Car chase
Hat
Bow tie
Exotic maps
Pictograms
Escape from rising water
Mystical artefacts
Someone that dies because he is greedy
Flying saucer
Aliens

Things that should have been there, but weren’t:
spiders
someone actually getting impaled
cleaned up bones after army-ant attack

I am sure there are hordes of things that I have missed…

I know almost nothing about frogs really and am happy to admire them from a distance. My mom always had a very positive attitude towards them: “If you can hear frogs in the garden, there (probably) aren’t any snakes.” and of course this was very useful as South Africa has some rather nasty snakes and children Played Outside.

I have just push live a Network Protocol entitled A method for quantifying phonotaxis in the concave-eared torrent frog which gives details for a method used in the Nature paper Ultrasonic frogs show hyperacute phonotaxis to female courtship calls. And was very pleased by the ideas of “phonotaxis” and “ultrasonic frog”.

You might want to check out this figure from the Nature paper. I wonder what that frog is tying to do to the loudspeaker…