Tools and tips for reproducible science from Rich FitzJohn

Rich FitzJohn, a computational biologist and director of puppets, made a very nice slideshow of how to produce reproducible science using a few tools revolving around R. It’s a great read!

You can download the slideshow here, but the gist is in this slide I think (which I have stolen from the slideshow, hope it is okay):

Tools for greating reproducible research with R

Tools for greating reproducible research with R

He uses an example from one of his own studies on wood which is very instructive – the makedown, knitr generated analysis page really shows how transparent and reproducible science can be.


1. Slideshow “Reproducible research – current challenges and future prospects” by Rich FitzJohn

Scientific calculator on the desktop

Emulation of the good ol' TI-83 on a mac

Emulation of the good ol' TI-83 on a mac

I love my old TI-83 calculator but it is getting increasingly… well weird. So I was pretty excited to learn that it is possible to setup an emulator of my good old companion on the desktop instead, using a software called Wabbitemu.

Here’s what you do:
1. Download Wabbitemu for mac
2. Download a rom-image from your calculator. There is a good guide here on how to do it. Unfortunately you need a pc. Alternatively, you can try and google them – but I am not certain these are legal.
3. Open the rom-image from Wabbitemu.

As it turns out, there are a number of other emulators for other platforms listed here.

Near-haploid and haploid cell lines

Haploid vs dipoloid

Haploid vs dipoloid

Haploid mammalian cell lines are useful for forward genetics experiments, the idea being that new phenotypes (ie induced by mutations or knock-out) would be exposed immediately.

I haven’t been able to find good lists of such cell lines, so instead I have compiled a non-exhaustive list here. Very few are available, even though haploid cancers are known to arise in humans and some authors mention that many cell lines become hypodiploid or even near-haploid as they are passaged. If anybody knows of more, I would be happy to know.

Name Cancer Non-haploid chromosomes Reference
KBM-7 Chronic myeloid leukemia 8, 15*, Y* Kotecki et al, 1999
HAP1 Derived from KBM-7, but fibroblast-like Carette et al, 2011
NALM-16 Acute lymphoblastic leukemia ? Kohno et al, 1980
MMLAL Myeloma 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 18, 19, 20, 21, 22, X Wong et al, 2013

* Varying descriptions as to whether these chromosomes are diploid or not.

1. Haploid vs diplod image from Wikimedia user Ehamberg.
2. Haploid genomes illustrate epigenetic constraints and gene dosage effects in mammals, Epigenetics & Chromatin 2013, Leeb and Wutz.

Old-school cool flow

Check out this old-school image from a flow cytometry experiment:

Neat old-school flow cytometry image

Neat old-school flow cytometry image

It’s from an 1991 article, back when it must have payed off being handy with glue and scissors.

Citat om døden

Torch Race with Prize Hydria; Three Youths, c. 430 BC-420 BC

Torch Race with Prize Hydria; Three Youths, c. 430 BC-420 BC.

Citat fra Michel de Montaigne:

“Go out of this world as you entered it. The same passage that you made from death to life, without feeling or fright, make it again from life to death. Your death is part of the order of the universe; it is part of the life of the world.

Our lives we borrow from each other… and men, like runners, pass along the torch of life.”

Citat fra “The Swerve” af Stephen Greenblatt.
Billede af vase fra Harvard Art Museum.

© 2014 Mike Barnkob

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