6,626 reputation
13162
bio website blahah.net
location Cambridge, UK
age 28
visits member for 2 years, 7 months
seen Sep 10 at 13:08

PhD student in Plant Sciences at Cambridge working on dissecting the molecular basis of C4 photosynthesis. Formerly plant biologist, data analyst, bioinformatician and programmer at the Millennium Seed Bank.

My expertise is in plant biology, genomics, transcriptomics and computational biology.

I write software in Objective-C, C++, Ruby, Python, Javascript and R.

Solvers.io is my attempt to help highly skilled developers use their skills to benefit the world's poorest, or to help solve crucial scientific problems.


Oct
13
comment What does “delineate” mean in this context?
Didn't think of that!
Oct
13
awarded  Citizen Patrol
Oct
13
answered What does “delineate” mean in this context?
Oct
13
comment What does “cellular” mean in this context?
Diatoms are generally porous, so perhaps that's why they thought it might mean that. But I've never known 'cellular' to mean porous.
Sep
21
awarded  Custodian
Sep
20
comment Transcript(omics) terminology: cDNAs, ESTs, RNA-seq, etc
I think RNA-Seq assembly prior to alignment is common in non-model species, where you need to first describe the features you align the reads to.
Sep
20
comment Does culling badgers restrict the spread of bovine tuberculosis?
Much better :) +1 For an even better answer you could summarise the main points?
Sep
20
comment Does culling badgers restrict the spread of bovine tuberculosis?
This doesn't answer the question...
Sep
10
comment How exactly are game theoretical evolutionary models described during implementation for computer simulations?
Probably both. Berkeley Madonna is specifically for modelling, but it's horrible, so it's not that widely used.
Sep
10
comment How exactly are game theoretical evolutionary models described during implementation for computer simulations?
It's not the chance of both eggs being excluded that Dawkins talks about, he talks about the chance of having an egg excluded. It's still true that it would be worth cheating for the first few birds. The wider point about the trait not being an ESS might be true, but his specific explanation is not. In your specific example, if there are 105 eggs and 5 are excluded, each egg has a ~5% (more precisely, 4.76%), not ~1%, chance of being excluded. In any case, your question was interesting so I'm writing a model of the Guillemot situation. I'll report back when done :)
Sep
10
comment Difference between genetic engineering and synthetic biology
PCR is not synthetic; although it involves biological synthesis, it has to start from a template. Synthesis as in synthetic biology involves artificial gene synthesis, i.e. starting just with a sequence on a computer and ending with biological sequence.
Sep
10
comment Difference between genetic engineering and synthetic biology
The parts registry, and BioBricks are key examples of synthetic biology. And Randy's is the correct answer, except that there's no reason to exclude sequences found in nature, as long as they are ab-initio synthesised. The clue is in the name... synthetic biology involves synthesised, not cloned, biological sequences. Synthetic biology is still a subset of genetic engineering.
Sep
10
comment How exactly are game theoretical evolutionary models described during implementation for computer simulations?
This. I would say most people use the language they know best, so for non-programmer scientists that's python or perl, for mathematicians it's matlab, mathematica, or berkeley madonna, and for programmers it's c or some descendant.
Sep
10
comment How exactly are game theoretical evolutionary models described during implementation for computer simulations?
Let's hope R doesn't become standard for anything other than stats - it's the ugliest programming language since J.
Sep
10
comment How exactly are game theoretical evolutionary models described during implementation for computer simulations?
Unfortunately the guillemot example is a bad one - Dawkins was wrong about it (and very obviously so). He forgets to account for the fact that if a bird lays twice as many eggs as any other in the colony, his eggs are twice as likely to be excluded from care.
Sep
3
comment Has anyone tried Gibson Assembly Optimizations?
I've just joined the Gibthon team, so if you need any more specific help let me know.
Aug
30
reviewed Approve suggested edit on Evolutionarily speaking, why do humans have 46 chromosomes
Aug
29
comment Does age affect the frequency of flatus?
Agree this is really a comment.
Aug
28
awarded  Good Answer
Aug
26
comment How does a plant decide when to grow a branch?
I answered this in some detail in response to another question... biology.stackexchange.com/a/2646/430