drj11

Amazon Lightsail: Amazon are going after the low-end server market with a consolidated product. Primarily targetted at users of other VPS hosting services like Dreamcloud. Not useful for us yet. We'll keep an eye out.

AWS Research Cloud Program: Useful. Am signing up. There's a bundle of goodies, but in particular free network traffic for downloads to JISC (so all UK universities), and invoiced billing instead of credit card.

Refinery Groups: Anyone can create a group, they are the owner and can then add members to that group.

drj11

from hypothesis import given
from hypothesis.strategies import floats

@given(floats())
def test_divide(p, q):
    if q == 0: return
    assert p / q == p * (1 / q)

if __name__ == '__main__':
    test_divide()

drj11

a-acute: guaraná

a-dots: jäger, hälleflinta, ländler, schwärmerei

a-grave: déjà vu (phrase, alas)

a-hat: pâté, râle

a-ring: Ångström, ås

drj11

Why Doesn't my webserver work?

What ports are being listened on?

netstat --listen --inet # warning IPv4 only

netstat --numeric --listen --tcp

netstat -peanut

drj11

conda iceberg rapid

module load apps/python/conda conda create --name aws . activate aws

to install awscli I had to

conda install -c bioconda awscli

drj11

A short experiment on copying big files

File size is 1412908312

According to https://www.kernel.org/doc/Documentation/sysctl/vm.txt

/bin/echo 3 | sudo tee /proc/sys/vm/drop_caches

is used to remove file data and metadata from (kernel) RAM. We'll use it so we can get timings for copying a file cold,

drj11

bcbio for Dummies

(like me)

download template. This creates a directory (in the example below, the directory is my_dummy_dir), in which you will find a .yaml file.

bcbio_nextgen.py -w template illumina-rnaseq my_dummy_dir

(where is this documented?)

drj11

Dear Teen Vogue, attention Hanna Howard,

I think you should get more into coding.

Following, is an elaboration of that.

I am one of your readers (Twitter and Web). I doubt that I am a typical reader: I am a grumpy middle aged man who works as a programmer in a science lab in a university in the North of England.

drj11

From a conversation with roryk about gemini and extasy on 2017-02-28

gemini does 2 things: 1) gather data from a bunch of sources to make a VCF file; and, 2) let's you query over that VCF.

The two things are separable.

So if we have a bunch of annotations, then if they are in a VCF file we can add them to Gemini's VCF using cvf2anno (which is scriptable in lua, yay!).

drj11

My CV is available online at https://github.com/drj11/cv

Open Source has created an incredibly valuable ecosystem. So far, this ecosystem is software tools for professional programmers. I'm keen to see Open Source create value in the scientific community.

Life sciences are being revolutionised by a tsunami of data, personal omics being just one example. Using this data to deliver valuable services to society (without being crushed under the tsunami!) will involve computation and computing skills.