Learning Python

I'm going to try and get my arse in gear and learn Python, it will be a useful glue for anything I want to get done, bioinformatics, data analyses, Django (for web development) and much more. An initial thought is to write a Twitter bot, so I'm making a note of this here.

2017/05/09 13:38 · neil

Transparent Backgrounds

Needed to make the background of an image transparent in GIMP, found this, it worked.

2017/03/28 22:43 · neil

Something to Read

A Sci-Fi story with some climbing in Taklamakan by Bruce Sterling

2016/09/21 21:00 · neil

New Troos

Possible place for new trousers

2016/05/20 11:00 · neil


emerge -av letsencrypt

Configure lighttpd

Based on instructions here

mkdir -p /tmp/letsencrypt/public_html/.well_known

Modify /etc/lighttpd/lighttpd.conf to include the following…

## Used for letsencrypt validation
$HTTP["url"] =~ "^/.well-known/" {
    server.document-root = "/tmp/letsencrypt/public_html/.well-known/"
    alias.url = ( "/.well-known/" => "/tmp/letsencrypt/public_html/.well-known/" )
    dir-listing.activate = "disable"

Restart your server…

/etc/init.d/lighttpd restart

Obtain Certificate

Look for your basedir in /etc/lighttpd/lighttpd.conf

grep base /etc/lighttpd/lighttpd.conf

Use your domain name, and the basedir the above returns…

letsencrypt certonly --webroot -w /var/www/localhost -d kimura.no-ip.info

As advised backup the created /etc/letsencrypt/ directory to somewhere secure.


2016/04/16 13:15 · neil

Reproducible Research

I came across Hartgerink CH, van Aert RC, Nuijten MB, Wicherts JM, van Assen MA. (2016) Distributions of p-values smaller than .05 in Psychology: What is going on? PeerJ PrePrints 4:e1642v2 (https://doi.org/10.7287/peerj.preprints.1642v2) and aside from the subject matter thought it was a really nice way of transparently sharing the code that underpinned the work of the paper.

The code and the data are both available for others to view and build upon. I think it would have been nice if they'd turned their R code into a package, the process of which is massively simplified by Hadley Wickhams devtools and his excellent Packages book.

2016/01/16 22:43 · neil


Secure File Transfer Protocol (sFTP) is a method of transferring files between computers. It utilises SSH to ensure that passwords are sent encrypted rather than as plain text when FTP is used which is insecure as the password could be intercepted en-route compromising the security of the remote server.

Getting an Account

First step is to have an account on the remote system setup for you by the administrator. They will email you your username and password. Both will be case-sensitive so be careful when you are typing them.


If you are using GNU/Linux then there are command line tools such as sftp that are part of OpenSSH or you can find graphical interfaces such as gFTP (or the Qt based equivalent). Consult your distributions package management system, on Gentoo use eix ftp to see what programs are available then emerge your choice.


If you are using M$-Windows then a good client is WinSCP, download, scan for viruses and install it.

Establishing a Connection

The WinSCP documentation should guide you through setting up your connection. You'll need to know either the IP Address or the server name to which you want to connect (in addition to your account details). By default the port used is 22 but its possible the system administrator may have changed this, if so they will tell you what port to use.

Transferring Files

Once you've established a connection WinSCP will show you two panes/windows similar to the usual File Explorer. One of these is the remote system to which you have connected, the other is the local system on the computer you are using. Its then as simple as navigating around and dragging and dropping files from one system to another (or you can right-click on directories on the remote system and select to Download).

2015/12/10 07:35 · neil


A few useful sites when shopping around for Books, CDs and DVDs in the UK are…

2015/12/07 10:45 · neil

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