slack

aiptek_usb_tablet

Sun, 07 Dec 0000 21:29:49 +0000

I picked up one of these free thanks to RogerB who was getting rid of his. The challenge then was to get it working under Gentoo GNU/Linux. To be fair I didn't do anything for a good year or so, until I decided to have a clear out of crap. I was going to get rid of this having never used it but thought I'd check out first whether I can actually get it working. Turns out I can, and here's how.

blog

Mon, 29 Jun 0000 21:37:42 +0000

climbing

Mon, 29 Jun 0000 21:37:42 +0000

Climbing is a great way to relax. This may seem counter-intuitive as many would consider putting yourself in a dangerous situation to be quite stressful, but its not, it forces you to focus on only your immediate surroundings and actions, and in doing so you put everything else in your life to one side and forget about anything that might have been worrying you.

fugue

Mon, 29 Jun 0000 21:37:42 +0000

Fugue is a program from the Abecassis Lab at the Center for Statistical Genetics, University of Michigan. Its used to reconstruct haplotypes from high density human genetic data derived from platforms such as Affymetrix SNPchip or Illumina Bead Array, and is capable of handling population based data (i.e. unrelated individuals) or family based data (i.e. related individuals) and as such was used to derive the haplotype maps of human chromosomes 19 and 22

genetics

Mon, 29 Jun 0000 21:37:42 +0000

Since reading wp>The Selfish Gene when I was about 16 I developed a strong interest in Genetics. This led to me stuyding BSc Zoology & Genetics at The University of Sheffield (sadly they no longer run this excellent complementary dual-honors course) and then for an MSc Genetic Epidemiology, again in Sheffield (I was one of four students who took the course in its first year of running).

gentoo

Mon, 06 Apr 0000 19:46:26 +0000

Gentoo is a GNU/Linux distribution that is highly configurable. Detailed here are ebuilds for some software that I have written in the past. System Maintenance * NFS Portage : If you've multiple computers running Gentoo lighten the load on the rsync servers by only syncing one and sharing portage. * NFS Layman : Using Gentoo overlays on a networked server that isn't running Gentoo. * Local Overlays : Setting up and maintaining your own local overlay. * Updating daily : simple step-b…

gentoo_on_dell_lattitude_x300

Sun, 17 May 0000 14:41:18 +0000

This laptop is in my opinion brilliant, its as thin as, and preceded the fancy apples but a fraction of the cost, has all the ports and harware that you need on the go and looks damn funky. Obviously I had to install my favourite distribution on it, so this page documents various aspects of running Gentoo on the laptop.

gentoo_on_playstation_3

Mon, 03 Aug 0000 08:53:35 +0000

I'd been wanting to build a home media center for a while, and a month or so ago Paula and I were in town wandering through Zavvi looking for some bargain CD's and DVDs when I noticed they were selling off their PS3 stock at £250 which seemed like a fairly good deal, and after a quick bit of searching it appeared it would probably fit well as the media center....after a Gentoo install of course!

howto_create_diptych_s

Mon, 20 Oct 0000 12:37:33 +0000

Taking pictures of climbing I've started combining a series of pictures into diptrychs or triptych to show a sequence of moves on a climb or the subtely invovled in using the holds. These were created using The GIMP and the following HowTo describes the process.

hyperwrt_thibor15c

Sun, 04 Jan 0000 12:06:28 +0000

This is a very neat firmware for extending your NSLU2. Unfortunately development seemes to have ended some time around October 2007, fortunately the WayBack Machine has archives of the site. Links * Thibor (last mirror of the site from October 2007). * HyperWRT/Thibor Firmware Archive * Linksysinfo.org knowledgeable forums.

installing_dokuwiki

Mon, 29 Jun 0000 21:37:42 +0000

You must first have unslung your NSLU2 to SlugOS-4.8 BE on an external drive and added the Optware packages which provide a large number of additional packages for installation, in this case DokuWiki. Install DokuWiki and Dependencies Unfortunately the package for DokuWiki under SlugOS-4.8 BE doesn't pull in all of the necessary required dependencies so some have to be installed manually. Further no web-server pulled is pulled in as a dependency as there are a number of choices. As the NSLU2…

installing_transmission

Mon, 29 Jun 0000 21:37:42 +0000

Requirements Before proceeding ensure that you have * Unslung your NSLU2 with SlugOS-4.8 BE * Installed Optware an additional package repository for SlugOS-4.8 BE If you have not done so then these instructions may work, but there are no guarantees.

keysonic_540bt_mini_wireless_keyobard

Sat, 11 Apr 0000 12:58:59 +0000

Picked up one of these to go with the Playstation 3 and it after pairing it works straight off. Next challenge was to get it working with Linux so that I could use it after I installed Gentoo to the PS3. Kernel I enabled the following options for Bluetooth in the kernel (tuxonice-2.6.28)

latex

Tue, 17 Mar 0000 12:28:04 +0000

LaTeX is a type-setting software suite that allows you to produce exceptionally elegant documents, letters, posters and presentations. The beauty of LaTeX is that is separates the content from the style, freeing you from the hassle of formatting the content as you go.

linksys

Sun, 08 Feb 0000 17:26:50 +0000

No, I'm not a criminal, here the term wp>hacker (computing) is used in the context of a home computing enthusiast. I first picked up a wp>WRT54G (Version 2) a number of years ago and being a keen Linux enthusiast quickly started upgrading the firmware to one of the derivatives that had been developed after Linksys released their source code (which they hadn't initially done, but were obliged to release it under the terms of the GNU GPL.

maintaining_your_world_file

Mon, 29 Jun 0000 21:37:42 +0000

Gentoo's portage package management system uses a simple text file located at /var/lib/portage/world to record packages that are explicitly emerged. Over time this can become cluttered with dependencies that have failed and have required explicit emergeing.

mediatomb_upnp

Wed, 11 Feb 0000 17:24:39 +0000

Mediatomb is an open source uPnP Media Server that makes your images, music and movies on your NSLU2 available to uPnP clients such as the PlayStation 3. Installation Installation is simple as a Mediatomb is maintained in the Optware package repository.

merlin

Sun, 05 Oct 0000 20:15:33 +0000

Merlin is a program from the Abecassis Lab at the Center for Statistical Genetics, University of Michigan. Its used for parametric and non-parametric linkage analysis in diploid populations. Its algorithms utilise a sparse 'tree' for representing gene flow within pedigrees and its is particularly well geared towards handling dense marker maps. There are a wide range of options to choose from when analysing your data and when used in conjunction with SimWalk2 provides a powerful set of tools f…

microsoft_natural_ergonomic_keyboard_4000

Sun, 15 Feb 0000 14:24:23 +0000

I spend a lot of time in front of a computer, both at home and at work. As normal keyboards are smaller in width than my shoulders I find using them forces me to twist my hands to get my fingers on the base keys for touch-typing. Imagine putting your hands out in front of you, palms down, now pretend there is a pivot through the base of your thumb and rotate your hands outwards, i.e. your little fingers towards the forearm, this is the twisting I, and no doubt many others, have to do to get th…

nfs_layman

Sun, 04 Jan 0000 11:37:03 +0000

After setting up NFS Portage I found that it was annoying not to have the Overlays that I used updated nightly on my network storage and got lazy with syncing the overlays when my main computer was running. Fortunately though, since Layman is essentially just a set of Python scripts for managing the various overlays and it uses SVN, CVS, Git or Mercurial to actually synchronise the local copy of the overlay with those made available on-line its relatively straight-forward to set up a CRON job …

nfs_portage

Sun, 04 Jan 0000 12:25:42 +0000

Gentoo etiquette asks that users don't sync their Portage no more than daily to avoid over-loading the rsync servers. But what if you have several Gentoo systems and you want to update each daily? The simple solution is to have one computer synchronise daily and then share Portage as a Network File System (NFS) that the other systems then mount and use transparently.

nokia_n95

Tue, 12 May 0000 10:52:37 +0000

I finally bit the bullit earlier in the year and signed up for a mobile contract. My change in attitude was mainly down to envy and desirability of some of my friends Nokia N95 that seems to be able to do pretty much everything I might want from a phone/PDA.

nslu2_overview

Sun, 04 Jan 0000 10:45:42 +0000

The NSLU2 or Slug as it is affectionately known by hackers is a brilliant piece of hardware from Linksys. Its basically a small computer built with the ARM processor, 32Mb RAM, an ethernet port and two USB ports. You can plug any USB storage device into it, plug it into your router turn it on, and hey presto, you have additional network storage device.

openwrt

Mon, 29 Jun 0000 21:37:42 +0000

OpenWRT is a highly flexible generic operating system that works on a range of devices. I opted to install this on my second WRT54g to play around with and it seems to have the greatest flexibility. Installation The easiest method of installing OpenWRT is either to use the “Flash Firmware” functionality of the already installed distribution, or if you've bricked your router then you can use the tftp method (my preference).

photography

Sun, 19 Oct 0000 20:31:02 +0000

I enjoy snapping pictures, mainly of landscapes and inanimate objects, but I do enjoy snapping pictures when out climbing too. Hardware I use a wp>Nikon D50 with various lenses, primarily the 18-200 mm f/3.5-5.6G ED-IF AF-S VR DX, but also the wp>Nikon 50 mm f/1.8D AF Nikkor and the kit lens 18-55 mm f/3.5-5.6G ED AF-S DX. For convenience, I'll also snap pictures with my wp>Nokia N95.

plink

Mon, 29 Jun 0000 21:37:42 +0000

PLINK is a program from the Shaun Purcell er al. at the Center for Human Genetic Research, Massachusetts General Hospital. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. It intigrates with haploview and a graphical interface gPlink to aid in the visualisation an anotation of results. PLINK also integrates with R to facilitate analysis.

qtdt

Mon, 29 Jun 0000 21:37:42 +0000

QTDT is a program from the Abecassis Lab at the Center for Statistical Genetics, University of Michigan. Its used for detecting linkage and association with quantiatitve traits in nuclear families. Ebuild The ebuild is shown below # Copyright 1999-2008 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ DESCRIPTION="Linkage and Association testing of Quantitative Traits in.\ nuclear families." HOMEPAGE="http://www.sph.umich.edu/csg/abecasis/qtd…

snphap

Mon, 29 Jun 0000 21:37:42 +0000

Snphap is a program from the David Clayton Its used for estimating haplotype frequencies via an EM-algorithm. Ebuild The ebuild is shown below # Copyright 1999-2005 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ DESCRIPTION="Hapltoype frequency estimation via EM-algorithm." HOMEPAGE="http://www-gene.cimr.cam.ac.uk/clayton/software/" SRC_URI="http://www-gene.cimr.cam.ac.uk/clayton/software/${P}.tar.gz" SLOT="0" LICENSE="Artistic" KEYWORDS…

start

Sat, 21 Mar 0000 00:54:17 +0000

Welcome to slack here you will find sections on Gentoo, LaTeX, Photography, Climbing, Statistics, Nokia N95, Genetics, hacking Linksys products and the occasional blog update.

statistics

Mon, 29 Jun 0000 21:37:42 +0000

Statistics are the useful numbers that get called upon in any number of situations. Sadly they're often misused and abused mainly by politicians, spin-doctors and the media who have an agenda. Statisticians per se are a fairly honest bunch (at least those I've met, and I'm including myself in that!).

updating_daily

Thu, 09 Oct 0000 21:31:28 +0000

Syncing Portage In order to update your system you need to syncrhonise your local portage tree (and overlays) with those on the central servers (or its mirrors). If you've multiple Gentoo servers on your home network then you should ideally be using a centralised portage tree that you are sharing over NFS. You can use a cron job to synchronise your portage tree automatically, whether its on your local machine, or your NFS portage.

wrt54g_overview

Mon, 06 Oct 0000 23:22:20 +0000

Firmware Which firmware you opt for will be influenced by a number of factors such as your familiarity (or willingness) to use the command line interface (CLI) to edit and manage the software, or if you'd rather stick with a web-based user interface (WebUI). I've used two different firmwares on my WRT54G so provide some details. Other alternatives are listed.

x_keymapping

Sun, 12 Apr 0000 21:45:17 +0000

On occasions I found that after emerge -uDN @world that my keymappings under X had gone awry and reverted to US, despite no changes to my /etc/X11/xorg.conf. Thing were fine under a TTY, but not under X. Why? This happens when you upgrade to a version of Xorg >1.5 as input devices such as keyboard, mouse and touchpads are now controled by HAL and .