FoAM - biology

HapStar

dave — Thu, 07 Jan 2010 16:31:40 +0000

About

Haplotype Networks and Minimum Spanning Networks are commonly used for representing associations between sequences. HapStar is a tool for viewing both types of networks, and is designed to directly use the output data generated from Arlequin. HapStar is unique in that it automatically lays out the network for optimal visualisation, and provides the option to calculate a Minimum Spanning Network from a list of alternative connections. HapStar provides a user-friendly interface, and publication-ready figures can be exported simply.

Installing

HapStar works on Windows, Linux or OSX and requires python to be installed on your computer - which you can find here.

Download the current version:

hapstar-0.6.zip (Windows)
hapstar-0.6.tar.gz (Linux/OSX)

To run, simply extract the zip or tar archive and double click on "hapstar.py". Under OSX operating systems, ctrl click and select "open with" and choose "python launcher".

Source Code

HapStar is released under the GPLv3 licence. The source is availible in the FoAM git repository.

Publications

Teacher AGF. Griffiths DJ (2010) HapStar: automated haplotype network layout and visualization. Molecular Ecology Resources, online.

The pre-print version is available here.

Funding: European Union FP7 ERA-NET program, BiodivERsA

Bitesize lecture with Brian Degger

maja — Sat, 21 Jun 2008 18:31:30 +0000

Start: 2005-06-14 00:00 Europe/Brussels

Brian Degger's Stories from the flesh factory

Whilst building my art practice, i have been working at a fish factory, this has given me various inspirations for bioart projects Working with fish calls into question sustainability of harvesting
these organisms. In the case of Orange Roughy, a deepsea fish, we know more about how to catch them than their basic biology. My two drives are making the "barely visible obvious" and beauty through decay" I undertake this through re-purposing waste streams and utilizing fish as media. I am intrigued by the relationship between human and underwater ecosystems. This talk will cover past art visual art projects and further directions into bioart. In particular i will discuss a project BioOceanBalls that i wish to develop with Foam.

I am a formally trained biotechnologist, achieving a PhD(2002) in the production of recombinant fish growth factors. I have became intrigued by the growing synergies between art and science, have developing a practice in time-based video art, and am moving towards realization of a number of bio-art projects. In 2004 I undertook an attachment with Blast Theory (UK) being involved in the production of a mixed reality game/performance titled 'I like Frank' for the Adelaide Fringe Festival. I also attended a master classes by video artist Craig Walsh (Au) and, John Cleater of the Builders Republic(US). Although not formally trained in new media I have become familiar with this area through attendance of a number of international Art&Science events including the Biennale of Perth 2002&2004, Converge, Adelaide 2002, and Transmediale, Berlin 2005. My video/ image based work has been exhibited in Adelaide (SALA 2003, 2004 and Downtown Arts Space, 2004), Melbourne (Drivers Lane, 2004)
and Dublin (Epoch, Meeting Square Temple Bar, 2005). The current project, BioOceanBalls, draws on my fascination for fish, and the possibility of reseeding underwater environments.

Bitesize lecture with Catherine Watling and Angelo Vermeulen

maja — Sat, 21 Jun 2008 18:26:48 +0000

Start: 2005-12-01 20:00 Europe/Brussels

End: 2005-12-01 23:00 Europe/Brussels

Our two guests in the last 'bite-size-lecture' for 2005 are experts in artistically grown ecologies and ecologically inspired arts. They talked to us about what happens when you depend on living (or recently living) organisms to become cooperative partners in your artistic process...

Angelo Vermeulen, a visual artist and biologist will present both a recent and an upcoming project, dealing with art and ecology. "Blue Shift [LOG. 1]" is a Darwinian art project that was conceived for the exhibition "Hot ReStrike" earlier this year in De Warande in Turnhout (B). The project was realised together with biologist Luc De Meester from the University of Leuven and engineers from Philips. "Blue Shift [LOG. 1]" is an interactive installation with a living model ecosystem at its core. Using single-cell algae, water fleas, fish and water snails, a compact biological community is set up in the exhibition space. The whole system is designed in such a way that the visitor automatically induces a gradual microevolution of the light-responsive behaviour of the water fleas. Video footage, photos and biological data was used to demonstrate the working process of the project. The concept and first preparations of a new project for the upcoming exhibition "Bruegel Revisited" in 2006 was also presented. It’s a site-specific installation and video project conceived for the Belgian National Botanical Garden in Meise. The projects aims to link historical notions of overconsumption, decadence and diversity to a contemporary ecological and artistic context.

Transcript of Angelo's lecture

Interdisciplinary artist Catherine Watling is working in collaboration with Professor Paul Pearson, Head of the Palaeoclimatology Group at the University of Cardiff Department of Earth, Ocean and Planetary Sciences where she is Artist in Residence. Together they have been working on the development of a series of 3d movies imaged using the Environmental Scanning Electron Microscope (ESEM), a microscope that allows you to view objects that are no more than one million of a millimetre in size. They have been exploring the possibility of using microscopic foraminifera, imaged using the (ESEM), to explore themes of environmental change and evolution in a series of artworks. These artworks have so far taken the form of 2d stop-frame animations and very short 3d films, some of which were showcased at Fo.am in December 2003. Catherine will be presenting their collaborative work to date and discussing their desires to allow people to experience the wonder of scientific discovery. The work attempts to re-create the hyper-real moment when you view, for the first time, an object that is incomprehensibly small and breathtakingly beautiful under the eye of an Electron Microscope and is also an exploration of the use of the Environmental Scanning Electron Microscope as an artistic tool.