a project co-produced by MedialabMadrid and the Protein Design Group from the Centro Nacional de Biotecnologia (CBN / CSIC) at the Universidad Autonoma de Madrid.
Research project in digital and physical interfaces for visualization, navigation and experimentation with genetic networks.
Santiago Ortiz [moebio.com]
Luis Rico [MediaLabMadrid] [banquete.org]
Alfonso Valencia [Protein Design Group]
ARS electronica Festival 2005: HYBRID, living in paradox
4th european conference on Computational Biology, Madrid, España
Network topology has become a paradigmatic field in sciences (as well as mathematics, social sciences and arts) since it studies the way in which many they are organized. The interaction between genes is a specific example of scientific studies where this is demonstrated. The network structure formed by molecular interactions defines functional genetic aspects of great importance.
Scientists in biology, genetics and bioinformatics whose fields of research include genetic networks, have to deal with huge amounts of relational information. The management of this information, its visualisation and in general, the way in which scientists relate to it, determines the direction of their research. The information is inert, scientists have to establish a relationship with it, and in that process play role many parameters, some can be controlled and some can even be created.
Wattson and Crick (Nature April 2, 1953) decided to continue their search for the basic way in which information is stored in the DNA molecule after having built a physical model of the double helix. This example illustrates how the relation with information can be revealing and diverse in a sensorial way, especially when it has a particular structure.
The aim of this project is to develop digital interfaces for the exploration of genetic networks, where the term exploration comprehends the following possibilities:
- To be able to move within the network, affecting the motion’s direction with gestures. This is then the order in which the nodes are navigated.
- To equip the visitor with different mechanisms of displacement, as well as different speeds and visualization systems.
- To offer a wide and continuous range of possibilities and a number of options to control the navigation.
- In the case of routes established at low control levels, a combination of two factors is considered, these are: chance and deterministic algorithms.
- To offer immersion in a metaphoric spatial construction, a spatial navigation experience. In other words: to offer different possibilities of navigating the network from the inside.
I. Stage one: oracle & landscape / genetic interaction network in the bacteria Escherichia Coli.
Oracle & landscape
The first stage of the project will result in the production of two interfaces for exploring the genetic interaction network of E. Coli, based on the interfaces developed for the Quiasma project. These are:
Oracle interface: A circular interface of high control level over the node selection, where the entire network of relations can be visualised.
······ Landscape interface: A three-dimensional interface for spatial navigation, based on the metaphor of a journey over a flat and infinite landscape, where the navigation takes place between interrelated nodes.
For images of the staging for Quiasma click here
Genetic interaction network
The Escherichia Coli is a historically important organism in genetics because its genome was the first to be completely sequenced, opening the door to a new era in genetic studies.
······ SEM image of Escherichia Coli group
The genome of the E. Coli has approximately 4300 genes, which have around 8700 identified functions.
The interaction network involves 720 genes, with 1350 relations that describe the inhibition and expression of each of the genes. Each relation in the network describes one of the following three possibilities:
1. Gene expression
2. Gene inhibition
3. Dual state
The following is the data with which the interfaces are being developed (provided by the Protein Design Group):
····> Escherichia Coli’s complete genome
····> Function code of Escherichia Coli’s genes
····> Identification and functional classification of E. Coli genes
····> E. Coli’s network of gene interaction
First approach to the representation of the network
······ this circular approach is the first graphical representation (oracle) of the network of interactions; It represents each gene with coloured segments associated to the structural description of the gene’s main function. The colour of the relation curves express the nature of relation, and the traces external to the circle establish a relation of auto regulation.
GNOM at ARS electronica Festival 2005
A first version of GNOM will be presented at the international electronic art festival ARS Electronica Festival 2005, GNOM will be exhibited in parallel with Quiasma (Q+G).
For information and staging schematic of Q+G click here.
II. Stage two: open lines of research
Throughout the development of the first stage in which GNOM is attached to Quiasma, new possibilities for the future development of the project as a stand alone installation will be noted. At present we have identified new areas of research that can be explored to enhance the sensorial experience visually and sonically.
Once the oracle and landscape interfaces are completed and presented at ARS Electronica in September as Q+G, we will start a new phase in which the resources of the installation are dedicated to the exploration of genetic networks, searching for new possible ways to visualize and spatially display the information within the network.
2. Hyper-structural relations between networks
As aforementioned in the introduction, networks have become a multi-paradigmatic pattern. The network approach to a problem gives priority to the relations between its components, since this effectively occurs in genetic networks, the relations and the topology which they form are themselves (or keep within themselves) dynamic information.
Once the two problems have been analysed with a network approach, it is possible to compare both structures from a common point of view: the graph and network theory.
The research carried out by Uri Alon, Ron Milo and co-workers (Science Vol. 298, 824-827, 2002. Science Vol. 303, 1538-1542, 2004) have given interesting results that allow us to compare very different networks, not only in their semantics but also in their structure and size. Their research is based on the search for “network motifs” (simple building blocks of complex networks) that appear in real networks in a significant way. This means that their probability of appearing in an aleatory network of similar structure is much lower. Taking this into account, the research team has set out guidelines to define super-families of networks and ways to compare different kinds of networks. Such as: genetic networks, neural networks, social networks or the internet.
······ significant motifs in different networks: genetic, neural, social, the internet and syntactical in different languages.
The dynamic visualisation of the correlation between networks of different natures whereby one can navigate the networks as well as perceive the relations between them is an interesting challenge.
The correlation between networks of different nature raises interesting challenges for their dynamic visualisation, where not only one can navigate the networks but also the relations between them are made explicit.
For Alon’s group’s papers click here
For Alon’s group’s different studied networks click here
A great family of networks that has not been explored in Alon’s work are the musical works of different eras and cultures (each with their own different tonal and atonal systems). For example an analysis identical to that of syntax developed through text can be achieved with musical scores.
Visualisation of “information spaces” is not the only line of research. It would be interesting to explore how sound can relate to information within the network. The ear is an amazing receptor of information, which alongside with certain parts of the brain carries out two different tasks of interest to us: recognition of patterns emitted by other individuals and spatial interpretation of sounds (some times these two processes can be performed at the same time, for example we may try to recognise someone by the sound of their steps). If we make sound work in conjunction with light (images), new ways to cruise within spatial representations of information can be explored.
For sound structure developed by Santiago Ortiz click here
From the comparative study of motifs in different kinds of networks, including those of a sonorous and musical nature, the creation of new network structures form those already existing can be achieved. Genetic networks and functional information in general can be used as foundations that would enable us to construct new sound structures which could bring the motifs found in the network to the acoustic field.
Interaction networks are dynamic by definition: using them as a departure point, we can create basic models where this dynamic nature is simulated. A simple model of this kind works as a cellular automaton moving through the network. This way, we create a dynamic pattern which can be expressed easily as sound. How does a dynamic interaction network sound from the inside?