Art and Science Exhibition


ISMB/ECCB 2013 brings together scientists from a wide range of disciplines, including biology, medicine, computer science, mathematics and statistics. In these fields people are constantly dealing with information in visual form: from microscope images and photographs of gels to scatter plots, network graphs and phylogenetic trees, structural formulae and protein models to flow diagrams; visual aids for problem-solving are omnipresent. Some of the works of the first such exhibition at the ISMB 2008 in Toronto combine outstanding beauty and aesthetics with deep insight that perfectly proves the validity of our approach or goes beyond the problem's solution. Others were surprising and inspiring through the transition from science to art, opening our eyes and minds to reflect on the work that we are undertaking.

The Art & Science Exhibition 2013 presents the artworks that have been generated as part of research projects. They are also soliciting images resulting from creative efforts that involve scientific concepts or employ scientific tools and methods.

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Art & Science Images

Sean O'Donoghue
CSIRO Mathematics, Informatics & Statistics, Australia
The Genetic Code Redisplayed, with Amino Acid Abundance
For most life forms on Earth, the standard genetic code translates the four bases of DNA into the twenty amino acids that are the building blocks of all proteins.

The circular arrangement we present here groups codons first by the central base, represented in the center of the layout, then first and third base. This displays the amino acids encoded by six codons (Leucine, Serine, and Arginine) as contiguous segments of the circle, and even brings all three stop codons together. The result is a visual aid that makes it easy and intuitive to discern non-synonymous nucleotide mutations.

The abundance percentage of amino acids was calculated for each kingdom of life (archaea, bacteria, eucaryota, and viruses) from a database of ca. 6 million proteins.

Sean O'Donoghue
CSIRO Mathematics, Informatics & Statistics, Australia
The Hungry Microbiome
"The Hungry Microbiome" is an animation currently in production which will depict the process of bacterial degradation of resistant starch granules within the large intestine. The animation will explore the potential molecular mechanisms by which the end products of bacterial metabolism can protect from diseases of the large intestine. The animation is aimed at providing detailed information about cellular and molecular biology processes in a way that is both accurate and visually compelling. This image is the first concept artwork for the animation project.

Jan Aerts
University of Leuven, Belgium
Cosmopolitan Chicken Research Project
The Cosmopolitan Chicken Project by Belgian artist Koen Vanmechelen aims to explore the phenotypic and genetic evolution of chicken breeds as a proxy for human evolution and diversity (http://www.koenvanmechelen.be/cosmopolitan-chicken-project). This project has created several generations of hybrids based on purebred domestic chickens.

In this data-driven sculpture, we visualize the genetic heterozygosity of one particular hybrid ("Mechelse Ancona") which descends from 12 different purebreds, including Mechelse Koekoek, Poulet de Bresse and Ancona. After genotyping, the number of homozygous and heterozygous loci were counted at their chromosomal positions, and translated as peaks in 3-dimensional space. Each chromosome is laid out in a circle, connecting at the starting position. Peaks pointing towards the centre represent homozygous genotypes; peaks pointing outward show heterozygous regions. As a result, inbred chickens generate smoother outlines whereas crossbred ones result in a form with many outward-pointing spikes. The 3D models were developed in Processing, an open source programming language and integrated development environment based on Java.

Marcio Acencio
Institute of Biosciences of Botucatu -- Universidade Estadual Paulista, Brazil
Stress spots in a cancer network on fire!
Cancer network (constructed by integrating cancer-related interactions from KEGG Pathways) visualized as a functional landscape. Brighter areas are network regions comprised by nodes with higher stress values; darker areas are network regions comprised by nodes with lower stress values. This landscape is similar to the visible surface of the Sun including sunspots (darker regions) and solar faculae (brighter regions). While solar faculae are produced by concentrations of magnetic field lines, here faculae are produced by the concentration of shortest paths in certain regions of this cancer network. The inset figure is the traditional visualization of this network.

Forbes Burkowski
University of Waterloo, Canada
Seashell
Seashell
The image was created using the VRML utilities in UCSF Chimera. The surface was defined parametrically as:
X(u,v) = (A – v) cos(2v) (1 + cos(u)) + (8pi/5) cos(2v)
y(u,v) = (A – v) sin(2v) (1 + cos(u)) + (8pi/5) sin(2v)
z(u,v) = B + (A – v) sin(u)
0 < u < 2pi, -2pi < v < 2pi, with constants A and B chosen to give a recognizable “snail architecture”.
The surface is comprised of approximately 1.4 million triangles. This provides enough resolution to define an intricate surface pattern that is painted by using a one-dimensional binary cellular automaton. For this particular rendering the chosen automaton is Wolfram’s “Rule 30” which gives an appearance that is similar to that seen in the Conus textile snail species.

Forbes Burkowski
University of Waterloo, Canada
Insulin's Hydrophilic center
Usually one thinks of a protein as having a central hydrophobic core. In the case of insulin (PDB ID 1ZNJ) the structure is a “trimer of dimers”. Each of the trimers has a hydrophobic core but the entire structure surrounds a center that contains a hydrophilic “cage” structure containing two zinc atoms (one of which is seen in the image as a green sphere).
The image was created using VRML facilities in UCSF Chimera. Each of the residues is represented by a sphere that is given a color corresponding to the residue’s position in the Kyte-Doolittle hydrophobicity - hydrophilicity range. The corresponding color range is a linear interpolation going from orange to white to blue. Spheres having centers that are within a distance of 9 Angstroms are joined using a spindle.
For this image, all the spheres corresponding to hydrophobic residues were removed along with any incident spindles. The result reveals a compelling symmetric structure that arises from the original 3-fold symmetry of the protein.

Forbes Burkowski
University of Waterloo, Canada
Lissajous in 3-space
If you have ever watched those old science fiction movies out of the ‘50’s, the mad scientist always had a cheap oscilloscope that invariably displayed some simple Lissajous closed curve (determined by two slightly out-of-phase sinusoidal inputs with frequencies corresponding to a ratio of two simple integers). With current technologies, a graphics program can create Lissajous curves that are also periodic, but more complicated and existing in a 3-dimensional space. The simple line can be replaced with a locally cylindrical surface that can be colored. In this image, the center line of the surface is a curve parametrically defined as:
x(t) = 6 sin(t*pi/3),
y(t) = 4 cos(t*pi) + 3 sin(2t*pi) cos(t*pi/3),
z(t) = 1 + 2 cos(t*pi).
Periodic functions were also used to determine both cylinder radius and coloration with color ranges chosen to give a compelling abstract impression for the final rendering. The image was created using the VRML utilities of UCSF Chimera.

Forbes Burkowski
University of Waterloo, Canada
Op Art C2
From Wikipedia:
Op art, also known as optical art, is a style of visual art that makes use of optical illusions. "Optical art is a method of painting concerning the interaction between illusion and picture plane, between understanding and seeing [John Lancaster]. Op art works are abstract, with many of the better known pieces made in black and white. When the viewer looks at them, the impression is given of movement, hidden images, flashing and vibration, patterns, or alternatively, of swelling or warping".

In this Op art experiment the VRML utilities in USCF Chimera have been used to set up an array of spheres with centers that are on a flat grid. Coloration of the spheres has been computed using trigonometric functions that vary the intensity and color values to construct the impression of a 3-dimensional toroid placement of the spheres.

Robin Haw
OICR, Canada
The Reactome Planetarium
Reactome (http://www.reactome.org) is an open-source, manually curated and peer-reviewed resource of core pathways and processes in human biology. The database can be used by biologists as an online encyclopedia of biology, or by bioinformaticians to make discoveries about biological pathways. Reactome Planetarium is a visual representation of the entire Reactome data set. The known Reactome universe can be viewed as a radial layout, displaying the total number of participating proteins and small molecules in a particular top-level pathway (node size) and the degree of similarity between top-level pathways (edge thickness). Reactome Planetarium can be used to navigate through the universe of human pathways and is invaluable to visualize connections between pathways, including many connections between domains of biology conventionally seen as unrelated. Illustration by Heeyeon Song.

Nadezda Kryuchkova
University of Lausanne, Switzerland
Mouse in the Correlation Net
We study how anatomy influences the evolution of protein-coding genes. The picture shows correlations between different protein parameters in mouse. Yellow lines show positive correlations and blue negative correlations, calculated with partial Pearson coefficient. The picture was done using Circos (Krzywinski et al. 2009). The parameters shown are gene expression level in 22 different organs, intron length and intron number, protein length, gene GC content and evolutionary rate (omega). Expression data were taken from ENCODE (The ENCODE Project Consortium 2007) and all other data are from Ensembl (Flicek et al. 2011).

Sebastian Salentin
Technische Universität Dresden, Germany
SHADOW DRUG
The artwork video "SHADOW DRUG" shows molecular interactions in the style of a modern chinese shadow theatre. This kind of play using the shadows of flat and three-dimensional figures for storytelling has a long history in southeast Asia. In the "SHADOW DRUG" animation, proteins and ligands seem to be moved on sticks behind a translucent screen. Lights, sounds and music are used for telling the story of a drug and its effects in an entertaining way. The play features the heat shock protein Hsp27 and the small molecule drug BVDU, which are a focus of research in our group.

[Video]

Theodore Alexandrov
University of Bremen / Steinbeis Innovation Center SCiLS Research / University of California San Diego, Germany
Woman and Man
Christopher M. Rath, Amina Bouslimani, Carla Porto da Silva, Mingxun Wang, Guo Yurong, Antonio Gonzalez Pena, Donna Berg-Lyons, Gail Ackermann, Gitte Christensen, Kathleen Dorrestein, Richard Gallo, Nuno Bandeira, Rob Knight, Theodore Alexandrov, Pieter C. Dorrestein

Despite a variety of advanced molecular techniques has been developed in the last decade, a systems biology large-scale analysis of a human is still a formidable challenge. We present an artistic representation of results of our project on 3D molecular and microbial analysis of the surface of the human skin. The molecular maps visualize distribution of molecules on the human skin.

Disclaimer: The tree of life visualization used in this art piece is authored by Ivica Letunic and is released into the public domain through Wikipedia Commons (available at http://en.wikipedia.org/wiki/File:Tree_of_life_SVG.svg).

Davide Bau
Centro Nacional de Analisis Genomica, Spain
Chromatin
Structural Bioinformatics

Structural bioinformatics is the branch of bioinformatics that deals with the analysis and determination of the 3D structure of biomolecules such as protein, RNA and DNA.
This image represents the merging between informatics and biology and how the integration of biochemical data and computational methods can help in understanding the mechanisms that take place in living cells.

(Image: A region of Human Chromosome 2.)

Vera Pancaldi
Spanish National Cancer Research Center, Spain
The essence of pombe
This is the cover image of the April 2012 issue of G3: Genes, Genomes and Genetics and it represents the first predicted interactome of the fission yeast, Schizosaccharomyces pombe. The network was predicted using maching learning and hundreds of protein and gene features. It is visualized using Cytoscape, where the nodes are colored according to the proteins' functional characterization terms. The network is superimposed on a microscopic image of a fission yeast cell where the nucleus has been replaced by a smaller version of the predicted network (See V. Pancaldi, Ö.S. Saraç, C. Rallis, J.R. McLean, M. Převorovský, K. Gould, A. Beyer, J. Bähler (2012) Predicting the fission yeast protein interaction network. G3 2(4), 453-467)

Milana Frenkel-Morgenstern
Spanish National Cancer Research Centre (CNIO), Spain
The expression of chimeric transcripts and the production of chimeric proteins
Numerous putative human chimeric transcripts have been identified using high throughput RNA sequencing. These chimeric RNAs are significantly more tissue-specific than non-chimeric transcripts and, although, they often incorporate highly expressed parental genes, most chimeric RNAs are weakly expressed. Nevertheless, 12 novel chimeric proteins have been detectable in multiple shotgun mass spectrometry experiments. Many such chimeras incorporate trans-membrane domains and signal peptides, altering the cellular localization of these proteins.

The cover is an artist's representation of the "gene expression landscape" that is identified by high throughput RNA sequencing. The "chimeric" RNAs are represented by two-tone sequence fragments, while the shape of the landscape represents different levels of the gene expression. Among the protein products, the "chimeric" proteins are represented by the red and blue volcanic eruptions. Overall, the picture gives us an idea of the relatively small proportion of chimeras that might be generated with respect to their normal protein counterparts, represented by the blue or red fire emitted by the volcanoes. The human data have been mainly taken from human cell lines, theoretically derived from the central human figure shown on the cover (Cover Illustration by Bureau Design Studio and Multi-Player Laboratory Ltd, for details see Frenkel-Morgenstern et al., 2012, Genome Research)

Alaa Abi Haidar
Universite Pierre et Marie Curie, Paris, France
Spirals
From DNA structure to galactic anatomy, spirals have inspired us with their universal form of a curve around a fixed center point that increases or decreases in distance from this point.

In this series, I focus on botanic spirals that is often in harmony with spirals from the animal kingdom, as shown in my main submission with a furn coupled with a snail shell.

More poetically, the fern slowly unfolds to express its gratitude to the sun.

I am a postdoctoral fellow at the university of Pierre and Marie Curie and the Centre de Recherche National in Paris. I work on artificial immune systems and pursue photography as a hobby.

Alaa Abi Haidar
Universite Pierre et Marie Curie, Paris, France
Unfolding Spirals
From DNA structure to galactic anatomy, spirals have inspired us with their universal form of a curve around a fixed center point that increases or decreases in distance from this point.

In this series, I focus on botanic spirals that is often in harmony with spirals from the animal kingdom, as shown in my main submission with a furn coupled with a snail shell.

More poetically, the fern slowly unfolds to express its gratitude to the sun.

I am a postdoctoral fellow at the university of Pierre and Marie Curie and the Centre de Recherche National in Paris. I work on artificial immune systems and pursue photography as a hobby.

Alaa Abi Haidar
Universite Pierre et Marie Curie, Paris, France
Fractal Spirals
From DNA structure to galactic anatomy, spirals have inspired us with their universal form of a curve around a fixed center point that increases or decreases in distance from this point.

In this series, I focus on botanic spirals that is often in harmony with spirals from the animal kingdom, as shown in my main submission with a furn coupled with a snail shell.

More poetically, the fern slowly unfolds to express its gratitude to the sun.

I am a postdoctoral fellow at the university of Pierre and Marie Curie and the Centre de Recherche National in Paris. I work on artificial immune systems and pursue photography as a hobby.

Niv Scott
Weizmann Institute of Science, Israel
A splash of Neurons
Picture of neurons from mouse brain. The green neurons are dopaminergic neurons infected with virus containing Green Fluorescence Protein (GFP). The red neurons are neurons that contain a certain hormone marked with anti-bodies. The picture was taken with Two-photon microscope.

Manjari -
Centre for DNA Fingerprinting and Diagnostics, India
Global and local hubs go Merry-go-round
A protein having high number of interacting partners is known as hub. The protein-protein interaction network shown here is of hubs and their partners in human. Size of the node shows its degree and color shows its breadth of 'hubness' across the tissue. Nodes with larger size are highly interacting nodes which are either centered in between or arranged outside the yellow non hub circle. Using tissue-specific gene expression data of human and based on tissue-specific interactions a hub can be hub in only few tissues also known as Tissue-specific hubs (TSH) which are shown in orange color and hubs which are hub in many tissues also known as Housekeeping hubs (HKH) shown with violet color. Edge is colored based on the number of tissues the partner (target) is conserved in the tissues where the protein (source) is hub. Orange color shows maximum conservation of partners and violet shows least conservation across the tissue. TSHs are having conserved partners compared to HKH which frequently changes the partners. TSHs which are expressed and hub in only few tissues mostly conserve their partners and may act as 'party hub' whereas HKHs which are globally expressed and hub in most of the tissues often switch the partners and may act as ‘date hub’.


Reference of the tool used to design the artwork: Bastian M., Heymann S., Jacomy M. (2009). Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media.

Monica Zoppè
Scientific Visualization Unit, Italy
The Challenge of HIV Research
The Challenge of HIV Research is a short movie developed as a means to sensitize people about HIV and the need of research to find a cure.The problem of HIV and AIDS, although not much visible in western societies, is still a major one for many other Countries.The short starts with an idyllic cellular scene, of everyday, regular life, with proteins idling on the surface of a white blood cell (among them experts may recognize the Toll Like receptor, ICAM and CD4).However, unknown to the white blood cell, somewhere, in the same body, another cell has been infected, and is emitting viral particles at high speed, releasing them into the bloodstream.Many of the single viral particles are defective (a finding that virologists have known for many years), and cannot initiate an infection. Yet, even if only 1% of virus is active, it is more that enough to spread the infection to other cells, continuing the disease.Many details are known of the complex process that, starting with binding of a virus to its receptor on the surface of the cell, will lead to the virus entering the cell, releasing its outer coat, and finally taking over the cellular process to its own benefit.

Juana Canul Reich
Universidad Juárez Autónoma de Tabasco, Mexico
An image that can save a life.
A mammogram showing a lesion classified with BIRADS 4. Left side is the original mammogram, while right side is the same image after undergoing computational algorithms for improvement to be used for diagnosis.

Herman van Haagen
LUMC, Netherlands
Big Data and literature mining
In 2009 we discovered a physical protein-protein interaction between the proteins CAPN3 and PARVB (Haagen et. al. , PlosOne). We studied a disease called Limb-girdle muscular dystrophy type 2A (LGMD2A) with is caused by defects in the human CAPN3 gene. We were searching for novel associations with this gene/protein and found one namely PARVB.

The discovery was done using concept profiles, a literature mining technique to find implicit or indirect links between concepts (medical terms). This image shows the network of all directly related concepts for CAPN3 and PARVB and the implicit links between the two "information clouds". CAPN3 and PARVB have never been explicitly co-mentioned in an article before we discovered it.

In this era of 'Big Data' this image is a good example that illustrates the enormous amount of information contained in text. Normally this is too much information to grasp as humans but not for a computer. The network (or information cloud) of CAPN3 contains 2634 concepts, the network of PARVB contains 548 concepts, and the shared implicit layer that drives knowledge discovery contains 281 concepts.

Vidhi Patel
Nanyang Technological University, Singapore
Protein, Love, Peace
This is a herpes viral protein, the structure of which is solved using crystallography. Fiddling around with protein structure is like solving a 3D puzzle posed by Nature. A simple act of rotating the structure in a different direction resulted in a Heart perimeter.
For me, personally, I see it as a junction of Science (a physical thing governing the law of Nature) and art (an imaginary event/situation which can be interpreted by many in many ways). I do not see a better way to observe the conglomeration of both science and art evoking the emotion of "Love", which forms the basis of human existence and cooperation. We might be blinded by our foolish fantasies at the macro level, while deep within science still teaches us to care and love

Imogen Smith
University of Reading, United Kingdom
Memories of a Machine
'Memories of a Machine' is a collaboration between Imogen (Immy) Smith, a scientist and artist from UK, and Luca Rossi, an artist from Italy. It is an 'exquisite corpse' - a form of drawing experiment where one person draws half a picture, covers it except for a thin strip, and sends to another artist to complete from the small visible strip. The final drawing is only unwrapped when the second half is complete, and in this way surprising combinations of elements may be placed together because of the hidden nature of part of the work.

The left-hand side of this drawing was made first by Luca Rossi, covered except for a small 2cm strip in the centre, and mailed to Immy Smith who completed the right-hand side before unwrapping the finished work.

Luca Rossi is a surrealist artist. Immy Smith is a neuroscientist in addition to being an artist, and studies human neuronal cell cultures using multi-electrode array (MEA) technology. The two have never met, but collaboration allows them to share their ideas and artwork without borders. Further work by both Immy and Luca can be found via collaborativecorpse.deviantart.com and imaginingscience.com

[Video]

Shailesh Tripathi
Center for Cancer Research and Cell Biology, United Kingdom
Cancer Network of B-Cell Lymphoma: NetBioV
The network shows a gene regulatory network of B-­-Cell lymphoma inferred with BC3NET from gene expression data. The color-­-highlighted modules correspond to biological pathways defined by the Gene Ontology database and the connecting paths correspond to the shortest connections on which information can be exchanged between these pathways. For the visualization we used NetBioV, an R package we developed for the graphical representation of large networks in biology and medicine.

Victor Padilla-Sanchez
The Catholic University of America, United States
T4 bacteriophage infection of Escherichia coli cells
Description: Model of bacteria during infection by T4 viruses where one cell (2 μm x 0.5 μm) is enlarged to show the infection and bacterium details including a polyribosome, T4 DNA packaging, nucleoid and phages during attack. The T4 bacteriophage (200 nm x 90 nm) model shows its molecular architecture counting about 50 proteins where the packaging machine is composed of pentameric ATPase motor with 2 domains (PDB: 3EZK), dodecameric portal protein (pseudoatomic homology model), dsDNA where the portal-motor interactions are colored yellow and red forming an intercalating pattern 2-1-1-1-1 interacting subunits and 2-1-1-1-1 non interacting subunits. See Journal of Virology 2012 issue 8 cover and featured article.

Image: This image is a composite of four models (bacteria group during infection, enlargement of one infected E. coli, enlargement of T4 bacteriophage and packaging machine) constructed with the molecular visualization software UCSF Chimera and enhanced with Adobe Photoshop CS6 where the only components are X-ray structures (PDBs) and 3D reconstructions (EMDBs).

Author: I am Victor Padilla-Sanchez, PhD Student in the Biology Department of The Catholic University of America at Washington DC where I have been working on the structure and function of the portal protein gp20 of Bacteriophage T4 while my interests are in Structural Biology, Virology, Bioinformatics and Molecular Modeling. Contact: 70padillasan@cardinalmail.cua.edu

Saket Navlakha
Carnegie Mellon University, United States
The Loneliness of the Young, Unnormalized Synapse
2300 synapses extracted from electron microscopy images of the developing mouse somatosensory cortex. "Variability" in the images (left) can be reduced using computational alignment and "normalization" (right). This improves "classifier" performance, but at what "cost"?

The title and theme is inspired by Alan Sillitoe's famous short story, "The Loneliness of the Long Distance Runner".

Liddy Hubbell
The Jackson Laboratory, United States
Retina Three
This collage focuses intently on the landscape of the retina at an unusual confluence of the visual and tactile senses. It is the complexity and richness of that juxtaposition that interests me.

The palm-sized work of spun silk, linen, wool and cotton might be taken as a garden, an abstract expression, or even a landscape. Yet the fibers echo the forms of the three basic stages of processing of the circuit that captures light and translates it into signals the brain can understand. The physical nature of collage materials demands attention to connections, layering and texture. The very delicacy of the threads, which crudely mimic the far finer matrices of the cells themselves, underscores the complex nature of the microscopic worlds within each of us.

This piece references work of Robert Burgess of the Jackson Laboratory in Bar Harbor, Maine, USA. Rooted in observation, my work proceeds beyond illustration further into the abstract realm of interpretation. I use my art to convey complex scientific concepts in ways which compel fresh observation and inquiry, raise awareness of science and pose questions that we don’t normally ask.

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