Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?

The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from the genomic data from Plasmodium falciparum, but using also the millions of genomic data from other species. Drug candidates are sought in a chemical space containing the millions of small molecules stored in public and private chemolibraries. Data management should therefore be as reliable and versatile as possible. In this context, we examined five aspects of the organization and mining of malaria genomic and post-genomic data: 1) the comparison of protein sequences including compositionally atypical malaria sequences, 2) the high throughput reconstruction of molecular phylogenies, 3) the representation of biological processes particularly metabolic pathways, 4) the versatile methods to integrate genomic data, biological representations and functional profiling obtained from X-omic experiments after drug treatments and 5) the determination and prediction of protein structures and their molecular docking with drug candidate structures. Progresses toward a grid-enabled chemogenomic knowledge space are discussed.Comment: 43 pages, 4 figures, to appear in Malaria Journa

Dataremix: Aesthetic Experiences of Big Data and Data Abstraction

This PhD by published work expands on the contribution to knowledge in two recent large-scale transdisciplinary artistic research projects: ATLAS in silico and INSTRUMENT | One Antarctic Night and their exhibited and published outputs. The thesis reflects upon this practice-based artistic research that interrogates data abstraction: the digitization, datafication and abstraction of culture and nature, as vast and abstract digital data. The research is situated in digital arts practices that engage a combination of big (scientific) data as artistic material, embodied interaction in virtual environments, and poetic recombination. A transdisciplinary and collaborative artistic practice, x-resonance, provides a framework for the hybrid processes, outcomes, and contributions to knowledge from the research. These are purposefully and productively situated at the objective | subjective interface, have potential to convey multiple meanings simultaneously to a variety of audiences and resist disciplinary definition. In the course of the research, a novel methodology emerges, dataremix, which is employed and iteratively evolved through artistic practice to address the research questions: 1) How can a visceral and poetic experience of data abstraction be created? and 2) How would one go about generating an artistically-informed (scientific) discovery? Several interconnected contributions to knowledge arise through the first research question: creation of representational elements for artistic visualization of big (scientific) data that includes four new forms (genomic calligraphy, algorithmic objects as natural specimens, scalable auditory data signatures, and signal objects); an aesthetic of slowness that contributes an extension to the operative forces in Jevbratt’s inverted sublime of looking down and in to also include looking fast and slow; an extension of Corby’s objective and subjective image consisting of “informational and aesthetic components” to novel virtual environments created from big 3 (scientific) data that extend Davies’ poetic virtual spatiality to poetic objective | subjective generative virtual spaces; and an extension of Seaman’s embodied interactive recombinant poetics through embodied interaction in virtual environments as a recapitulation of scientific (objective) and algorithmic processes through aesthetic (subjective) physical gestures. These contributions holistically combine in the artworks ATLAS in silico and INSTRUMENT | One Antarctic Night to create visceral poetic experiences of big data abstraction. Contributions to knowledge from the first research question develop artworks that are visceral and poetic experiences of data abstraction, and which manifest the objective | subjective through art. Contributions to knowledge from the second research question occur through the process of the artworks functioning as experimental systems in which experiments using analytical tools from the scientific domain are enacted within the process of creation of the artwork. The results are “returned” into the artwork. These contributions are: elucidating differences in DNA helix bending and curvature along regions of gene sequences specified as either introns or exons, revealing nuanced differences in BLAST results in relation to genomics sequence metadata, and cross-correlation of astronomical data to identify putative variable signals from astronomical objects for further scientific evaluation

Using machine learning to support better and intelligent visualisation for genomic data

Massive amounts of genomic data are created for the advent of Next Generation Sequencing technologies. Great technological advances in methods of characterising the human diseases, including genetic and environmental factors, make it a great opportunity to understand the diseases and to find new diagnoses and treatments. Translating medical data becomes more and more rich and challenging. Visualisation can greatly aid the processing and integration of complex data. Genomic data visual analytics is rapidly evolving alongside with advances in high-throughput technologies such as Artificial Intelligence (AI), and Virtual Reality (VR). Personalised medicine requires new genomic visualisation tools, which can efficiently extract knowledge from the genomic data effectively and speed up expert decisions about the best treatment of an individual patient’s needs. However, meaningful visual analysis of such large genomic data remains a serious challenge. Visualising these complex genomic data requires not only simply plotting of data but should also lead to better decisions. Machine learning has the ability to make prediction and aid in decision-making. Machine learning and visualisation are both effective ways to deal with big data, but they focus on different purposes. Machine learning applies statistical learning techniques to automatically identify patterns in data to make highly accurate prediction, while visualisation can leverage the human perceptual system to interpret and uncover hidden patterns in big data. Clinicians, experts and researchers intend to use both visualisation and machine learning to analyse their complex genomic data, but it is a serious challenge for them to understand and trust machine learning models in the serious medical industry. The main goal of this thesis is to study the feasibility of intelligent and interactive visualisation which combined with machine learning algorithms for medical data analysis. A prototype has also been developed to illustrate the concept that visualising genomics data from childhood cancers in meaningful and dynamic ways could lead to better decisions. Machine learning algorithms are used and illustrated during visualising the cancer genomic data in order to provide highly accurate predictions. This research could open a new and exciting path to discovery for disease diagnostics and therapies

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

"Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve. We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer interaction trends that would enable for enhancing visualization further

Interactive visualisation and exploration of biological data

International audienceno abstrac

The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Abstract Here, we introduce the 3D Genome Browser, http://3dgenome.org, which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure

Knowledge visualization: From theory to practice

Visualizations have been known as efficient tools that can help users analyze com- plex data. However, understanding the displayed data and finding underlying knowl- edge is still difficult. In this work, a new approach is proposed based on understanding the definition of knowledge. Although there are many definitions used in different ar- eas, this work focuses on representing knowledge as a part of a visualization and showing the benefit of adopting knowledge representation. Specifically, this work be- gins with understanding interaction and reasoning in visual analytics systems, then a new definition of knowledge visualization and its underlying knowledge conversion processes are proposed. The definition of knowledge is differentiated as either explicit or tacit knowledge. Instead of directly representing data, the value of the explicit knowledge associated with the data is determined based on a cost/benefit analysis. In accordance to its importance, the knowledge is displayed to help the user under- stand the complex data through visual analytical reasoning and discovery