The Data-Omics Era: Introducing the 2017 "Bringing Maths to Life" workshop
(Source: Pan European Networks: Science & Technology 22: 78-79 - http://www.paneuropeannetworkspublications.com/ST22/files/assets/basic-html/pa...)
"The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them,” said Sir William Henry Bragg (1862-1942; Physics Nobel Prize for Xray crystallography). In the early decades of the 20th Century, the publications of many scientists, physicists, mathematicians, biologists and geneticists - such as Jacques Monod (1910-1976), François Jacob (1920-2013), Ronald Aylmer Fisher (1890-1962), Erwin Schrödinger (1887-1961), and Alan Mathison Turing (1912-1954), for example - contributed to the foundations of biomathematics, a new discipline able to develop analytical and predictive models of biological systems. In the past 15 years, advances in high-throughput technologies have again revolutionised the approach to understanding biological phenomena and generating torrents of data. Known as ‘big data’, and initiating ‘the -omics era’, the suffix ‘-omics’ refers to the novel technologies emerging to enhance the acquisition and analysis of big datasets (genomic, transcriptomic, proteomic, metabolomic, metagenomics and nutrigenomics, amongst others).
The data explosion
The development of new measurement tools has driven an explosion of applications of diverse branches in mathematics, statistics, physics and biology to deal with big volumes of data.The generation of techniques, technologies, models, storage infrastructures and collaborative platforms is crucial to capturing the often unexpected features of complex biological systems. Furthermore, the increasing diversity of experimental techniques, the high dimensionality of the resulting data, the noise in high-throughput measurements, and the nature of the underlying biology result in substantial additional challenges in -omics data analyses.
However, while big datasets promise to discover and understand new patterns, their vastness can result in a sea of irrelevant or uncodifiable information. Therefore, the analyses of large-scale -omics datasets require the integration of these data under mathematical and relational models that can describe, mechanistically, the relationships between their components.
Discussing existing cases to identify gaps, or to share existing solutions, should help these disciplines in successfully linking up.
Bringing Maths to Life
Because of this, four enthusiastic researchers from different disciplines and institutions have come together and begun a discussion to improve the interface between life sciences and mathematics.
A workshop entitled ‘Bringing Maths to Life’ (BMTL - http://www.bmtl.it) has been developed from this to establish connections between the two fields and, indeed, to pinpoint needs, broaden views, exchange ideas, and share knowledge.
Participants of the past two editions of the BMTL workshop discussed these issues. During the workshops, case studies are discussed to identify gaps and share existing solutions, helping different disciplines in successfully linking up. For the past successful editions of 2014 and 2015, the meeting attracted more than 100 attendees, half of which had biological backgrounds (e.g. neurobiology, population genetics, cancer disease, environmental studies) and the other half mathematica and physical backgrounds applied to biological problems. With a list of confirmed speakers coming from leading European universities, the workshop is now approaching its third edition.
Addressing key challenges
Also this year, BMTL provides an occasion for biologists and mathematicians to join forces in addressing key areas in biology that face demanding mathematical challenges.
The workshop, as a mélange of different fields, will consist of keynote lectures and selected contributions for open discussion to present and confront the most updated results at the interface of mathematics and biology. The workshop is structured in three sessions based on main models components:
- Data: the acquisition, pre-processing and storage of different -omics datasets. The goal of this session is to discuss effective ways of acquiring, processing, and storing data as a starting point for any kind of analysis. Two large-scale projects will be presented within this session. The first project, SardiNIA, recruited more than 1.5 million Sardinians across the island to gather enough cases and controls to investigate genetic factors for a wide range of conditions and diseases (https://sardinia.nia.nih.gov/). The second, MetaSUB (Metagenomics & Metadesign of Subways & Urban Biomes), includes scientists tracking the microbes in city subways to describe their diffusion on an interactive map (http://metasub.org/);
- Information: data analysis, novel -omics technologies, and the application of deep learning to different -omics datasets. The integration of experimental data prior to their analysis requires full understanding of the algorithms that need to be used in order to ensure a correct application in answering biological questions. Case studies of this session are two examples of metagenomics analyses. The first is the analysis of data collected during the Tara Oceans expedition, including samples from 210 stations across the world’s oceans (http://taraexpeditions-it.blogspot.it/). The project is deciphering how the most complex organisms evolved from primordial bacteria, and in the future it will tell us about the fate of the myriad organisms that are present today. The second concerns the analysis of the human gut microbiome; and
- Knowledge: integration of different -omics data and system biology of -omics data. Methods for the integrative analysis of multi-omics data are required to draw a more complete and accurate picture of the dynamics of molecular systems. Unveiling the interactions between diverse types of data allows full exploitation of their information. The keynote lectures of this session will show the integration of genomic, biochemical and metabolic data under comprehensive mathematical models.
2017 BMLT workshop
The 2017 Bringing Maths to Life workshop, held from 7-9 June in Naples, Italy, in the magnificent Capitolo Hall of St Domenico Maggiore Convent - one of the most important spaces created during the renovation started by the Prior Ruffo (17th Century) - is being organised by Vincenza Colonna (Institute of Genetics and Biophysics), Mario Guarracino (High Performance Computing and Networking Institute), Alessandra Rogato (Institute of Bioscience and BioResources), and Valeria Zazzu (formerly Institute of Genetics and Biophysics) of the Italian National Research Council. The initiative is supported by the Italian National Research Council.
Confirmed speakers include:
- Dr Valeria D’Argenio, University of Naples Federico II, Italy;
- Professor Antti Honkela, University of Helsinki, Finland;
- Dr Daniele Iudicone, Zoological Station of Naples A. Dohrn, Italy;
- Dr Carlo Sidore, Institute of Genetic and Biomedical Research - CNR, Italy;
- Professor Klas I Udekwu, The Wenner-Gren Institute Stockholm University, Sweden;
- Professor Hans Westerhoff, University of Amsterdam, the Netherlands.