Session 1: Presentation 1

Jane Zheng, University Ulster

Towards multi scale computing in systems medicine

In this talk, Prof. Zheng will introduce the goal, mission and tasks in multiscale computing working group (WG4) in the OpenMultiMed COST ACTION. Challenges and opportunities of multiscale computing in systems medicine will be discussed. Examples of multiplex networks approaches to multiscale computing in systems medicine will be presented. The presentation will conclude with an open invitation to a survey of multiscale computing.

Biography: Huiru (Jane) Zheng is a Professor of Computer Science with School of Computing and Mathematics, a full member of Computer Science Research Institute and a Fellow of the UK Higher Education Academy. She was awarded a PhD in Computer Science (Data Mining) in 2003 and a Postgraduate Certificate in Teaching in Higher Education in 2005 from Ulster University. Within her broad interests in data mining, data integration, machine learning and healthcare decision support, Prof. Zheng has a particular research interest and expertise in integrative data analysis, complex network analysis, pattern recognition, assistive technology to support health and wellbeing, and behavior analysis. She has a successful track record of winning research funding as a Principal Investigator and has been a grant holder of research projects funded by EPSRC, TSB, DEL, NHS, Invest NI and European Commission including SMART Self Management, NOCTURNAL, CLARCH COPD Self Management, Self Management Platform for Connected Health, CardioWorkBench, SenseCare(H2020), MetaPlat(H2020) and OpenMultiMed (COST Action). The products of her research have been reflected in her over 200 peer reviewed journal and conference publications. Prof. Zheng is a Senior Member of IEEE. She serves on the editorial board of several international journals and serves as co-chairs and program committees of a number of international conferences.

Session 1: Presentation 2

Peter V Coveney, University College London

Biomedical high performance computing within and outside clouds

CompBioMed is concerned with Computational Biomedicine using techniques that span time and length scales from the macro, through the meso- to the nano- and microscales. In pursuing these research interests, we routinely make use of combinations of globally distributed petascale computing resources together with high performance visualisation, and high bandwidth, low latency networks. To fully exploit the vast range and scale of resources available, we have had to develop mechanisms to automate and manage the execution of complex chains of high performance simulations through workflow tools. In addition, our methods both rely on and produce vast amounts of data, which need to be moved carefully and rapidly. Our work —including drug discovery and selection as well as blood flow, in both of which we work with industry and healthcare providers—requires careful attention to verification and validation, as well as management of confidential data. Speed to solution and quality of service are of paramount importance. As a consequence, we have become increasingly interested in what cloud infrastructures operating at scale can offer to support our research.

Biography: Prof Peter V. Coveney holds a chair in Physical Chemistry, is an Honorary Professor in Computer Science at University College London (UCL) and is Professor Adjunct at Yale University School of Medicine (USA). He is Director of the Centre for Computational Science (CCS) at UCL. Coveney is active in a broad area of interdisciplinary research including condensed matter physics and chemistry, materials science, as well as life and medical sciences in all of which high performance computing plays a major role. He has published more than 400 scientific papers and co-authored two best-selling books (The Arrow of Time and Frontiers of Complexity, both with Roger Highfield) and is lead author of the first textbook on Computational Biomedicine (Oxford University Press, 2014). Coveney is a founding member of the UK Government’s E-Initiative Leadership Council and a Medical Academy Nominated Expert to the UK Prime Minister’s Council for Science and Technology on Data, Algorithms and Modelling which has led to the creation of the London based Turing Institute.

Session 1: Presentation 3

Johannes Schmidt, University Vienna

Bridging the gap between clinician scientists, basic researchers and computational scientists

Most of the life-threatening diseases of our civilization are caused and influenced by multiple factors, which build complex networks and feedback circuits. Moreover, the diseases themselves and their comorbidities exhibit multifaceted interrelations and dependencies thereby forming disease networks. Systems medicine aims at elucidating these nets and in particular their crucial nodes to identify potential points of therapeutic interference, which can be targeted
Synergistically. This requires new strategies and above all an interdisciplinary approach
linking specialists from different fields in a cooperative manner to identify the biologically relevant principles, to collect “big data” at molecular, cellular, pre-clinical and clinical levels and to apply
computational methods that are able to depict “patterns in the noise” of biological variation. For that purpose, it is essential to bridge the language gap between the various disciplines and to initiate a vivid and fruitful communication. Our experience is that biologists, biochemists or clinician scientists need computational tools that are rather easy to use, with a steep learning curve and a fast pay-off in terms of new results that can also generate novel intriguing hypotheses, so that they
can focus on the biological or medical aspects. This can be provided by commercial tools such as Ingenuity Pathway Analysis, Metacore or Genevestigator, but also by free platforms like GSEA (Gene Set Enrichment Analysis) or Genemania and network analysis or visualization tools such as CytoScape. A challenge for the future will be to define standards and primary instruments in the diversity of computational methods, which are equally accepted by the different communities so that the language gap can be bridged efficiently. Furthermore, it will be necessary to establish new
tools for visualization and analysis of complex multifactorial data, with an intuitive user interface, allowing for instance medical doctors to make treatment decisions based on rich molecular, cellular and clinical data. Prototypes for that are already available but need further refinement to pave the way for precision systems medicine.

Biography: J. Schmid received a training in biotechnology, biochemistry and molecular biology at the University of Natural Resources and Life Sciences in Vienna, Austria and focused on medical aspects already early in his career for the Master thesis. He did his PhD at the medical
faculty of the Univ. Vienna in a cell biology topic and had the first postdoctoral fellowship at the Novartis Research Institute. After that he joined the Vascular Biology Institute of the Medical University Vienna focusing on aspects of inflammation, cancer and thrombosis. His
international experiences comprise fellowships at the Research Inst. of Scripps Clinic, USA, Carnegie Mellon Univ., Pittsburgh, USA, EMBL Heidelberg and a sabbatical at the Immunobiology Dept. of Yale Univ. Medical School. He was cofounder of a new Ludwig Boltzmann Inst. of
Cancer Research and is currently speaker of a special research program (SFB-F54, Inflammation and Thrombosis, http://inthro.meduniwien.ac.at) of the Austrian Science Fund, heading a network of 10 pre-clinical and clinical research groups. His research interests focus on cooperativity
of signaling processes in inflammation, cancer and thrombotic diseases such as atherosclerosis or myocardial infarction. His group uses transgenic mouse models, as well as analyses of patient material with high-end microscopy. Furthermore, novel strategies of quantitative multiparameter microscopy and tissue cytometry are applied, as well as systems biology approaches. (personal website: http://www.meduniwien.ac.at/user/johannes.schmid/)

Session 1: Presentation 4

Mariano Vazquez, Barcelona Supercomputing Centre

HPC-based tools for multi scale simulations in biomedicine

In this talk we will describe the research achievements and future path of ComBioMed center of excellence related to multi-scale simulations in biomedical research. We will describe three different research exemplars: cardiovascular, molecular and neuro-musculo-skeletal, through different test cases. After a general description of all the exemplars, this talk will be specially focused on the cardiovascular CompBioMed research lines.

Session 2: Presentation 1

Derek Groen, Brunel University London

Multiscale computing and human brain blood flow simulation

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. I will present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from laptops to petascale supercomputers, including combinations of these. As part of my talk, I will reflect on a range of multiscale applications, with a particular focus on cerebrovascular bloodflow scenarios, where we combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1–10% of the total execution time.

Biography: Derek Groen is a Lecturer in Simulation and Modelling at Brunel University and a Visiting Lecturer at the Centre for Computational Science at University College London. Derek completed a PhD in Computational Astrophysics at the UvA and Leiden University in 2010, and worked as a post-doctoral researcher at UCL on multiscale bloodflow and materials modelling. He is PI on the PiTFLOW project, which aims to create a parallel-in-time implementation of the HemeLB bloodflow solver, and currently participates in the ComPat H2020 project and the OpenMultiMed COST initiative. Derek has published more than 20 peer-reviewed journal papers in diverse venues such as IEEE Computer, IEEE CiSE, Advanced Materials, Phil. Trans. R. Soc. A., Physics Review E., the Astrophysical Journal and eLife. In addition, Derek won the ARCHER Early Career Impact Award in 2015. Lastly, Derek has organized a range of Science Hackathons to efficiently establish new interdisciplinary collaborations, including one at CERN in Geneva in 2017.

Session 2: Presentation 2

Wil Mayers, Alces Flight

Agile HPC for bioinformatics in the cloud

Bioinformaticians are turning to cloud as a means to tackle ‘office hours HPC projects.’ These projects stand away from persistent work, allowing researchers the ability to launch as and when needed, leaving only minimal infrastructure in place for the times when the project is not live. Alces Flight, in collaboration with St. Mary’s Hospital, Manchester, are working to create pre-configured HPC clusters complete with scheduler, applications and a pipeline in place ready to launch at a click of the button. This talk outlines the work Alces Flight and St. Mary’s are doing to simplify access to resources and create environments for their researchers to achieve their goals in ways originally thought only possible through hardware.

Biography: Wil Mayers is Technical Director at Alces Flight, and has 20 years experience in high-performance compute and storage systems having built large environments for UK government, University and commercial customers. He has worked for both corporates and SMEs, helping customers to optimise their scientific computing workflows across many different domains including engineering, bioinformatics, physics, media and finance. Wil holds a degree in Computer Science, Biochemistry and Artificial Intelligence from Durham University in the UK. In 2010 Wil joined Alces Software, a software development and system integration company based in the UK. At Alces, Wil is responsible for building and delivering solutions for customers utilising wide a range of open-source and custom-developed software. Armed with its team of software developers Alces are rewriting the rule book on high-performance computing making it more approachable, scalable and accessible than ever before on platforms like AWS.

Session 2: Presentation 3

Jan Baumbach, University of Southern Denmark

Systems biomedicine – Network-enhanced disease profiling in the big data era

Recent advances in omics technology allow for profiling the expression of all kinds of biological entities (genes, proteins, metabolites, miRNAs,…) on a large scale and in spatiotemporal resolution. This massive data, if analyzed in isolation, has often limited explanatory power when investigating complex diseases, such as cancer. So-called network enrichment approaches attempt to de-isolate biomolecular expression patterns from the metabolic and signaling networks controlling them. I will introduce the first multi-omics network enricher KeyPathwayMiner 5.0 (keypathwayminer.compbio.sdu.dk) and its application to several different omics profiles and complex diseases. I will also present the first time-series network enricher TiCoNE (ticone.compbio.sdu.dk) and how it can be used to unravel temporal systems biology response patterns of human lung cells after Influenza vs. Rhino virus infection. Finally, we will illuminate the power of network-based biomarkers for boosting computational breast cancer subtyping using massive gene expression and DNA methylation data sets (pathclass.compbio.sdu.dk).

Biography: https://www.baumbachlab.net/head

Introduction

Harald Schmidt, Maastricht University

Biography: Harald H. W. Schmidt is a Professor in Pharmacology and Chairman of the Department of Pharmacology and Personalised Medicine. With a double degree in Medicine and Pharmacy Harald Schmidt has a passion for innovative drug discovery and therapy. As an ERC Advanced Investigator, Europe’s most prestigious research award, he performs high risk/high potential benefit research in areas of major medical need. His multi-national leadership experience in Academia and Industry has led to excellent scientific achievements (Hirsch-index 77) with high socio-economic impact such as patents and biotech spin-offs. He is a reputed drug expert, successful entrepreneur, dedicated teacher and team leader.