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Tutorials

The following information is still subject to change.

Registration
Attendance to tutorials for workshop participants is free, but subject to the limitations listed below. Workshop participants must specify their interest for one or more tutorials in the workshop registration form.
In order to register for the tutorial ONLY, you must send an email to nettab.workshops@gmail.com.
Please note that for some tutorials a limited number of attendees will be accepted. Priority will be given to workshop participants on a first-come/first-served policy.

List of tutorials

Tutorial 1, Monday October 16, 2017, 10:00 – 12:30
An introductory tour on Big Data, Big Data technologies, and Big Data applications in Biology and Medicine
Simona Rombo, University of Palermo, Italy

Tutorial 2, Monday October 16, 2017, 10:00 – 12:30
Biological network-based analysis of "-omics" for precision medicine: overview, interaction databases and network diffusion approaches
Ettore Mosca, Institute of Biomedical Technologies / CNR, Segrate (MI), Italy
Tutorial offered by CNR InterOmics Flagship project

Tutorial 3, Wednesday October 18, 15:00 – Thursday October 19, 17:00
Biological Networks: data analysis, visualisation and medical application (provisional title)
Alberto Calderone, ELIXIR-IIB, Italy
Inna Kuperstein, Institut Curie, Paris, France
Luana Licata, ELIXIR-IIB, Italy
Tutorial offered by ELIXIR-IIB, the Italian ELIXIR node.


Tutorial 1, Monday October 16, 2017, 10:00 – 12:30

Simona Rombo,
University of Palermo, Italy

Simona E. Rombo is Assistant Professor at the Department of Mathematics and Computer Science (DMI) of the University of Palermo (Palermo, Italy) since September 2012. Her main research activities focus on Bioinformatics, Algorithms and Data Structures, Data Mining. She co-authored more than 50 scientific publications appearing in established journals and conferences proceedings in these fields. In particular, she worked on local/global alignment and querying of biological networks, clustering of protein-protein interaction networks, analysis of biological sequences and 2D arrays, analysis and management of biological big data. She contributed to develop and/or coordinated the development of several software tools related to these topics. She serves as a member of the Program Committee for several international conferences (e.g., GECCO, EvoBio, Bioinformatics) and she is on the Editorial Board of Journal of Big Data, The Open Bioinformatics Journal and others. She was invited lecturer and/or visiting scientist at several prestigious institutes, such as Oxford University (Oxford, UK), National Institute of Health (Bethesda, USA), College of Computing of the Georgia Institute of Technology (Atlanta, USA), Purdue University (West Lafayette, USA). She contributed with her research to many national and international research grants.

An introductory tour on Big Data, Big Data technologies, and Big Data applications in Biology and Medicine
In this tutorial we aim at providing an overview on the Big Data technologies, by specifying some technical aspects and by illustrating how these technologies may be applied in the bioinformatics/biomedical context.
In particular, the first part of the tutorial will focus on introducing the audience to the notion of "Big Data". Then the Map-Reduce paradigm will be explained, by also discussing how it has been implemented on the Apache Hadoop and Spark frameworks. Moreover, the two frameworks will be compared in terms of their advantages and drawbacks, by explaining when each of them is more suitable to be applied than the other one.
In the second part of the tutorial, it will be explained why the relational model cannot be applied for database design in the Big Data era, and the notion of NoSQL databases will be illustrated as well as some of the most famous examples, such as Cassandra, MongoDB, HBase, etc.. Finally, some applications of Big Data technologies in the context of Biology and Medicine will be showed.


Tutorial 2, Monday October 16, 2017, 10:00 – 12:30
Tutorial offered by CNR InterOmics Flagship project

Ettore Mosca,
Institute of Biomedical Technologies / CNR, Milan, Italy

Ettore Mosca is a permanent researcher at the Institute of Biomedical Technologies of the National Research Council of Italy since March 2014. He received the BS in Molecular Biotechnologies, MS in Bioinformatics and PhD in Computer Science from the University of Milan-Bicocca. His main research activities focus on "-omics" data analysis and biological networks.
In particular, he worked on the analysis of different types of "-omics" (exome sequencing, SNP arrays, gene expression microarrays, RNA-seq, small RNA-seq and protein expression data), biological network-based and pathway-based methods, multi-omics data integration, modeling of biological pathways as dynamical systems, implementation of software packages.
He spent a few months as visiting scientist at the University of Edinburgh and at the University of Cambridge. He has been involved in several Italian and European projects (BIOINFOGRID, EGEE, NET2DRUG, MIMOMICS). He trained students of Biotechnologies, Biomedical Engineering and Applied Physics in collaboration with Italian Universities. He is a full member of the Bioinformatics Italian Society (BITS) and National Association of Italian Biotechnologists (ANBI). He is the author of more than 30 papers in peer-reviewed international scientific journals and several speeches at scientific conferences.

Biological network-based analysis of "-omics" for precision medicine: overview, interaction databases and network diffusion approaches
This tutorial aims at illustrating how the known molecular interactions can be useful in the interpretation of "-omics" data for precision medicine, with a main focus on data referable to genes.
In the first part, we will introduce broad objectives and principles of biological network-based analyses of "-omics" data. Then, we will overview the state-of-the art of current datasets from which networks can be defined, their completeness in relation to the coverage of high-throughput technologies and the issues in mapping "-omics" data to biological networks.
In the second part, we will focus on network diffusion-based approaches and illustrate how the principles behind this class of methods have been recently applied to several problems, including patient stratification and gene module extraction.
Throughout the tutorial, we will underline benefits, limitations and open issues in the field of network-based analysis, including also software availability and computational cost.


Tutorial 3, Wednesday October 18, 15:00 – Thursday October 19, 17:00
Tutorial offered by ELIXIR-IIB, the Italian ELIXIR node.

Alberto Calderone,
ELIXIR-IIB, Italy
Inna Kuperstein,
Institut Curie, Paris, France
Luana Licata,
ELIXIR-IIB, Italy

Biological Networks: data analysis, visualisation and medical application (provisional title)