Important dates
- Deadline for applications: early registration: September 23, 2017; on-line registration: October 8, 2017
- Register through the Application form even if you register for the Workshop
- Priority will be given to workshop participants on a first-come/first-served policy. For the participants ONLY to the tutorials, those with an adequate profile will be accepted immediately, especially if they come from other countries (to allow them to find reasonably cheap flight tickets)
- Course date: 18-19 October 2017
Venue
Istituto di Calcolo e Reti ad Alte Prestazioni (ICAR-CNR) of the Italian National Research Council in Palermo, Via Ugo La Malfa, 153.
Fee
No fee.
Speakers
- Luana Licata – Bioinformatics and Computational Biology Unit – Molecular Genetics Laboratory – Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy
- Alberto Calderone – Bioinformatics and Computational Biology Unit – Molecular Genetics Laboratory – Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy
- Inna Kuperstein – Computational Systems Biology of Cancer group, Institut Curie, Paris, France.
Organisers
- Allegra Via (ELIXIR-IIB Training Coordinator, CNR, Italy)
- Luana Licata – University of Rome Tor Vergata, Rome, Italy
- Alberto Calderone – University of Rome Tor Vergata, Rome, Italy
- Inna Kuperstein – Institut Curie, Paris, France.
Learning objectives
Course participants will be introduced to the fields of protein-protein interactions, biochemical reactions and causal interactions. During the course participants will be exposed to the literature curation principles and methods. In addition, there will be a session dedicated to common standards and ontologies adopted to formally describe data retrieved from the literature. A large number of molecular interaction resources and methodologies to analyze them will be introduced during hand-on sessions.
Participants will get a general understanding of network construction, data analysis and modelling in bio-medical research. In particular, participants will be involved in hands-on session where they will be asked to analyse a dataset in the context of network analysis and modelling. Attendees will develop an understanding not only on static networks but also on discrete and continuous dynamical networks and how to simulate basic systems in order to derive meaningful information related to cancer.
Target audience
PhD students, postDoc and PIs in Life Sciences, Biomedicine and Bioinformatics with little or no knowledge of network biology tools, who are interested in learning how to apply such tools in their research.
Learning objectives
Participants will gain an understanding of:
- protein interaction, biochemical reactions networks and pathway resources
- tools and standards for literature curation and network construction
- methods of network-based data analysis
- different approaches of mathematical modeling of networks
They will also learn:
- how to perform biological network reconstruction, visualization, and analysis
- how to integrate and visualize multi -omics data
- how to perform pathways enrichment
- applications in bio-medical research
Course prerequisites
Knowledge of the following concepts:
- Proteins, Protein-protein interactions, Pathways, Signaling data, Basic computer skills.
Programme
18 October 2017
Afternoon session: 14.30-18.00
Introduction lecture (Licata L.) (15 min)
An introduction lecture on networks, data types and how to analyze omics data.
Session 1: Protein interaction networks and pathway resources
This session will present the state of art of the available resources in the field of molecular interaction networks, such as IMEx resource, SIGNOR and Reactome. Standard data formats, data coverage, sources of information, annotation rules and cross-citations of different sources will be discussed in details.
IMEx resources (20 min) (Licata L.)
SIGNOR (20 min) (Licata L.)
Reactome (20 min) ( Licata L.)
Coffee break
Introduction to Biological networks and Modelling (A. Calderone)
Practical: How and where to collect data to build networks (A. Calderone, Licata L., backed up by Kuperstein I.)
19 October 2017
Morning session: 9.00-13.00
Session 2: Analyzing biological networks to understand human disease
Modelling biological system: static, discrete and continuous (A. Calderone) (30 min)
Practical: Static Networks and Boolean Networks (Cytoscape and GINsim) (A. Calderone) (1.30h)
Coffee break
Session 3: From network construction to data analysis and interpretation in cancer
The purpose of this session is to demonstrate how biological networks can be used in cancer research. The session will start with a short introduction to the main principles of knowledge formalization in a form of network, an example of ACSN as cancer signaling encyclopedia; RECON2 as metabolic pathways resource. The major tools for network manipulation (BiNoM), navigation and data visualization (NaviCell, NaviCom) will be introduced and pathway enrichment rationale will be explained.
Tools and standards for network construction. (Kuperstein I.) (20 min)
Practical: Network construction using standards: small example of texts from different papers on signalling that have to be represent in a form of network in CellDesigner (30 min)
Afternoon session: 14.00-17.30
ACSN as cancer signaling encyclopedia (Kuperstein I.) (20 min)
RECON2 as metabolic pathways resource (Kuperstein I.) (20 min)
NaviCell, NaviCom (Kuperstein I.) (20 min)
Practical 2: Data visualization and analysis in the context of network (ACSN and RECON2): perform enrichment test in NaviCell, visualize multi-level omic data, compare samples, groups, retrieve deregulated processes (Kuperstein I.) (30 min)
Coffee break
Tools for network manipulation (BiNoM) (Kuperstein I.) (20 min)
Practical: Structural analysis of network in BiNoM: perform path analysis, model reduction, network of modules, network merging using small example network. (Kuperstein I.) (30 min)
Closing lecture: Networks applications in cancer medicine (Kuperstein I.) (20 min)
