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InBiMedDoctoralCourse 2013

Contents

UNIMIB Joint Informatics, Biology and Medicine Short Doctoral Course 2013


Two short doctoral courses on Bioinformatics and Systems Biology topics will be held in September 2013 at the Università degli Studi di Milano Bicocca, organized by: BIMIB DISCo and BtBs (Schoo of Sciences) and DIMET (School of Medicine).

The two course will be held at the Department of Informatics, Systems and Communication, U14 Viale Sarca 336, 20126, Milan (MI) Italy. Directions about how to reach the venue can be found here (en) and here (it).


September 9 and 10, 2013 - Gene Lists, Networks and their Enrichment Analysis

Dr. Daniele Merico, Molecular and Cellular Biology Informatics Core Manager, The Centre for Applied Genomics (TCAG), and the Hospital for Sick Children, Toronto, Canada.


Dates

September 9 and 10, 2013


Venue

The course will be held in Aula Seminari, First Floor, Dipartimento di Informatica Sistemistica e Comunicazione, U14 Viale Sarca 336, 20126, Milan (MI) Italy.


Target audience

This course is geared towards biologists working with Omics data (e.g. gene expression, protein expression, molecular interactions, large-scale genetic screens and other omics data) from human and model Eukaryotic organisms who are interested in interpreting large gene lists resulting from their experiments. Concepts will be applicable to omics data from non-eukaryotic organisms, but software and demonstrations will not cover them.

Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).


Course Objective

Many research programs often slow or stall after generating a gene list. The course covers the bioinformatics concepts and tools available for annotating and determining functional enrichment of a gene list and analyzing networks. The workshop is focused on the principles and concepts required for analyzing and conducting pathway analysis on a gene list from any organism, although focus will be on human and model Eukaryotic organisms. Specifically, we will focus on 1) getting more information about a gene list, 2) finding out how a set of genes is connected, 3) discovering what's enriched in a gene list (and using it for hypothesis generation) and 4) extending or refining a gene list. An analysis flow chart will be developed throughout the course.


Course Prerequisites, Material and Requirements

Important!

  • Students are required to come with their own laptop and have Cytoscape already installed [1].
  • It is highly recommended that students follow the course with data they are interested in analyzing. E.g., if a student is looking at some particular set of gene-expression data in her/his research activity it is highly recommended to have such data at hand during the course.

Course Outline and Preliminary Timetable

Day 1, September 9th - Gene Lists

  • 8:30 - 9:30 Registration and WiFi credential distribution.
  • 9:30 Welcome address.
  • 9:45 Module 1: Brief introduction to gene lists
    • Ice breaking session for participants (to promote networking)
    • Gene list analysis overview presenting a workflow of concepts and tools from gene list to pathway analysis
    • Where do gene lists come from?
    • Working with gene function information o Definition, sources (e.g. Gene Ontology) and issues (e.g. quality of annotation transfer, evidence codes, working with multi-functional genes)
    • Overview of pathway analysis
  • Laboratory: Practical aspects of working with gene lists
    • Workflow of tools and steps
    • Practical: review of Cytoscape tutorial
  • 10:30 - 11:00 Break
  • 11:00 Module 2: Finding over-represented pathways in gene lists
    • Over-representation analysis (ORA)
    • Use of DAVID tool Statistics for detecting over-representation e.g. hypergeometric test, GSEA
    • Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR
    • Filtering Gene Ontology e.g. using evidence codes
    • Text based enrichment analysis (Wyeth Wasserman)
  • 12:30 - 14:00 Lunch
  • 14:00 Laboratory: Performing over-representation analysis
    • Workflow of tools and steps
    • Gene Set Enrichment Analysis (GSEA) and Enrichment Maps software tool
    • DAVID tool for over-representation analysis
    • Practical: Running gene enrichment tools on your gene list
  • 15:30 - 16:00 Break
  • 16:00 Module 3: Pathway and Network Analysis
    • Overview of pathway and network analysis
    • Basic network concepts
    • Types of pathway and network information

Day 2, September 10th - Networks

  • 9:30 Module 4: Network Visualization
    • Introduction to network visualization
    • Visualizing omics data on a network or pathway
  • 10:30 - 11:00 Break
  • 11:00 Laboratory: Tutorials on Cytoscape
    • Workflow of tools and steps
    • Tutorial: Cytoscape and selected plugins
  • 12:30 - 14:00 Lunch
  • 14:00 Module 5: Gene Function Prediction
    • Functional association networks and gene function prediction
    • Functional relationships, similarity space Homology based prediction Guilt-by-association
  • 15:30 - 16:00 Break
  • 16:00 Laboratory
    • Workflow of tools and steps
    • Practical: Using GeneMANIA to assess gene and gene list function
  • (TBD) Module 6: Cytoscape plugin development in Java
    • Overview and resources


September 23 and 24, 2013 - Modeling and Simulation of Cellular Systems

Prof. Jim Schaff, The Richard D. Berlin Center for Cell Analysis and Modeling (CCAM), University of Connecticut Health Center, Farmington, CT, USA


Dates

September 23 and 24, 2013


Venue

The course will be held in Room T024 (Ground Floor), U14, Dipartimento di Informatica Sistemistica e Comunicazione, Viale Sarca 336, 20126, Milan (MI) Italy.


Target audience

This workshop is geared towards biologists working with Omics data (e.g. gene expression, protein expression, molecular interactions, large-scale genetic screens and other omics data) from human and model Eukaryotic organisms who are interested in learning how to employ sophisticate modeling and simulation tools in order to incorporate these tools and techniques in their Systems Biology research activities.

Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).


Course Objective

The simulation of biological systems is one of the most foundational parts of any Systems Biology integrative approaches to biomedical research. There are many systems available for the development of biological simulations based on different underlying paradigms. The goal of this short course is to acquaint users with the VCell system, one of the prominent systems for biological simulations. A few different biological models will be presented alongside the various possibilities offered by VCell pertaining their simulations. ´┐╝ A link to VCell is listed below (pre-installation on your system is advised): VCell tool

Timetable

Monday 23, 2013 at 9:45
Tuesday 24, 2013 at 9:45