Courses

Courses The training activities are held both in Milan and Naples. Check out the corresponding schedules:

Teachers: Paola Galimberti (UNIMI) & Arnaud Ceol (IEO). Dates: 22-24-30 November 2022; 1 December 2022

Aim of the course: the course will provide useful tools for researchers to respond to the new paradigm in handling and sharing research results, from open access publications to research data management. A variety of training methodologies will be used, such as plenary sessions, hands-on sessions, the completion of assignments and complementary e-learning materials.

The course is organized in the context of the ENABLECARES European project (https://enablecares.eu/).

Timetable
9.30-11.00
Lesson Argument
  1.  Introduction
  2. Definitions
  3. The different colors of open access: examples
  4. Editorial workflow
Lesson Location
Meeting Room 1+2
Timetable
11.15-12.45
Lesson Argument
  1.  Open science policies at the University of Milan
  2. Focus on the available resources:  AIR (Research Institutional Archive)
  3. Funders’ requirement
Lesson Location
Meeting Room 1+2
Timetable
9.30-11.00
Lesson Argument
  1. A deep view: Predatory journals, ethics aspects, evaluation, management of rights and licences etc
  2. Tools: Sherpa; DOAJ, CORE; Unpaywall etc.
Lesson Location
Meeting Room 1+2
Timetable
11.15-12.45
Lesson Argument
  1. Meeting with a researcher (Federico Zambelli, prof. @UNIMI and Technical Coordinator @ EliXir IT)
Lesson Location
Meeting Room 1+2
Timetable
9.00-11.00
Lesson Argument
  1. Aim of the Data management session
  2. Introduction: The Data Management Plan (DMP)
  3. Data management: who is involved?
Lesson Location
IFOM - Conference Room
Timetable
11.15-12-45
Lesson Argument
  1. Presentation of a DMP (Dorina Dobi, phd @UNIMI)
  2. Analysis of a DPM, focus and relevant sections
  3. Data
Lesson Location
IFOM - Conference Room
Timetable
9.00-11.00
Lesson Argument
  1. Open science & FAIR data
  2. Data storage
  3. Documenting your data
Lesson Location
Meeting Room 1+2
Timetable
11.15-12.45
Lesson Argument
  1. Data management good practices
  2. Research ethics and data protection
  3. Writing a Data Management Plan, Conclusions
Lesson Location
Meeting Room 1+2

Teacher: M. Fumagalli (IEO) - Dates: 19 December 2022; 10-17-24- 31 January 2023; 7-14 February 2023

Aim of the course: the course seeks to empower junior scientists by giving them the tools to explore their potential as entrepreneurs in life sciences and their interest in pursuing careers in business or innovation management, thereby increasing their employability in academia or beyond.

Location: Meeting Room 1-2, IFOM

The course is organized in the context of the ENABLECARES European project (https://enablecares.eu/).

Timetable
9.00-12.00
Lesson Argument

Introductive lesson – Welcome. Technology transfer in the biomedical sector: an overview

Teachers

Marzia Fumagalli

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
9.00-15.30 with lunch break
Lesson Argument

Module 0 – Introduction to Entrepreneurship

9.00 - 10.00 Lecture
Coffee Break
10.15 - 12.15 Assignment  & time for team work
Lunch together
13.30 - 15.30 Workshop & discussion (groups presenting the assignment)

Teachers

Marzia Fumagalli

Affiliations

IEO

Lesson Location
Meeting Room 1+2
Timetable
9.00-15.30 with lunch break
Lesson Argument

Module 1 – Basics of Innovation 

9.00 - 10.00 Lecture
Coffee Break
10.15 - 12.15 Assignment  & time for team work
Lunch together
13.30 - 15.30 Workshop & discussion (groups presenting the assignment)

Teachers

Tiago Oliveira Botelho

Affiliations

IRB - Barcelona

Lesson Location
Meeting Room 1+2
Timetable
9.00-15.30 with lunch break
Lesson Argument

Module 2 – Product Development: customer value proposition, analysis and strategy

9.00 - 10.00 Lecture
Coffee Break
10.15 - 12.15 Assignment  & time for team work
Lunch together
13.30 - 15.30 Workshop & discussion (groups presenting the assignment)

Teachers

Tiago Oliveira Botelho

Affiliations

IRB - Barcelona

Lesson Location
Meeting Room 1+2
Timetable
9.00-15.30 with lunch break
Lesson Argument

Module 3 – Intellectual Property.Management & Strategy 

9.00 - 10.00 Lecture
Coffee Break
10.15 - 12.15 Assignment  & time for team work
Lunch together
13.30 - 15.30 Workshop & discussion (groups presenting the assignment)

Teachers

Marzia Fumagalli

Affiliations

IEO

Lesson Location
Meeting Room 1+2
Timetable
9.00-15.30 with lunch break
Lesson Argument

Module 4 – Organisation. Team development, Key partners, Funding & Financials

9.00 - 10.00 Lecture
Coffee Break
10.15 - 12.15 Assignment  & time for team work
Lunch together
13.30 - 15.30 Workshop & discussion (groups presenting the assignment)

Teachers

Piergiorgio Mastroberardino

Affiliations

IFOM

Lesson Location
Meeting Room 1+2
Timetable
9.00-15.30 with lunch break
Lesson Argument

Module 5 - Pitch & Reflection. Case Studies/Real World

9.00 - 10.00 Lecture
Coffee Break
10.15 - 12.15 Assignment  & time for team work
Lunch together
13.30 - 15.30 Workshop & discussion (groups presenting the assignment)

Teachers

Marzia Fumagalli & Piergiorgio Mastroberardino

Affiliations

-

Lesson Location
Meeting Room 1+2

Teacher: Rosella Visintin - Dates: 9-11 January 2023

Format: Lectures and practical activities

Location: Human Technopole, Milan

Timetable
9.30-10.00
Lesson Argument

Welcome

Timetable
10.00-11.00
Lesson Argument

Critical reading of the literature

Timetable
11.00-12.15
Lesson Argument

How to do a Journal club

Timetable
9.30-10.30
Lesson Argument

Experimental design - From hypothesis to conclusions

Timetable
10.30-11.30
Lesson Argument

Case Study

Timetable
11.30-12.30
Lesson Argument

Gender diversity in scientific experiments

Teachers

Susanna Chiocca

Affiliations

IEO

Timetable
9.30-11.30
Lesson Argument

Research integrity module:

  • Shared values in scientific research;
  • Running and recording experiments (labnotebook);
  • Generating and manipulating data (scientific misconduct - falsification; fabrication and plagiarism);
  • Time management
Timetable
11.30-12.30
Lesson Argument

Famous cases of alleged scientific misconduct

Organizers: Ylli Doksani & Marina Mapelli

Dates: 16-19 January 2023

The course aims at providing theoretical knowledge and practical principles on the main forefront strategies used for genome editing and biochemistry.

Timetable
9.00-10.00
Lesson Argument

Expression of coding and non-coding genes in mammalian genome

Teachers

Francesco Nicassio

Affiliations

IIT

Timetable
10.00-11.00
Lesson Argument

Challenges in measuring RNA expression

Teachers

Matteo Marzi

Affiliations

IIT

Timetable
11.00-12.00
Lesson Argument

Working with mammalian genomic DNA

Teachers

Ylli Doksani

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-15.00
Lesson Argument

Visualization of DNA structures in Electron Microscopy

Teachers

Massimo Lopes

Affiliations

UZH

Timetable
15.00-16.00
Lesson Argument

DNA Cloning strategies

Teachers

Chiara Bruckmann

Affiliations

Enthera Pharmaceuticals

Lesson Location
Meeting Room 1+2
Timetable
9.00-10.30
Lesson Argument

CRISPR technology and its applications in drug discovery (streamed online)

Teachers

Danilo Maddalo

Affiliations

Genentech

Timetable
10.30-11.30
Lesson Argument

Fundamentals of gene targeting

Teachers

Stefano Casola

Affiliations

IFOM

Timetable
11.30-12.30
Lesson Argument

Protein expression and purification

Teachers

Marina Mapelli

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
14.00-15.00
Lesson Argument

Biochemical and biophysical protein characterization

Teachers

Sebastiano Pasqualato

Affiliations

Human Technopole

Lesson Location
IFOM - Conference Room
Timetable
9.30-10.30
Lesson Argument

Measuring protein interactions "in vitro"

Teachers

Luigi Scietti

Affiliations

IEO

Timetable
10.30-11.30
Lesson Argument

Measuring protein interactions "in vivo"

Teachers

Sara Sigismund

Affiliations

IEO

Timetable
11.30-12.30
Lesson Argument

Working with Antibodies

Teachers

Simona Polo

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
15.00-16.00
Lesson Argument

Capturing specific protein–DNA interactions in biological systems by ChIP

Teachers

Ivan Dellino

Affiliations

IEO

Timetable
16.00-17.00
Lesson Argument

Protein-DNA interactions involved in DNA repair and DNA replication

Teachers

Vincenzo Costanzo

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
9.30-10.30
Lesson Argument

Principles of Enzymology

Teachers

Leonardo Pollegioni

Affiliations

University of Insubria

Timetable
10.30-11.30
Lesson Argument

Liquid-liquid phase separation

Teachers

Philipp Erdmann

Affiliations

Human Technopole

Timetable
11.30-12.30
Lesson Argument

Protein-RNA interactions

Teachers

Ana Casañal

Affiliations

Human Technopole

Lesson Location
Meeting Room 1+2
Timetable
14.00-17.00
Lesson Argument

Case studies

Lesson Location
Gold and Platinum Room

Organizers: Dario Parazzoli and Nils Gauthier - Dates: 23-25 January 2023

The course will cover all basic microscopy techniques and provide an overview of a broad range of innovative imaging approaches. Each lecture will include an overview of the topic and a presentation of the lecturer’s specific field of interest.

Timetable
9.00-10.00
Lesson Argument

Introduction

Teachers

Dario Parazzoli - Nils Gauthier,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.00-11.00
Lesson Argument

Sample preparation

Teachers

Sara Barozzi,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
11.00-12.30
Lesson Argument

Widefield Microscopy

Teachers

Dario Parazzoli,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-17.00
Lesson Argument

Flow Cytometry/Cell sorting

Teachers

Maria Grazia Totaro (IFOM), Simona Ronzoni (IEO) 

Lesson Location
IFOM - Conference Room
Timetable
9.00-10.00
Lesson Argument

Confocal Microscopy

Teachers

Simona Rodighiero,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
10.00-11.00
Lesson Argument

Sectioning:
- confocal
TIRF

Teachers

Dario Parazzoli,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
11.15-12.30
Lesson Argument

Multiplexing

Teachers

Simona Rodighiero,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
14.00-17.00
Lesson Argument

Big Sample

Teachers

Zeno Lavagnino,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
9.00-10.00
Lesson Argument

Electron Microscopy

Teachers

Alexander Mironov,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.00-12.30
Lesson Argument

Super resolution and Mechanobiology

Teachers

Andrea Ghisleni - Nils Gauthier,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room

Teachers: Riccardo Rossi (INGM), Valeria Ranzani (INGM), Nicola Pesenti

Dates: 30 January - 3 February 2023

Location: INGM

Timetable
9.30-16.30 with lunch break
Lesson Argument

Usable R fundamentals for biologists

 - Developing a scripting attitude: from GUIs to CLIs
 - IDEs, RStudio, packages and good practices
 - Anatomy of a command, standard output/error, batch & interactive mode
 - R data structures, basic operators, coercion, objects, classes
 - Reading data into R objects
 - The Tidyverse. When data are “tidy”?
 - Basic tabular manipulation with dplyr
 - Transformations between wide and long
 - Get quick summarizations with pipes and “group_by"

Teachers

Riccardo Rossi - INGM

Timetable
9.30-16.30 with lunch break
Lesson Argument

The grammar of graphics with ggplot & data visualization

 - The graphical packages of R
 - The generic R graphic devices, plot command, colours
 - Colours in R, R colour brewer and palettes
 - The grammar of graphics
 - The ggplot2 levels and hierarchy
 - Different types of geoms for different types of data (histograms, bar plots, pie charts, density plots, scatter plots, box plots)
 - Piping summarized data into ggplot
 - Special purpose graphics: volcano, heatmap
 - (optional) Other graphical packages

Teachers

Valeria Ranzani - INGM

Timetable
9.30-16.30 with lunch break
Lesson Argument

Fundamentals of descriptive statistics

 - Different kind of data, how to distinguish them
 - Basic descriptive indices
 - How to evaluate data position, variability and symmetry
 - How to interpret data position, variability and symmetry
 - Correlation and covariance
 - Missing data, their patterns and treatment

Teachers

Nicola Pesenti

Timetable
9.30-16.30 with lunch break
Lesson Argument

Bases of statistical inferences

 - Research hypotheses and tests
 - Choosing the most fitting test to answer a question
 - Differences between parametric and non-parametric tests
 - Differences between independent and paired tests
 - What’s in a p-value?
 - (optional) Type I and II errors and power of a test
 - How to choose a test
 - Meaning of parametric/non-parametric and independent/paired tests
 - What’s in a p-value?
 - (optional) Missing data, their patterns and treatment

Teachers

Nicola Pesenti

Timetable
9.30-12.00
Lesson Argument

Wrap up, Q&A session

Teachers: U. Pozzoli, F. Iannelli, M. Cereda

Dates: 6-10 February 2023

Location: IEO

Teorethical lessons and practicals

Timetable
9.30-10.00
Lesson Argument

Course Introduction: description and objectives

Timetable
10.00-12.30
Lesson Argument

Programming Languages: origins, similarities and differences

Timetable
14.30-17.30
Lesson Argument

R basics: language structure, data types, object-oriented programming

Lesson Location
Coral Room
Timetable
9.30-12.30
Lesson Argument

Programming techniques

Timetable
14.30-17.30
Lesson Argument

Data manipulation

Lesson Location
Coral Room
Timetable
9.30-12.30
Lesson Argument

Code writing and performance testing

Timetable
14.30-17.30
Lesson Argument

Bioconductor for genomic & transcriptomic data

Lesson Location
Coral Room
Timetable
9.30-12.30
Lesson Argument

Writing R Extensions

Timetable
14.30-17.30
Lesson Argument

Data Visualization

Lesson Location
Coral Room
Timetable
9.30-12.30
Lesson Argument

Data Communication

Timetable
14.30-15.30
Lesson Argument

Implementing a data analysis pipeline using Bioconductor and R Markdown

Timetable
15.30-17.30
Lesson Argument

Build interactive web app: Shiny

Lesson Location
Coral Room

Organizers: Francesco Ferrari (IFOM) & Martin Schaefer (IEO) - Dates: 13-16 February 2023

Timetable
10.00-12.30
Lesson Argument

Genomics sequence search and alignment

Teachers

Fabio Iannelli,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-16.30
Lesson Argument
  • Mutations calling (including copy number variations and structural variants)
  • Cancer genomics resources and databases (e.g. cancer genome portal, TCGA, ICGC resources and datasets)
Teachers

Fabio Iannelli,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
10.00-11.30
Lesson Argument

Bulk transcriptomic data analysis (RNA-seq - including also expression quantification and splicing)

Teachers

José Davila Velderrain,

Affiliations

 Human Technopole

Lesson Location
Human Technopole - Auditorium
Timetable
13.30-16.30
Lesson Argument

Single cell transcriptomic data analysis

Teachers

José Davila Velderrain,

Affiliations

Human Technopole

Lesson Location
Human Technopole - Auditorium
Timetable
10.00-13.00
Lesson Argument

Bioinformatics data analysis for ChIP-seq and other techniques to study 1D chromatin organization, transcription factors binding sites, epigenomic profiles, chromatin states

Teachers

Francesco Ferrari,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
15.00-16.30
Lesson Argument

Bioinformatics data analysis for Hi-C and other techniques to study 3D chromatin organization

Teachers

Francesco Ferrari,

Affiliations

 IFOM

Lesson Location
IFOM - Conference Room
Timetable
14.00-16.30
Lesson Argument

Computational analysis of large cohorts towards the identification of disease variants (GWAS, polygenic risk scores etc)

Teachers

Nicole Soranzo,

Affiliations

Human Technopole

Lesson Location
ONLINE LECTURE

Organizers: D. Pasini, A. Bachi, T. Bonaldi - Dates: 20-24 February 2023

Timetable
10.00-12.00
Lesson Argument

Journal Club Genomics

Lesson Location
IFOM - Conference Room
Timetable
10.00-12.00
Lesson Argument

Journal Club Genomics

Lesson Location
IFOM - Conference Room
Timetable
9.30-11.00
Lesson Argument

Introduction to MS proteomics

Teachers

Angela Bachi,

Affiliations

IFOM 

Lesson Location
IFOM - Conference Room
Timetable
11.15-12.45
Lesson Argument

Quantitative Proteomics

Teachers

Alessandro Cuomo,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
15.15-16.30
Lesson Argument

Targeted Proteomics

Teachers

Vittoria Matafora,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
16.45-17.45
Lesson Argument

Single Cell proteomics

Teachers

Angela Bachi,

Affiliations

IFOM

Lesson Location
IFOM - Conference Room
Timetable
9.30-11.15
Lesson Argument

Proteomics in clinical research and Drug Discovery + Debriefing on the RT "Clinical Proteomics"

Teachers

Roberta Noberini, Tiziana Bonaldi,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
11.30-13.00
Lesson Argument

Interaction and modification proteomics

Teachers

Tiziana Bonaldi,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
14.00-15.15
Lesson Argument

MALDI imaging for spatial proteomics profiling

Teachers

Andrew Smith,

Affiliations

UNIBicocca

Lesson Location
IFOM - Conference Room
Timetable
15.15-16.30
Lesson Argument

Conformational/structural proteomics: basic principles

Teachers

Andrea Graziadei,

Affiliations

IEO & HT

Lesson Location
IFOM - Conference Room
Timetable
16.30-17.30
Lesson Argument

Working Group (WG) assembly and discussion for project preparation

Lesson Location
IFOM - Conference Room
Timetable
9.30-11.30
Lesson Argument

Data Analysis tutorial

Teachers

Alessandro Cuomo,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
11.30-13.30
Lesson Argument

WG for project preparation

Lesson Location
IFOM - Conference Room
Timetable
15.30-17.30
Lesson Argument

Project presentation by WGs

Lesson Location
IFOM - Conference Room

Organizer: Myriam Alcalay & Ugo Cavallaro IEO Milan

Dates: 27 February - 1 March 2023

The course aims to provide a link between the molecular pathogenesis of cancer, experimental approaches for genetic analysis, and the clinical relevance and applications of cancer genetics in oncology.

Timetable
9.30-10.45
Lesson Argument

Genomics and big data, from science to medicine and back

Teachers

Giovanni Tonon, HSR - Milan

Lesson Location
IFOM - Conference Room
Timetable
11.00-12.15
Lesson Argument

Genetic screens

Teachers

Luisa Lanfrancone, IEO

Lesson Location
IFOM - Conference Room
Timetable
16.00-17.15
Lesson Argument

Modeling cancer genetics

Teachers

Alberto Ciccia, Columbia University 

Affiliations

 

Lesson Location
ONLINE LECTURE
Timetable
11.00-12.30
Lesson Argument

Aneuploidy and cancer

Teachers

Stefano Santaguida, IEO

Lesson Location
ONLINE LECTURE
Timetable
14.00-15.30
Lesson Argument

Alternative splicing in cancer

Teachers

Juan Valcarcel, CRG - Barcelona

Lesson Location
ONLINE LECTURE
Timetable
15.30-17.00
Lesson Argument

Viral oncogenesis

Teachers

Susanna Chiocca, IEO

Lesson Location
ONLINE LECTURE
Timetable
9.30-11.00
Lesson Argument

Harnessing genetic alterations in cancer therapy

Teachers

Alberto Bardelli, IFOM

Lesson Location
Meeting Room 1+2
Timetable
11.00-12.30
Lesson Argument

Cancer genetics in the clinic: implications and applications

Teachers

Bernardo Bonanni, IEO

Lesson Location
Meeting Room 1+2
Timetable
14.30-16.00
Lesson Argument

The impact of cancer genetics on precision oncology

Teachers

Pier Francesco Ferrucci, IEO

Lesson Location
Meeting Room 1+2

Teachers: Rosella Visintin, IEO, & Myriam Alcalay, IEO 

Dates: 6-7-8-13 March 2023

Timetable
9.30-11.00
Lesson Argument

Preparing and Delivering an Effective Presentation

Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
11.15-12.45
Lesson Argument

Preparing a good poster

Teachers

Rosella Visintin,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
9.30-11.00
Lesson Argument

Principles of Effective Writing

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
11.15-12.45
Lesson Argument

Grammar in Scientific English

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
14.00-15.30
Lesson Argument

Exercises (performed individually by students)

Timetable
9.30-11.30
Lesson Argument

Writing an original manuscript

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
11.45-12.45
Lesson Argument

Plagiarism and Copyrights

Teachers

Myriam Alcalay,

Affiliations

IEO

Lesson Location
IFOM - Conference Room
Timetable
9.30-13.00
Lesson Argument

Discussion of Abstracts and Presentations before/after

Lesson Location
IFOM - Conference Room

Dates: 14-15-16 March 2023

The aim of this course is to help students acquire new skills in the analysis of microscopy images mainly using ImageJ/Fiji and its macro language. Lectures and hands-on sessions on different applications will get across the basics and theoretical concepts of most demanding analysis topics, and will provide students the practical tools to perform quantitative image analysis.

Timetable
9.00-10.45
Lesson Argument

Introduction to digital images
•    How an image is obtained, sampling, monochromatic and color images, Fourier transforms

Teachers

Zeno Lavagnino,

Affiliations

IFOM

Lesson Location
Meeting Room 1+2
Timetable
11.00-13.00
Lesson Argument

Introduction to Fiji and objects segmentation:

  • Introduction to Fiji’s key functionalities: installation, basic options, opening of images (Bio-Formats Import), management of simple images, export of analysed images
  • Measurements of images: image calibration, set measurements parameters, creation of selections and Region Of Interest
  • Processing images: geometric transformations, filters, mathematical operations
  • Binarization of images: image thresholding methods, processing of binary images
  • Objects segmentation and detection: Analyse particles/Find Maxima functionalities
Teachers

Chiara Soriani,

Affiliations

IEO

Lesson Location
Meeting Room 1+2
Timetable
14.00-17.00
Lesson Argument

Hands-on: Nuclear segmentation and spots detection:

  • Step-by-step creation of an image analysis workflow for nuclear segmentation and nuclear spots detection
  • Step-by-step recording of macro commands within the analysis workflow
Teachers

Serena Magni,

Affiliations

IFOM

Lesson Location
Meeting Room 1+2
Timetable
9.00-12.30
Lesson Argument

Introduction to Macro Language

  • Introduction to macro language: What is a macro? Why do we need macros?
  • How can move from a set of recorded commands to a macro for batch processing?
  • Built-in functions in FIJI: basics imaging analysis functions
  • Basics of programming in Fiji macro language with examples: variables, arrays, loops, conditional statements
  • Import and export of files: bio-formats and bio-formats macros extensions
  • Hands-on: Generalization of a series of recorded commands to create a macro for batch nuclear segmentation
Teachers

Mattia Marenda (IEO), Fabrizio Orsenigo (IFOM)

Lesson Location
Meeting Room 1+2
Timetable
14.00-17.00
Lesson Argument

Colocalization:

  • Introduction to the concept of colocalization
  • Co-occurrence
  • Hands-on: co-occurence batch analysis
  • Intensity correlation coefficient-based analyses object-based colocalization
  • Hands-on: the JACoP plugin
Teachers

Simona Rodighiero,

Affiliations

IEO

Lesson Location
Meeting Room 1+2
Timetable
9.00-9.50
Lesson Argument

Images for publication and guidelines for best practices in image processing

Teachers

Fabrizio Orsenigo,

Affiliations

IFOM

Lesson Location
Meeting Room 1+2
Timetable
10.00-12.30
Lesson Argument

Tracking in Biology:

  • Introduction to the concepts of tracking and biological motivation: tracking of cells and intra-cellular objects (chromatin, proteins, exogenous probes)
  • Introduction to TrackMate Software
  • Technical details for tracking: objects detection & trajectories reconstruction
  • Evaluation of parameters from trajectories: displacement, velocity, directionality, etc
  • Mention of advanced features in tracking: mean square displacement to calculate the motion type (free-diffusion, confined, active motion) and environment material properties
  • Hands-on: Tracking of nuclei using Trackmate
Teachers

Mattia Marenda,

Affiliations

IEO

Lesson Location
Meeting Room 1+2
Timetable
14.00-16.00
Lesson Argument

Collective Motion:

  • Introduction to the concepts of collective cellular mobility and motivation
  • Different ways and parameters to study collective cell motility:
    Wound Healing, Cell Streaming, Particle Image Velocimetry to evaluate speed of wound closure, velocity and coordination of movement
  • Hands-on: Wound Healing speed of closure extraction using Fiji
Teachers

Emanuele Martini,

Affiliations

IFOM

Lesson Location
Meeting Room 1+2
Timetable
16.30-17.00
Lesson Argument

Wrap-up and Discussion

Lesson Location
Meeting Room 1+2

Organizer: M. Mapelli (IEO) & A. Casanal (HT) - Dates: 17-20 April 2023

Venue: Human Technopole, Milan

The course will focus on how to analize the structures and on structural biology projects. There will be a day dedicated to Cryo-EM with practicals at the microscope.

Timetable
9.30-11.30
Lesson Argument

Crystallization theory and practical

Teachers

Sebastiano Pasqualato (HT) & Luigi Scietti (IEO)

Lesson Location
Human Technopole - Auditorium
Timetable
11.45-12.45
Lesson Argument

Basis of crystallography

Teachers

Marina Mapelli,

Affiliations

IEO

Lesson Location
Human Technopole - Auditorium
Timetable
14.00-15.00
Lesson Argument

Structure based drug design

Teachers

Mario Milani,

Affiliations

CNR - Biophysics Institute

Lesson Location
Human Technopole - Auditorium
Timetable
15.00-17.00
Lesson Argument

Pymol tutorial

Lesson Location
Egg Rooms, 4th floor, PITA
Timetable
9.30-10.20
Lesson Argument

Principles of Cryo-EM SPA

Teachers

Francesca Coscia,

Affiliations

Human Technopole

Lesson Location
Human Technopole - Auditorium
Timetable
10.40-11.30
Lesson Argument

Anatomy of the microscopes and sample preparation

Teachers

Paolo Swuec,

Affiliations

Human Technopole

Lesson Location
Human Technopole - Auditorium
Timetable
11.45-12.45
Lesson Argument

Challenges of a SPA project “How to recognize and package mRNA?"

Teachers

Clemens Plaschka,

Affiliations

IMP, Vienna

Lesson Location
Human Technopole - Auditorium
Timetable
14.00-14.30
Lesson Argument

Working with Cryo-EM microscopes

Teachers

Paolo Swuec,

Affiliations

Human Technopole

Lesson Location
Egg Rooms, 4th floor PITA
Timetable
14.30-15.00
Lesson Argument

Group 1: Visit to microscopes

Group-2 will alternate with Group-1 for the microscopes’ visit and negative staining tutorial

Teachers

Simona Sorrentino & Malan Silva,

Affiliations

Human Technopole

Lesson Location
Egg rooms 4th floor PITA
Timetable
15.00-15.30
Lesson Argument

Group 1: Negative staining tutorial

Group-2 will alternate with Group-1 for the microscopes’ visit and negative staining tutorial

Teachers

Paolo Swuec & Simona Sorrentino,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
15.30-17.00
Lesson Argument

Model building tutorial: Coot for model building and structure interpretation of cryoEM maps

Teachers

Ana Casañal,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
9.30-10.20
Lesson Argument

CLEM: correlative light and electron microscopy

Teachers

Malan Silva,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
10.40-11.30
Lesson Argument

Principles of Cryo-ET: sample prep and theory

Teachers

Philipp Erdmann,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
11.45-12.45
Lesson Argument

A Cryo-ET story: “The Molecular Structure of Anterograde Intraflagellar transport trains”

Teachers

Gaia Pigino,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
14.00-17.00
Lesson Argument

Cryo-ET workshop and tutorial

Teachers

Philipp Erdmann,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
9.30-10.20
Lesson Argument

Principles of NMR

Teachers

Giovanna Musco,

Affiliations

San Raffaele Hospital

Lesson Location
Human Technopole - Auditorium
Timetable
10.40-11.30
Lesson Argument

Mass Spectrometry for Structural Biology: XL-MS

Teachers

Andrea Graziadei,

Affiliations

IEO & HT

Lesson Location
Human Technopole - Auditorium
Timetable
11.45-12.45
Lesson Argument

Principles of Alpha-fold

Teachers

Andrea Graziadei,

Affiliations

IEO & HT

Lesson Location
Human Technopole - Auditorium
Timetable
14.00-15.30
Lesson Argument

Alpha-fold tutorial

Teachers

Helen Foster,

Affiliations

Human Technopole

Lesson Location
Egg Rooms 4th floor PITA
Timetable
15.30-17.00
Lesson Argument

Students’ presentation of articles

Teachers

Ana Casañal & Marina Mapelli

Lesson Location
Egg Rooms 4th floor PITA

Organizers: Alice Barbaglio (IEO) & Maria Francesca Mossuto (HT)

Venue: Mezzanino di Palazzo Italia, Human Technopole

Timetable
9.30-10.00
Lesson Argument

Speakers’ introduction and ice breaking

Timetable
10.00-10.30
Lesson Argument

- Proposal writing as a transferable skill and a career tool;
- Proposal writing vocabulary;
- Differences respect to a scientific paper.

Timetable
10.30-12.30
Lesson Argument

Proposal development plan: from scientific hypothesis development to proposal submission

Timetable
13.30-14.30
Lesson Argument

CV/personal statement preparation

Timetable
14.30-15.30
Lesson Argument

Funding opportunities for early stage researchers

Timetable
15.30-16.00
Lesson Argument

Decompression break

Timetable
16.00-18.00
Lesson Argument

Let's try: group work

Organizer: Fabio Stella, University Bicocca - Dates: 17-20 July 2023

The course aims to provide a gentle introduction to different components of machine learning. In particular, the course will first give the framework of machine learning and then will devote specific lectures to different models and techniques. Attention will be devoted to Bayesian networks, machine learning methods and models for the analysis of single cell data analysis, for analyzing the spread of infectious diseases, and to reinforcement learning.

The first lesson will be held at the IEO, Silver room (bldg. 13, 3rd floor); the rest of the course is online.

Timetable
9.00-12.00
Lesson Argument

What is Machine Learning?

Teachers

Fabio Stella,

Affiliations

University Milan Bicocca

Lesson Location
IEO Silver Room
Timetable
9.00-12.00
Lesson Argument

Building an Infectious Disease Model: SIR and Beyond

Teachers

Andrea Sottosanti,

Affiliations

University of Padua

Lesson Location
ONLINE LECTURE
Timetable
9.00-12.00
Lesson Argument

Practical Bayesian Networks for Clinical Data (part 1)

Timetable
14.00-17.00
Lesson Argument

Practical Bayesian Networks for Clinical Data (part 2)

Teachers

Marco Scutari,

Affiliations

Dalle Molle Inst. for Artificial Intelligence - Switzerland

Lesson Location
ONLINE LECTURE
Timetable
14.00-17.00
Lesson Argument

Basic Machine Learning for single-cells data analysis

Teachers

Marco Beccuti,

Affiliations

University of Turin

Lesson Location
ONLINE LECTURE

Organizer: B. Bodega (INGM) - Dates: 13-14-18 September 2023

The course will be held at INGM, c/o Padiglione Invernizzi, Via Francesco Sforza, 35 – Milan

Timetable
9.15-9.30
Lesson Argument

Introduction to the course

Teachers

Sergio Abrignani,

Affiliations

INGM

Timetable
9.30-11.00
Lesson Argument

Innate and adaptive immunity

Teachers

Sergio Abrignani,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
11.30-13.00
Lesson Argument

Immunological Tolerance

Teachers

Jens Geginat,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
14.00-15.30
Lesson Argument

Imaging Immunity

Teachers

Marco De Giovanni,

Affiliations

San Raffaele Institute

Lesson Location
INGM Conference Room
Timetable
16.00-17.30
Lesson Argument

Monoclonal antibodies and immunotherapies

Teachers

Antonio Lanzavecchia,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
9.30-11.00
Lesson Argument

Transposable elements dynamics regulate T-cell exhaustion in tumor microenvinroment

Teachers

Beatrice Bodega,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
11.30-13.00
Lesson Argument

CAR-T

Teachers

Andrea Biondi,

Affiliations

University of Milan Bicocca

Lesson Location
INGM Conference Room
Timetable
14.00-15.30
Lesson Argument

T Cells

Teachers

Samuele Notarbartolo,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
9.30-11.00
Lesson Argument

B cells

Teachers

Stefano Casola,

Affiliations

IFOM

Lesson Location
INGM Conference Room
Timetable
11.30-13.00
Lesson Argument

COVID-19: immune response and vaccines

Teachers

Sergio Abrignani,

Affiliations

INGM

Lesson Location
INGM Conference Room
Timetable
14.00-15.30
Lesson Argument

Genome editing in T cells for cancer immunotherapy

Teachers

Chiara Bonini,

Affiliations

San Raffaele Institute

Lesson Location
INGM Conference Room

Organizer: F. Ciccarelli - Dates: 25-26 September 2023

Format: 2-day course

Timetable
10.00-12.00
Lesson Argument

Introduction to network theory and its application to biomedicine

Teachers

Diego Di Bernardo,

Affiliations

TIGEM

Lesson Location
ONLINE LECTURE
Timetable
14.00-16.00
Lesson Argument

Building up small molecular networks step by step

Teachers

Andrea Ciliberto,

Affiliations

IFOM

Lesson Location
IEO Silver Room
Timetable
10.00-12.00
Lesson Argument

Network biology approaches to study cancer genes

Teachers

Francesca Ciccarelli,

Affiliations

King's College London

Lesson Location
IEO Silver Room
Timetable
14.00-16.00
Lesson Argument

Praticals on gene expression networks

Teachers

Hrvoje Misetic,

Affiliations

King’s College London

Lesson Location
IEO Silver Room

Dates: 27-28-29 November 2023

Venue: Human Technopole

The aim of this course is to help students acquire new skills in the analysis of microscopy images using advanced image analysis tools. Through theoretical and practical lessons, the course will cover topics related to python/jython programming in Fiji and the application of machine learning and deep learning algorithms for the analysis of microscopy data.

Timetable
9.00-12.00
Lesson Argument

Introduction to Python/Jython programming languages:

  • From ImageJ macro language to Jython programming language in Fiji
  • Python basics: syntax, statements, expressions, list, loops, conditional statements, functions
  • From Python to Jython: object oriented programming
  • Jython main APIs and Classes for Fiji
  • Python vs Jython: Pros and cons
Teachers

Emanuele Martini,

Affiliations

IFOM

Timetable
12.00-12.30
Lesson Argument

Hands-on: practice on a nuclei segmentation macro and comparison with Jython language

  • Implementation of nuclei segmentation
  • Focus on Regions Of Interest Manager
  • Creation of customized Results table
Teachers

Fabrizio Orsenigo & Serena Magni,

Affiliations

IFOM

Timetable
14.00-17.00
Lesson Argument

More complex image analysis and Analysis of Multiple Images

Hands-on: nuclei segmentation with spots count and intensity measurement

  • Bio-formats handling
  • User interaction
  • Multiple channel handling
  • Parent-children objects handling
  • Multiple Results Table management
  • Multiple images analysis
Teachers

Fabrizio Orsenigo & Serena Magni,

Affiliations

IFOM

Timetable
9.00-10.30
Lesson Argument

Introduction to machine learning and deep learning in image analysis

  • Theoretical introduction about machine learning and deep learning
  • Machine learning as tool for semantic segmentation/pixel classification
  • Deep Learning as tool for image restoration and instance segmentation
Teachers

Florian Jug,

Affiliations

Human Technopole

Timetable
11.00-12.30
Lesson Argument

Hands-on: Semantic segmentation/pixel classification with Labkit

Teachers

Florian Jug,

Affiliations

Human Technopole

Timetable
14.00-17.00
Lesson Argument

Image restoration and instance segmentation using Deep Learning in Python

  • Introduction to Jupyter (Python) notebooks and their use in cloud with ZeroCostDL4Mic
  • Deep Learning algorithms for image restoration and instance

Hands-on: Image restoration and nuclear segmentation with Deep Learning algorithms

  • Image restoration using Noise2Void algorithm; model training and application using Jupiter notebooks in ZeroCostDL4Mic
  • Nuclear segmentation using 2D and 3D Stardist using Jupyter notebooks in ZeroCostDL4Mic
Teachers

Damian Edward Dalle Nogare,

Affiliations

Human Technopole

Timetable
9.00-12.00
Lesson Argument

Segmentation in tissues using Stardist with QuPath software:

  • Introduction to QuPath for tissue sections analysis
  • Cell segmentation in tissues

Hands-on: Cell segmentation in tissues using Stardist and cell-type classification in different populations

Teachers

Chiara Soriani,

Affiliations

IEO

Timetable
14.00-17.00
Lesson Argument

Cell segmentation using Cellpose software in Python:

  • Introduction to conda environments and their utility for using local Jupyter (Python) notebooks
  • CellPose Deep Learning software for cell and nuclear segmentation

Hands-on: Segmentation of cells and nuclei using CellPose and evaluation of cytoplasmic signal using local Jupyter notebooks

Teachers

Mattia Marenda,

Affiliations

IEO