• Istituto di Biologia e Patologia Molecolari

Elixir European Training

• European post-doctoral training  

ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers. The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living organisms work. ELIXIR includes 23 European countries and over 220 research organisations. 

The ELIXIR Italy Node (ELIXIR-IIB) is organized as a Joint Research Unit (JRU) coordinated by the National Research Council (CNR), and currently includes 22 partners, among which are several universities and High Performance Computing (HPC) providers.
The ELIXIR-IIB Training Platform is specifically designated to support researchers and professionals in acquiring specialised bioinformatics, computational and data analysis skills. 

More information and the complete list of our training courses can be found at: 
https://elixir-iib-training.github.io/website/.

Allegra Via, Italian Training Coordinator, Elixir European Infrastructure 
Loredana Le PeraELIXIR-IIB Deputy Training Coordinator  (CNR-IBIOM, c/o IBPM Bioinformatics and Computational Biology Group)



ELIXIR-IIB is pleased to announce the upcoming Winter School organised in collaboration with MSCA-RISE IDPfun.

“Disorder in Disorders: Pathogenic mechanisms of Intrinsically Disordered Proteins"

27-31 January, 2020

Università degli Studi di Padova -  Casa della Gioventù,
Via Rio Bianco,12
39042 Bressanone-Brixen (BZ), Italy.

COURSE DESCRIPTION

During lectures and practicals, experts of the field will provide students with an overview of IDP biological mechanisms that develop pathogenic phenotypes. They will explore the concepts of folding, unfolding and misfolding, highlighting their differences and similarities. Practical exercises aim at transferring to students basic skills for the study of IDPs using bioinformatic tools to solve complex problems. The school includes a half-day workshop on ELIXIR interoperability services and support for the IDP community.
 
Should you have any questions, do not hesitate to contact the organisers at: idpfun@ngp-net.bio.unipd.it





ELIXIR-IIB is pleased to announce the course"International Summer School on Rare Disease Registries and FAIRification of Data."

“International Summer School on Rare Disease Registries and FAIRification of Data."

23-27 September, 2019

Istituto Superiore di Sanità, Rome, Italy

COURSE DESCRIPTION

The training course is open to the international research community, clinicians, medical specialists, registry curators, database managers, healthcare professionals and rare disease patients representatives. 
 
Registration is possible for:
· the first training module (“Rare Disease Registries”, September 23-25, 2019)
· the second training module (“FAIRification of Data”, September 26-27, 2019)
· the entire course (“Rare Disease Registries” and “FAIRification of data”, September 23-27, 2019).
Online registration form is available at this link: 
 
For all the information, please visit the website: 

If you have questions please write to the course organiser Claudio Carta, PhD:


ELIXIR-EXCELERATE, in collaboration with ELIXIR-IIB and the National Research Council of Italy, is pleased to announce a Train the Trainer (TtT) event.

“ELIXIR-EXCELERATE Train the Trainer"

30-31 May, 2019

University of Padua, Campus of Biology and Biomedicine “Fiore di Botta”, Italy

COURSE DESCRIPTION

The course is organized around four sessions, covering:
* Learning principles and how they apply to training and teaching
* Teaching techniques that can be used to enhance learner engagement and participation
* Lesson, course, and materials design
* Assessment and feedback in training and teaching
 
Examples and discussions will also focus on the challenges presented by academic teaching.
 
Full details at: ELIXIR-IIB Course

Should you have any question about organizational issues, do not hesitate to contact us at elixir.ita.training@gmail.com
If you have questions regarding the course goals and content, you may contact Allegra Via (allegra.via@gmail.com). 
 




ELIXIR-IIB (ELIXIR Italy), in cooperation with other ELIXIR Nodes (France, Sweden and Slovenia), and the National Research Council

“Genome Assembly and Annotation"

01-05 July 2019

University of Milano-Bicocca
Lab. 715, U7 Building
via Bicocca degli Arcimboldi, 8
20126 Milano, Italy 

COURSE DESCRIPTION

The course is aimed at researchers interested in learning more about genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue with a step-by-step description of all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using Unix/Linux command line. 

Full details at: ELIXIR-IIB Course
 
Should you have any question, do not hesitate to contact the local organiser Gianluca Della Vedova gianluca.dellavedova@unimib.it




ELIXIR-IIB and the National Research Council

“Docker and Reproducibility"

13-14 June 2019

University of Turin
Molecular Biotechnology Center
Via Nizza, 52
10126 Torino, Italy
https://www.mbc.unito.it/it 

COURSE DESCRIPTION

Docker is a container framework for Linux that allows a developer to make easier the creation, deployment and execution of applications by using containers. During the workshop, the participants will learn the core concepts of Docker and how to easily embed bioinformatic pipelines/workflows into a docker container.
Full details at: ELIXIR-IIB Course
 
For all kinds of queries, please contact the ELIXIR-IIB Training Team at: elixir.ita.training@gmail.com or the local organiser Raffaele Calogero at: raffaele.calogero@unito.it, tel: +39 0116706454, cel: +39 3333827080





ELIXIR-IIB, in collaboration with the Telethon Institute of Genetics and Medicine (TIGEM) and the National Research Council

“Single Cell RNA Sequencing and Data Analysis"

07-09 May 2019

Telethon Institute of Genetics and Medicine (TIGEM)
Via dei Campi Flegrei, 34
80078 Pozzuoli (NA)
Italy www.tigem.it

COURSE DESCRIPTION
Single-Cell Transcriptomics is improving the quality of biological investigations by enhancing the dissection of heterogeneity in complex tissues and cell cultures. 
This 3-day course aims to provide an overview of a complete Single-Cell RNA sequencing workflow: 
- A theoretical overview of all existing methods to perform Single-Cell RNA sequencing libraries with a focus on individual features and weaknesses. 
- A practical hands-on laboratory training to produce 10X Genomics 3’ Single-Cell RNA sequencing libraries. 
- A practical bioinformatics training that will provide guidelines and tools to process and analyze Single-Cell RNA sequencing libraries from raw sequences to visualization. 
 
Should you have any question, do not hesitate to contact the local organiser Barbara Zimbardi course2019@tigem.it





As part of the EXCELERATE ELIXIR-Carpentries agreement, ELIXIR-IT, in collaboration with The National Research Council Italy, will host the following course:

“ELIXIR Software Carpentry on February 11-12, 2019 at the at the IGB-CNR of Naples, Italy"

11-12 February 2019

IGB-CNR of Naples, Italy

Course attendance is free of charge.
More information at the workshop webpage. Here is the registration link.
Should you have any question, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training@gmail.com) and/or the local organiser Dr. Vincenza Colonna (vincenza.colonna@igb.cnr.it). 

The workshop  is aimed at biologists with little or no prior computational experience and is focused on Reproducible Scientific Analysis. The curriculum will include: The Unix Shell, R for Reproducible Scientific Analysis, Version Control with Git
For instance, after attending this workshop you will be able to: automate repetitive tasks, capture small data manipulation steps that are normally not recorded to make research reproducible, R data and plot manipulation, use a few easy-to-remember commands to do most day-to-day version control tasks.





As part of the EXCELERATE ELIXIR-Carpentries agreement, ELIXIR-IT, in collaboration with The National Research Council Italy, will host the following course:

“ELIXIR Data Carpentry on February 14-15, 2019 at the University of Milano-Bicocca, Milan, Italy."

14-15 February 2019

University of Milano-Bicocca, Milan, Italy

Course attendance is free of charge.
More information at the workshop webpage. Here is the registration link.
Should you have any question, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training@gmail.comand/or the local organiser Dr. Gianluca Della Vedova (gianluca@dellavedova.org).

The workshop is aimed at people from any area with little or no prior computational experience who need to develop skills for data organisation in spreadsheets, data cleaning with OpenRefine, data analysis and visualization in Python, data management with SQL.

The Carpentries are a fiscally sponsored project of Community Initiatives. They teach skills that are immediately useful for researchers, using lessons and datasets that allow researchers to quickly apply what they’ve learned to their own work. The target audience is learners who have little to no prior computational experience, and the instructors put a priority on creating a friendly environment to empower researchers and enable data-driven discovery. Even those with some experience will benefit, as the goal is to teach not only how to do analyses, but how to manage the process to make it as automated and reproducible as possible. 


 



The National Research Council Italy, in collaboration with ELIXIR-IIB and ELIXIR-EXCELERATE, is pleased to announce the upcoming:

“ELIXIR-EXCELERATE Train the Trainer (TtT) course"

27-28 September 2018

Italian National Research Council, p.le Aldo Moro 7, 00185 Roma, Italy

COURSE DESCRIPTION:

The course is made up of four sessions, covering:
1. Learning principles and how they apply to training and teaching
2. Teaching techniques that can be used to enhance learner engagement and participation
3. Assessment and feedback in training and teaching
4. Lesson, course, and materials design


Full details at: https://elixir-iib-training.github.io/website/2018/06/25/BITS_Docker_Torino.html




ELIXIR-IIB, in collaboration with the National Research Council Italy, is pleased to announce the upcoming 

“Workshop on Docker and Reproducibility, a satellite event held jointly with the BITS Annual Meeting 2018"

25-26 June 2018

University of Turin
Molecular Biotechnology Center
Via Nizza, 52 - 10126 Torino (Italy)


COURSE DESCRIPTION:

Docker is a container framework for Linux that allows a developer to make easier the creation, deployment, and execution of applications by using containers. Recently it is becoming a promising approach to computational biology research reproducibility by: 

• Saving time and expenses on human and computational resources allocated to already performed analysis;
• Boosting communication between computational biologists working on similar topics;
• Enhancing transparency within the community;
• Granting open access computational knowledge to the community.

During the workshop the participants will learn the core concepts of docker and how to easily embed bioinformatic pipelines/workflows into a docker container.

Full details at: https://elixir-iib-training.github.io/website/2018/06/25/BITS_Docker_Torino.html



ELIXIR-IIB, in collaboration with the National Research Council Italy, is pleased to announce the upcoming 

“Population Genomics: background and tools"

21-27 April 2018
09:00

Biblioteca 
Consiglio Nazionale delle Ricerche 
Istituto di Genetica e Biofisica “Adriano Buzzati-Traverso” 
via Pietro Castellino 111 
80131 Napoli - IT 
www.igb.cnr.it

COURSE DESCRIPTION:

Study methods in population genomics have been profoundly reshaped in the last few years thanks to the growing availability of complete genomic sequences at population level. The rapid and recent growth of data and methods calls for new approaches to become routine in evolutionary genomics laboratories. The objective of this Practical Course is to give an overview of state of the art methods in population genomics combining lecturing from outstanding experienced population geneticists and software developers. All conceptual innovation will be presented in lectures and applied in practice both individually and in group work.

Full details at: The ELIXIR-IIB Training Programme



ELIXIR-IIB, in collaboration with the National Research Council Italy, is pleased to announce the upcoming 

“Software Carpentry workshop"

22-23 February 2018
09:00

University of Milano Bicocca
Via Bicocca degli Arcimboldi, 8 
20126 Milano

COURSE DESCRIPTION:

This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. In particular, in this workshop we will cover the Unix Shell, programming in Python and version control with Git.

Full details at: The ELIXIR-IIB Training Programme



ELIXIR-IIB, in collaboration with the National Research Council Italy, is pleased to announce the upcoming training course on

“Linux shell scripting for high-throughput biological data processing on supercomputers"

16-17 January 2018
09:00

CINECA

Via dei Tizii 6b
00185 Roma, Italy

COURSE DESCRIPTION:

Biological big data increasingly require supercomputers for their processing and analysis. Running high-throughput (HTP) bioinformatics data pipelines on supercomputing machines requires advanced Linux shell command line and scripting skills. In this two-day course, we will introduce the Linux shell and, on day one, we will show how to navigate and work with files and directories, how to combine commands to do new things, how to perform the same actions on many different files, how to filter and selectively extract data from tables, and how to find objects in files. Moreover, we will show how to connect to a remote supercomputer and how to utilise a supercomputing environment to analyse big amount of biological data, run simple shell scripts and bioinformatics pipelines. Day 2 will be wholly practical.

Full details at: The ELIXIR-IIB Training Programme