• 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 



Mercoledì 28 aprile, ore 15-16:30

Il COVID-19 Data Portal è il portale voluto dalla Commissione Europea come punto di riferimento per lo scambio dati e prodotti scientifici su COVID-19. Lo scorso febbraio è stata lanciata la versione italiana, federata all’interno del portale europeo, con lo scopo di facilitare la condivisione e l’accesso alle diverse tipologie di dati su COVID-19. 

Chiunque produca o lavori con i dati della pandemia ha dunque a disposizione un punto di riferimento nazionale per reperire risorse e materiali prodotti da altri, per condividere i propri risultati e capire come farlo. 

Le caratteristiche principali del portale italiano saranno illustrare nel webinar “ll COVID-19 Data Portal italiano: un punto di riferimento nazionale per i dati della pandemia”, in programma per il 28 aprile 2021, dalle 15 alle 16.30. 

Saranno presentate le diverse sezioni, le tipologie di dati e relative linee guida. Inoltre si fornirà una panoramica dei servizi offerti e dei possibili modi di interagire con il portale e i suoi curatori.

Registrazione obbligatoria al seguente link: https://us02web.zoom.us/webinar/register/WN_3eccqJAJRpSUGzLF2txqGw

Programma:

• Introduce Emma Lazzeri, ricercatrice CNR-ISTI e GARR
• Matteo Chiara, ricercatore UniMI e ricercatore associato di CNR-IBIOM: “SARS-CoV-2 e condivisione dei dati. La situazione nel nostro paese. Focus: dati genomici”.
• Federico Zambelli, ricercatore UniMI e ricercatore associato di CNR-IBIOM, Technical coordinator di ELIXIR-IT: “ELIXIR-IT e condivisione dei dati COVID-19, l’esempio del COVID-19 Data Portal”.
• Marco Carraro, Università degli Studi di Padova “COVID-19 Data Portal Italy, creazione, stato dell’arte, prospettive future”
• Discussione

Il webinar fa parte del ciclo “Open Science e COVID-19, collaborare per contrastare la pandemia”. Per maggiori informazioni consultare: https://www.cnr.it/it/evento/17209 e https://www.openaire.eu/item/open-science-e-covid-19-collaborare-per-contrastare-la-pandemia

TW https://twitter.com/CNRsocial_/status/1382986738344333314
FB https://www.facebook.com/CNRsocialFB/posts/10158022068302727
IN https://www.linkedin.com/feed/update/urn:li:activity:6788754207613751296



ELIXIR-IIB is pleased to announce the course:

“Train the Trainer"

1-4 December, 2020

online course

COURSE DESCRIPTION

The course is made up of four sessions, covering:

  • Learning principles and how they apply to training and teaching
  • Lesson, course, and materials design
  • Teaching techniques that can be used to enhance learner engagement and participation
  • Assessment and feedback in training and teaching


Full details at:  https://elixir-iib-training.github.io/website/2020/12/01/train-the-trainer-italy-online.html



Lunedì 16 novembre, ore 15-17. Seconda edizione. 

Con la pandemia da COVID-19 è diventata evidente la necessità di condividere i dati e gli altri risultati della ricerca scientifica. Nel webinar si tornerà a parlare dell'urgenza di aderire a un modello di scienza aperto e collaborativo e degli aspetti specifici dell’Open Science per le ricerche su Covid-19 e Sars-Cov-2. Inoltre verranno illustrate le principali iniziative europee per la condivisione di dati e risultati di ricerca all'interno della comunità scientifica.

La registrazione è obbligatoria a questo link, in cui è possibile anticipare eventuali domande ai relatori. 

Programma:

• Allegra Via, ricercatrice CNR, coordinatrice della piattaforma di Training di ELIXIR-IT: “Le principali iniziative europee per la condivisione di dati e dei risultati della ricerca a supporto della comunità scientifica. ELIXIR (portale dati Covid-19), OpenAIRE, RDA”.
• Emma Lazzeri, ricercatrice CNR, Coordinatrice OpenAIRE NOAD e nodo italiano RDA: “L'efficacia del modello Open Science e il suo metodo di cooperazione nel contesto della pandemia in corso. Ruolo e azioni di OpenAIRE e RDA”.
• Graziano Pesole, Coordinatore di ELIXIR-IT, Professore UNIBA, associato CNR-IBIOM: “La condivisione dei dati al tempo del Covid-19: sfide e opportunità per l’Italia. Ruolo e azioni di ELIXIR”. 
• Discussione

L’incontro viene proposto per la seconda volta a distanza di tre mesi, e fa parte di una serie di webinar e tutorial organizzati dai nodi italiani di OpenAIREELIXIRRDA e EOSC Pillar in cui si illustreranno gli strumenti e le pratiche dell’Open Science per contrastare la crisi sanitaria in corso. In particolare si guarderanno aspetti e risorse specifiche per diversi tipi di dati - epidemiologici, clinici e omici - e altri prodotti della ricerca scientifica quali software, protocolli e altri strumenti di analisi.

Maggiori informazioni alla pagina sul portale di OpenAIRE e del CNR.

Un’ora prima dell’evento gli iscritti riceveranno via email il link per partecipare.




ELIXIR-IIB is pleased to announce the course:

“R for Reproducible Scientific Analysis"

14-17 July, 2020

online course

Registration deadline is 1 July 2020

COURSE DESCRIPTION
The goal of this workshop is to teach novice programmers to write modular code and best practices for using R for data analysis. R is commonly used in many scientific disciplines for statistical analysis and the emphasis of these materials is to give attendees a strong foundation in the fundamentals of R, and to teach best practices for scientific computing: breaking down analyses into modular units, task automation, and encapsulation. Note that this workshop will focus on teaching the fundamentals of the programming language R, and will not teach statistical analysis.

Should you have any question, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training@gmail.com) and/or Dr Loredana Le Pera (loredanalepera@gmail.com).

Full details at:  https://elixir-iib-training.github.io/website/2020/07/14/SWC_RforReproducibleScientificAnalysis-online.html




ELIXIR-IIB is pleased to announce the course:

“EMBO Practical Course on “Population Genomics: Background, tools, and programming"

1-8 April, 2020

Procida, Italy

Registration deadline is 28 January 2020

COURSE DESCRIPTION

This EMBO Practical Course will cover coalescent theory, the effect of demography in space and time, genetic clustering, the detection and quantification of admixture and selection. Lectures on these topics will be complemented by hands-on computer practicals introducing a wide range of software packages, both in R and Python.

This course is aimed at evolutionary biologists who already have basic bioinformatics skills. The main criterion for selection will be how much a candidate can benefit from the course. This implies that PhD students and Postdoc researchers will likely be favoured; however, applications from candidates at all levels will be considered.
Fellowships to cover travel expenses and for childcare are available.

Full details at:  https://elixir-iib-training.github.io/website/2020/04/01/population-genomics-procida.html




ELIXIR-IIB is pleased to announce the course:

“RNA-seq and single-cell RNA-seq Course"

9-13 March, 2020

University of Turin, Italy

COURSE DESCRIPTION

This course aims to provide participants with theoretical and practical knowledge on how to perform bioinformatic analyses of RNA-seq data using Bioconductor and other open-source software tools. A specific module will briefly describe the single-cell RNA-seq workflow, highlighting differences existing between bulk RNA-seq and single-cell sequencing. The course is suitable for life science researchers who are new to NGS technology, and no statistics prerequisites or computing experience are necessary for attending the course.

Full details at: https://elixir-iib-training.github.io/website/2020/03/09/RNAseq-and-single-cell_Turin.html

Should you have any question, do not hesitate to contact the Local organiser Raffaele Calogero (raffaele.calogero@unito.it) or the ELIXIR-IIB Training Team (elixir.ita.training@gmail.com)
 




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