PERCORSO FORMATIVO

Il percorso formativo del Corso di Dottorato in Biologia e Scienze Applicate prevede l’acquisizione di 180 CFU, di cui 120 CFU derivanti dall’attività di ricerca e 60 CFU dall’attività frontale. L’attività di ricerca costituisce la parte principale della formazione e consiste nello svolgimento di un progetto di ricerca all’interno dei temi trattati dai curricula di dottorato. Questo progetto viene assegnato dal corpo docente entro i primi tre mesi dall’inizio del corso e viene svolto sotto la supervisione di un tutor.

Per promuovere lo sviluppo delle capacità critiche degli studenti e favorire un solido consolidamento culturale, il programma di dottorato prevede l’acquisizione di 60 ECTS (European Credit Transfer and Accumulation System), che possono essere ottenuti attraverso diverse modalità:

  • Partecipazione a seminari, corsi e cicli di lezioni organizzati nell’ambito delle attività di dottorato. Il Collegio dei Docenti elabora annualmente un calendario di lezioni, workshop e seminari, che viene pubblicato nella sezione dedicata alla struttura didattica.
  • Presentazione dei risultati sperimentali in workshop, congressi e conferenze nazionali e internazionali. Questa opportunità permette ai dottorandi di condividere i propri risultati di ricerca con la comunità scientifica, ricevere feedback e ampliare le proprie conoscenze nel campo di interesse.
  • Periodo di formazione all’estero, previsto in base a un accordo tra il tutor, il dottorando e il coordinatore. Questa esperienza permette agli studenti di arricchire la propria formazione attraverso il confronto con altre realtà scientifiche e culturali.

Inoltre, per essere ammessi all’esame finale, è richiesta almeno una pubblicazione presentata su una rivista peer-reviewed. Altri prodotti valutabili che rappresentano gli output attesi dalle attività di ricerca dei dottorandi includono relazioni presentate in conferenze scientifiche, workshop, sessioni tematiche di congressi nazionali e internazionali, sviluppo di software e deposito di brevetti.

Attività didattica programmata

Name Hours Description Curriculum
Computer Vision: From Image Capture to Pattern Recognition 12 The aim of the course is to provide PhD students with the basics of Computer Vision and the related topics of Image Acquisition/Processing and Pattern Recognition, including application examples for different fields. Starting from the principles of still and video imagery, the students will be introduced to the fundamentals of image capture through digital imaging sensors, as well as to the main concepts behind image processing methodologies and algorithms such as: Brightness/Contrast/Saturation Adjustment, Foreground/Background Detection, Image Segmentation, Features Extraction, Motion Detection, Object Tracking. The students will also learn how these techniques can be used for acquiring salient features in geometric as well as in organic shapes, to the aim of recognizing specific patterns of interest. The theoretical elements will be accompanied by practical examples of computer vision applications in various application domains.  

CURRICULUM BIOLOGIA SCIENZE APPLICATE

Summary of the topics:

–  Digital image fundamentals, Pin-hole Camera.

–  Still image and video capture. Capture devices and their characteristics.

–  Foreground and background detection, image segmentation, pattern detection.

–  Different types of image features, features extraction.

–  Objects extraction, color-based object detection, Histogram of Oriented Gradients.

–  Introduction to tracking and main tracking methods

–  Dynamic scene analysis, motion-field and optical flow

–  Detection of moving objects, difference between frames, background subtraction.

–  Point features, Articulated Motion Models, Pose Estimation.

Design and Execution of Empirical Studies 12 The course aims to provide Ph.D. students with basic knowledge about commonly used techniques for conducting empirical studies. The course will span over both quantitative and qualitative analysis techniques. As for quantitative methods, the course will focus on surveys, case studies, and controlled experiments. As for qualitative methods, interviews, focus groups and record analysis will be treated. At the end of the course, the Ph.D. students will be able to autonomously decide which kinds of empirical studies are best suited for their specific studies. Also, they will be able to determine how to analyze the results and how to report them through tables and figures.

Summary of the topics:

–  Introduction to empirical research

–  Methodologies for designing quantitative studies: surveys and case studies

–  Methodologies for designing quantitative studies: controlled experiments

–  Examples of quantitative studies with exercises: plan and design your quantitative study

–  Methodologies for designing qualitative studies: interviews, focus groups, and record-keeping

–  Techniques for analyzing quantitative and qualitative data

–  Approaches for reporting the results of quantitative and qualitative studies

–  Examples of qualitative studies with exercises: plan and design your qualitative study

 

CURRICULUM BIOLOGIA SCIENZE APPLICATE

R basis 16 The course will provide the most important basic elements of R use (i.e. from the overall paradigm to coding principles) that will allow the students to get familiar with the software. Since R has now become the reference software among scientists and researchers for statistical analyses, the students will be given the opportunity to use an extraordinary tool to analyze the data they will gather during their Phd course. Moreover, R functionalities to generate high-quality graphics will allow the students to produce complex figures for their scientific manuscripts. Such abilities will be equally applicable by the students to any kind of data belonging to both molecular and environmental facets of biological sciences.

Summary of the topics:

–  Installing required softwares. Why R? Software overview. R Workspace. Help tool. R Packages. Reusing results

–  Data types. Importing data. Keyboard input. Exporting data. Viewing data. Missing data.

–  Creating a new variable. Operators. Built-in functions. Control structures. User-defined functions. Data sorting. Data merging. Aggregating data.

–  Base functions. Lattice/ggplot2 packages.

 

CURRICULUM BIOLOGIA SCIENZE APPLICATE

Industrial biotechnology for the production of recombinant proteins 12 The course will provide students with a thorough knowledge about the main methods and systems for the industrial production of recombinant proteins. Specific topics are:

–  Microorganisms of biotechnological interest. DNA cloning techniques: plasmids, cosmids and viruses as cloning vectors. Expression vectors for the production of recombinant proteins in prokaryotic and eukaryotic cells. Methods for promoting the solubility and renaturation of polypeptides.

–  Transgenic plants and their applications for the production of recombinant proteins. Notes on the expression of recombinant proteins in baculovirus. Expression of recombinant proteins in mammalian cells: transfection, viral and retroviral vectors.

Genetic targeting in mammals: zinc-finger nucleases, TALEN and CRISP-Cas9.

– Cell engineering applied to the creation of transgenic organisms. Scale-up cultures in mini- bioreactors for the production of monoclonal antibodies and proteins. Use of proteins in different industrial sectors. Selected examples of protein modifications for industrial interest aimed at improving specific properties.

 

CURRICULUM BIOLOGIA

Physical and numerical modeling in applied sciences 12 The course aims to illustrate the principles of modeling in applied sciences by exploiting the physical and numerical reproduction. It provides some basic tools for creating models of real objects and processes that allow studying the prototype under multiple conditions by simplifying it.

Numerical modeling supports the experimental part by exploring, for example, the influence of varying parameters that cannot be controlled in physical model tests. The extrapolation of the results of the experiments is often based on physical considerations in combination with a mathematical model. On the other side, numerical models need experiments for proper calibration. Through a combination of both approaches, the modeling can uncover information of interest that would be complementary. The course will go through the modeling process from conception to the final stage of results exploitation.

The principles discussed in this course will provide a framework for the modeling considering different options and with some practical examples; the part on the output exploitation will focus on the effective selection, organization, and presentation of the results for research purposes. These objectives are consistent with the Ph.D. program in Biology and Applied Sciences aiming at developing advanced scientific and technological profiles to autonomously conduct research activities by developing strategies for the analysis and solution of complex problems.

 

SCIENZE APPLICATE

Introduction to Numerical Methods for Ordinary Differential Equation 16 The main goal of the course is to provide the basic knowledge on the main approximation techniques that allow the simulation of real phenomena described by ordinary differential equations. In particular, the fundamental features of a generic numerical method will be introduced and the stability properties of some schemes belonging to the classes of linear multistep methods and

Runge-Kutta type methods will be analyzed. The importance of identifying efficient numerical schemes, and of adding reliable error estimation techniques, will be emphasized.

According to the presented concepts, appropriate numerical simulations will be carried out in Matlab environment, in order to experimentally analyze the performance of some solvers based on the methods illustrated in the course

 

CURRICULUM BIOLOGIA SCIENZE APPLICATE

Effective science communication: basic writing and communication techniques for doctoral students

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

8 The aim of the course is to provide PhD students with basic tools related to the techniques of writing and communication scientific results. The students will acquire the theoretical fundamentals useful to set up an effective reading and writing of a scientific article, paying particular attention to the evaluation of the manuscript draft towards the final version, to the stylistic and linguistic elements, in addition to the theoretical elements supporting the preparation of an oral preparation of scientific data and results.

The theoretical elements will be accompanied by practical, individual and group exercises, through which the student will acquire autonomy of judgment with respect to the communication strategies to be applied. Furthermore, the student will experience both written and verbal language and communication skills by interacting with the colleagues and with the teacher and through the presentation of scientific data and related results. Content of the course:

–  Scientific reading (scientific paper structure, reading strategies)*

–  Writing process (organizing ideas, the importance of the draft)*

–  Reader-centred writing (storytelling and the importance of title/abstract)*

–  “Five paragraph method” while writing*

–  Draft vs final version (peer-review process and how to give feedback)

–  Elements of style (shorten sentences, avoid jargon, hedge words, tautologies)*

–  Prepare your next presentation (focus on the audience, duration, timing and structure of talk and sentences, tips and advices)*

*  with practical session

 

CURRICULUM BIOLOGIA SCIENZE APPLICATE

Microorganisms and plants for bioremediation 16 The objectives of the Doctoral School of Biology and Applied Sciences, curriculum Biology, encompass the training of highly qualified personnel with an interdisciplinary preparation and capable of planning and carrying out autonomously basic and applied research for different biological systems. Consistently with these objectives, the “Microorganisms and plants for bioremediation” course is aimed at giving knowledge and understanding of the role of microorganisms and plants in the process of environmental remediation. Special attention is paid to the mechanisms of pollutant uptake/stabilization/degradation by plants and/or microorganisms, depicting technical scenarios and providing scientific guidelines for the application of viable plant/microorganism-based technologies for the decontamination or stabilization of different environmental contexts.

Upon completion of this course, students will understand the important role of plants and microorganisms in environmental restoration and will be able to assess/analyze the toxic effects of different sources of environmental contamination.

 

CURRICULUM BIOLOGIA

Sustainable timber structures in seismic areas: basis of design 16 Timber structures are high-efficient structural systems that, thanks to their prerogatives of easiness and quickness of construction, transportation, material sustainability, energy efficiency, eco-compatibility and good seismic response have become a valid alternative with respect to traditional structures. In addition to long-span roofs, bridges and floors, timber elements are effectively used to realize highly performing timber buildings for commercial and

residential destinations in seismic-prone areas and, more recently, for structural and energetic retrofitting of existing buildings.

The short course focuses on the general aspects concerning the basis of design of structural elements made with solid and glulam timber, subassemblies, and mechanical and carpentry connections in the framework of National and European standards emphasizing the research advancements. Thereafter, they will be treated both technological aspects and the seismic behaviour of the most common timber building typologies – i.e., CLT buildings, light and heavy timber frame buildings and blockhouse buildings – focusing on the role of traditional or innovative solutions for the connection systems to enhance the seismic resistance and the environmental sustainability.

Finally, the course addresses towards the recent research advancements concerning the use of timber products (i.e., solid or light timber panels, braces, etc.) for combined seismic and energetic retrofitting of existing buildings or for the structural rehabilitation of ancient timber members.

 

SCIENZE APPLICATE

Deep Learning in Python for image Recognition 12 The course aims to teach the fundamental concepts of using the Python programming language and the PyTorch library for image recognition in the field of deep learning on neural networks. It specifically focuses on the “Visual Transformer” and “Graph Neural Network” layers, providing in-depth understanding and practical knowledge.

 

Calendario attività didattiche

Attività per la formazione interdisciplinare, multidisciplinare e transdisciplinare

Questo percorso formativo mira a fornire agli studenti le competenze e le conoscenze necessarie per diventare ricercatori qualificati nel campo della biologia e delle scienze applicate.

Il percorso formativo del Corso di Dottorato in Biologia e Scienze Applicate si basa su un’articolata attività didattica disciplinare e interdisciplinare, mirata a offrire agli studenti la possibilità di approfondire le proprie conoscenze e competenze, nonché a facilitare l’acquisizione di 60 crediti di attività frontali. In questo contesto, sono previsti dei corsi obbligatori per tutti i dottorandi

Tipo di attività Descrizione dell’attività (e delle modalità di accesso alle infrastrutture per i dottorati nazionali)
Perfezionamento linguistico La lingua inglese rappresenta lo strumento più comune per lo svolgimento dell’attività di ricerca nell’ambito scientifico di riferimento. Si intende offrire attività di formazione dedicate al perfezionamento delle competenze linguistiche. Insegnamenti dedicati e seminari saranno finalizzati all’innalzamento delle
capacità di espressione scritta e orale dei dottorandi nei settori di ricerca di competenza.
Perfezionamento informatico Corsi e seminari per l’utilizzo di software e programmazione avanzata in diversi linguaggi e piattaforme selezionati in funzione delle esigenze curriculari. In particolare, il dottorando acquisirà conoscenze e abilità di base per individuare strategie adeguate alla soluzione di problemi, nonché analizzare dati e interpretarli utilizzando specifiche applicazioni informatiche e banche dati.
Gestione della ricerca e della conoscenza dei sistemi di ricerca europei e internazionali Cicli di seminari, svolti da specialisti interni all’Ateneo, sull’accesso ai bandi di programmi di finanziamento europei e nazionali. Corso intensivo sulla stesura di un progetto di ricerca scientifica di livello internazionale.
Valorizzazione e disseminazione dei risultati, della proprietà intellettuale e dell’accesso aperto ai dati e ai prodotti della ricerca Seminari e corsi pratico-teorici sugli strumenti e le metodologie utili alla comunicazione della ricerca scientifica.

Seminari di approfondimento sugli aspetti giuridici, economici, etici, e sociali della proprietà intellettuale dei risultati della ricerca scientifica.

Principi fondamentali di etica, uguaglianza di genere e integrità Cicli di seminari volti a promuovere la cultura delle pari opportunità, del rispetto e dell’inclusione. Nello specifico, gli obiettivi sono:

–  far comprendere la genesi degli stereotipi e dei pregiudizi;

–  sviluppare competenze per promuovere le pari opportunità;

–  favorire l’inclusione delle diversità e valorizzare le differenze in un’ottica di promozione della dignità della persona;

–  contrastare ogni forma di discriminazione e violenza;

–  implementare l’adozione di comportamenti eticamente corretti per una civile convivenza;

–  incoraggiare le buone pratiche per l’educazione alla biodiversità ed alla sostenibilità ambientale.