Tools for Advanced Data Analyses in Biology

Da lunedì 27 novembre a venerdì 1° dicembre presso il Polo della Memoria "San Rossore 1938" avrà luogo il workshop dal titolo "TADAB - Tools for Advanced Data Analyses in Biology".

Registrati (entro il 20 novembre)

L'evento, realizzato con i fondi di Ateneo per le attività scientifiche dei dottorandi, è aperto a studenti, dottorandi, post-doc e allievi di master.

La registrazione è obbligatoria e deve essere effettuata entro il 20 novembre. Saranno ammessi al massimo 25 partecipanti. In caso di sovrannumero verrà effettuata una selezione.

Il workshop è suddiviso in moduli. E' possibile scegliere quali moduli seguire, specificandolo al momento della registrazione.

Comitato organizzatore: Diana Cruz, Paola De Giorgi, Ana Escolano Moltó, Jacopo Franzoni, Manuel Tiburtini, Sara Verni.

Abstract

Data analysis is a crucial step for all research projects, especially in biology, in which the high variability and complexity of the study systems calls for a proper selection of analytical approaches. In particular, young scientist may have a strong biological background but a not-so-well-established statistical one, mostly in advanced techniques that can be handy in some situations. This could lead to difficulties in data analyses, struggle to find valuable scientific results or, worse, drawing wrong conclusions.

The TADAB workshop aims at improving general knowledge and practical skills of the attendees concerning some of the most up-to-date analytical tools for biological analyses. A solid theoretical basis will be provided to better interpret and understand the output of the practical sessions. Topics of the lectures will span from indepth regression and machine learning analyses to coalescent models for species delimitation. The proper management and visualization of data will be also included.

At the end of the workshop attendees should have a clear overview of some of the advanced techniques for data analyses in the biological field and should gain confidence in using devoted software and R packages.

Ph.D. students will be the main target of this workshop. Nevertheless, researchers of all grades, post-doc, master and bachelor students will be welcome.

I moduli

Regression analysis of biological data in ecology

(Sergey Rosbakh)

Topics:

• Gentle introduction into linear models (model selection and assumptions, output interpretation, residual check).
• Generalised linear models with different types of data. Residuals check with DHARMa package.
• Linear mixed-effect models. Fixed vs. random factors.
• Accounting for phylogenetic relatedness in linear models.
• Non-linear models in R.

Data preparation and missing data management

(Mariasole Calbi)

Topics:

• Missing data in functional traits databases.
• How to impute missing data: phylogenetic eigenvectors (PVR), missForest, RPhylopars, bayesian hierarchical matrix factorization (BHPMF).

Application and exploration of machine learning in biological data analysis

(Sina Gholami, Manuel Tiburtini)

Topics:

• The meaning of statistical learning.
• Linear and non-linear classification models.
• Unsupervised learning.
• Build better learners.

Coalescent models in phylogeny and species delimitation

(Salvatore Tomasello)

Topics:

• Coalescent models in phylogeny.
• Multispecies coalescent model and species delimiation theory.
• Coalescent modelling using BPP and BEAST.
• Species delimitation comparison, model diagnostics and evaluation.

Data visualization with ggplot2

(David Dolci)

Topics: advanced use of the package ggplot2 in R

Programma

27 November 2023

9:00-13:00 Regression analysis of biological data in ecology.

Aula B, Polo Nobili (via Alessandro Volta 4Bis)

14:00-18:00 Regression analysis of biological data in ecology.

Aula Lab PC, "Polo San Rossore 1938 Pisa" (via Risorgimento 9)

28 November 2023

09:00-13:00 Regression analysis of biological data in ecology.

Aula ES2, Polo Nobili (via Alessandro Volta 4Bis)

14:00-18:00 Application of machine learning in biological data analysis and exploration.

Aula Lab PC, "Polo San Rossore 1938 Pisa" (via Risorgimento 9)

29 November 2023

09:00-13:00 Data visualization with ggplot2.

Aula Lab PC, "Polo San Rossore 1938 Pisa" (via Risorgimento 9)

14:00-18:00 Data analysis in biology: a Ph.D. student perspective.

Aula Seminari (Aula X), via Derna 1, first floor

30 November 2023

09:00-13:00 Coalescent models in phylogeny and species delimitation.

Aula Seminari (Aula X), via Derna 1, first floor

14:00-18:00 Coalescent models in phylogeny and species delimitation.

Aula Lab PC, "Polo San Rossore 1938 Pisa" (via Risorgimento 9)

1 December 2023

09:00-13:00 Coalescent models in phylogeny and species delimitation.

Aula Lab PC, "Polo San Rossore 1938 Pisa" (via Risorgimento 9)

14:00-18:00 Data preparation and missing data management.

Aula Lab PC, "Polo San Rossore 1938 Pisa" (via Risorgimento 9)