Bioinformatics workshop 1: How to analyze scRNA-Seq data?

1. Speakers: Irene Soler Sáez and Fernando Gordillo Gómez. Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Center.
2. Date: Thursday, May 4, 2023, 4:00 p.m.-7:00 p.m. (3 hours).
3. Classroom: 3.1

Description of the workshop.

The application of omics techniques to individual cells allows the resolution of biological questions considering the particularities of each type cell phone. In this seminar, attendees will learn how to perform analysis of transcriptomic data from single cells (scRNA-seq). Specifically, the steps of quality control, normalization, selection of highly variable features, clustering, annotation of cell types, and differential expression analysis will be delved into. The seminar will present a high practical component, where attendees will be able to execute example code for the previously mentioned steps from their computer. For this purpose, it will be necessary to have R software with the following packages installed: SingleCellExperiment, Matrix, scDblFinder, scater, scran, ggplot2, PCAtools, celldex, SingleR, uwot, MAST and data.table

Bioinformatics workshop 2: Preparation of interactive reports in R, for the presentation of results bioinformatics.

1. Speakers: Carla Perpiñá Clérigues and Rubén Grillo Risco. Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Center.
2. Date: Thursday, May 11, 2023, 3:00 p.m. style="color:#222222">Requirements for attendees: laptop with R software (we will indicate the necessary packages for the practices).
3. Classroom: 3.1

Description of the workshop.

A clear and orderly presentation of the results obtained in a project or service is fundamental for their communication and interpretation. The objective of this seminar is to introduce attendees to the use of R Markdown, a very versatile tool that allows you to generate different types of documents. Likewise, it is easy to use, modify and reproduce, which translates into great time savings for the programmer. Specifically, the seminar will focus on creating HTML reports, dynamic documents with a professional appearance that offer the user an interactive experience that makes it easy to explore results. 

Bioinformatics workshop 3: Analysis of lipidomic data.

1. Speakers: Carla Perpiñá Clérigues and Rubén Grillo Risco. Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Center.
2. Date: Thursday, May 11, 2023, 5:30 p.m.-7:30 p.m. (2 hours)
3. Requirements for attendees: laptop with R software (we will indicate the necessary packages for practices).
4. Classroom: 3.1

Workshop description.

Lipidomics is gaining importance due to the structural role of lipids and their influence on signaling and inflammation processes, providing new perspectives in clinical and biomedical research. For this reason, this seminar will address a bioinformatics strategy with the aim of introducing participants to this field. The seminar will consist of two parts: i) a brief introduction to omics and the nature of data, with its advantages and limitations, and ii) the implementation of a bioinformatics strategy with a practical component that will be carried out in the R software (exploratory analysis, differential abundance, annotation and class enrichment). By the end of the seminar, participants will have a practical and theoretical understanding of the bioinformatics techniques necessary to carry out lipidomics analysis. style="text-align:justify">

Mini-CVs:

50. Francisco García García has a degree in Statistical Sciences and Techniques and a doctorate in Biomedicine and Biotechnology in the University of Valencia.  He has developed his technical and research career in different health institutions and during the last fifteen years he has been part of the team of the National Institute of Bioinformatics and the Bioinformatics platform for Rare Diseases, generating new functional enrichment analysis methods, designing and implementing web tools for the analysis of omics data and participating in numerous training activities in Bioinformatics and Computational Biology, aimed at professionals and university students.  He currently directs the Bioinformatics and Biostatistics Unit of the Príncipe Research Center. Felipe. Coordinator of the 2023 bioinformatics workshops together with Vicente Arnau, professor at the UV.

50. Irene Soler Sáez is a graduate in Biochemistry and Biomedical Sciences from the Universitat de València. After carrying out experiments from the bench in different research centers (IATA, IN, IBMCP), he decided to train in bioinformatics through the Master in Bioinformatics at the Universitat de València. Since the end of 2021, she has been carrying out her doctoral thesis at the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Center, where she investigates sex differences in multiple sclerosis using a multi-omics approach. In addition, it makes the development of the thesis compatible by collaborating with various research groups, as well as carrying out activities to praise bioinformatics in the RSG-Spain organization. style="list-style-type:lower-alpha">
50. Rubén Grillo Risco has a degree in biology from the University of Córdoba, and has a Master's degree in Biotechnology specialized in genetic analysis. He began his training in Bioinformatics by taking a Specialization Diploma in Bioinformatics Analysis at the Pablo de Olavide University, to later complete it with the Master's Degree in Bioinformatics at the University of Valencia. Since 2019 he has been working as a bioinformatics technician in the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Center, where he combines his doctorate with work and collaborations with different research groups.

50. Carla Perpiñá Clérigues is a graduate in Biology from the University of Valencia. During her internship at an in vitro fertilization center and in her years at the bench-based experimental laboratory (SBYBI-IATA), she discovered the great role of bioinformatics in different research fields. It was then when he decided to take the Master's Degree in Bioinformatics at the University of Valencia. Since the end of 2021, he has been carrying out his doctoral thesis in collaboration with the Faculty of Medicine of the University of Valencia and the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Center. Her research focuses on identifying sex differences in the effects of alcohol consumption, using a multi-omics approach. In addition, Carla is an active member of RSG-Spain, where she organizes activities and posts on social networks to share her passion for this fascinating discipline. style="list-style-type:lower-alpha">
50. Fernando Gordillo González graduated in Basic and Experimental Biomedicine at the University of Seville, where he completed his TFG on Alzheimer's. After that, he decided to expand his research training in the field of bioinformatics by completing the Master in Bioinformatics at the University of Valencia. Thanks to this training, he was able to work as part of the bioinformatics unit of the "López-Neyra" Institute of Parasitology and Biomedicine (CSIC), until, at the end of 2022, he began his doctoral thesis on the characterization of sex differences in Parkinson's through a multi-omics approach, in the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Center.