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Workshops 2023

  • April 25th, 2023
Workshops 2023

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

  1. Speakers: Irene Soler Sáez and Fernando Gordillo Gómez. Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre.
  2. Date: Thursday 4 May 2023, 16h-19h (3 hours).
  3. Room: 3.1

Workshop description

The application of omics techniques to individual cells allows answering biological questions taking into consideration the distinctive features of each cell type. In this seminar, the attendants will learn how to carry out a transcriptomic data analysis coming from individual cells (scRNA-seq). Specially, there will be more analysis on the steps of quality control, standardisation, selection of highly variable characteristics, clustering, taking note of cell types, and analysis of differential expression. The seminar will involve a high practical level, where attendants will be able to run an example code from their computers for the steps previously mentioned. With this aim, it will be necessary to have the R software with the following packages installed: SingleCellExperiment, Matrix, scDblFinder, scater, scran, ggplot2, PCAtools, celldex, SingleR, uwot, MAST and data.table

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

  1. Speakers: Carla Perpiñá Clérigues and Rubén Grillo Risco. Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre.
  2. Date: Thursday 11 May 2023, 15h-17h (2 hours)
  1. Requirements for attendants: laptop with R software (we will inform of the packages needed for workshops).
  2. Room: 3.1

Workshop description

A clear and organised presentation of the results obtained in a project or service is essential for they communication and interpretation. The objective of this seminar is introducing to attendants in the use of R Markdown, a very versatile tool that allows creating different types of documents. In addition, it is easy to use, modify and play, which is translated in time saving for the programmer. Specifically, the seminar will focus on the elaboration of HTML reports, dynamic documents with a professional aspect that offer to users an interactive experience which makes easier the results exploration.

Bioinformatics workshop 3: Lipidomics data analysis.

  1. Speakers: Carla Perpiñá Clérigues and Rubén Grillo Risco. Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre.
  2. Date: Thursday 11 May 2023, 17h30-19h30 (2 hours).
  3. Requirements for attendants: laptop with R software (we will inform of the packages needed for workshops).
  4. Room: 3.1

Workshop description

Lipidomics is gaining importance due to the structural role of lipids and its influence on the signalling and swelling processes, which provides new perspectives in clinical and biomedical research. For this reason, this seminar will cover a bioinformatics strategy with the objective of introducing the participants in this field. The seminar will be formed by two parts: i) a short introduction to omics and to the nature of data, with its advantages and disadvantages, 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 analysis, annotation and class enrichment). At the end of the seminar, participants will acquire a practical and theoretical knowledge of bioinformatics techniques in order to carry out a lipidomics analysis.

Mini-CVs:

  1. Francisco García García is graduated in Sciences and Statistical Techniques and was awarded a doctorate in Biomedicine and Biotechnology in the Universitat de València. He has developed his technical and researcher background in different health institutions and during the last fifteen years he has formed part of both, the National Bioinformatics Institute team, and of the platform of Bioinformatics for Uncommon Diseases. Not only has he created new methodological analysis of functional enrichment, but he has also designed and implemented web tools for omics data analysis. In addition, he has participated on several training activities in Bioinformatics and Computational Biology, addressed to professionals and university students. He currently runs the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre. Coordinator of bioinformatics workshops 2023 together with Vicente Arnau, lecturer of the UV.
  1. Irene Soler Sáez is graduated in Biochemistry and Biomedical Sciences by the Universitat de València. After conducting experiments from the bench of different research centres (IATA, IN, IBMCP), she decided being trained in bioinformatics through the Master’s Degree in Bioinformatics of the Universitat de València. Since the end of 2021, she is doing her doctoral theses in the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre, where she conducts researches of gender differences in multiple sclerosis through a multiomic approach. What is more, she coordinates the thesis development collaborating with several research groups, as well as with the development of activities for extolling bioinformatics in the RSG-Spain organisation.
  1. Rubén Grillo Risco is graduated in Biology by the University of Córdoba, and has a Master’s Degree in Biotechnology specialised in genetic analysis. He started his training in Bioinformatics studying a Diploma in Bioinformatics Analysis in the University Pablo de Olavide, for then completing it with the Master’s Degree in Bioinformatics of the Universitat de València. Since 2019 he works as a bioinformatics technician in the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre, were he coordinates his doctorate with works and cooperation with different research groups.
  1. Carla Perpiñá Clérigues is graduated in Biology by the Universitat de València. During her internships in an in vitro fertilization centre and during her years in the experimental laboratory in bench (SBYBI-IATA), she discovered the great role that bioinformatics plays in the different fields of research. It was then when she decided to study the Master’s Degree in Bioinformatics of the Universitat de València. Since the end of 2021 she is carrying out her doctoral thesis in cooperation with the Faculty of Medicine of the Universitat de València and the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre. Her research is focused on identifying the gender differences in the effects of alcohol consumption, from a multiomic approach. In addition, Carla is an active member of RSG-Spain, where she organises activities and publishes in social media for sharing her passion for this exciting discipline.
  1. Fernando Gordillo González is graduated in Basic and Experimental Biomedicine in the University of Sevilla, where she did her undergraduate degree final project in bench on Alzheimer. After this, she decided to extend their research training in the field of bioinformatics by studying the Master’s Degree in Bioinformatics of the Universitat de València. This training helped her being part of the Bioinformatics Unit of the Institute of Parasitology and Biomedicine “López-Neyra” (CSIC), until the end of 2022, when she started doing her doctoral thesis in the characterisation of gender differences in Parkinson through a multiomic approach, in the Bioinformatics and Biostatistics Unit of the Príncipe Felipe Research Centre.