The 1st Bioinformatics Workshop "Introduction to bioinformatics and omics data analysis" will take place in Xishuangbanna Tropical Botanical Garden (XTBG), Chinese Academy of Sciences (CAS). The course content comprises a series of topics that cover the fundamental principles of bioinformatics, genomic and transcriptomic analyses of NGS data, and analyses in population genomics. Each day of the workshop includes 3 hours of theory and 4 hours of practice, while the last day is entirely dedicated to the research topics of the students to facilitate their advancement. We hope that after the training, each participant will be able to use this knowledge and these methods proficiently and apply them appropriately to their own research. 

 Training time

February 10-14, 2025（5 days）

2.T raining Location

Xishuangbanna Tropical Botanical Garden (XTBG), Chinese Academy of Sciences (CAS) 

3. Training costs

The training fee is 800 RMB/person. 

The transportation to and from the Xishuangbanna Botanical Garden, and the board and lodging expenses during the training period are at the students' own expense.

4. Trainees

Young scholars, graduate students, master's students, PhD students, and XTBG staff. No more than 30 people.

5. Training language

English 

6.Course Schedule

Day 1:  Principals of Bioinformatics

•Principals of bioinformatics

•Introduction to Linux + Bash + R

•Reproducibility in bioinformatics

•The bioinformatics laboratory notebook

•GGplots for bioinformatics

Day 2: Introduction to NGS data analysis and transcriptomics

•NGS platforms

•NGS data types (fasta, fastq, bam, sam, vcf)

•Transcriptomics (mRNA, smallRNA, rRNA, tRNA, miRNA, siRNA, piRNA)

•Rules of experimental design

•Examples of potential problems seen in sequencing data

•Conceptual introduction to bioinformatic steps of transcriptomic analysis

Day 3: Genomics – de novo genomes

•basics of the evolution at the genomic level (point and structural mutations, orthologs vs paralogs)

•reference genomes

•annotations

•NCBI, Ensemble & UNIPROT

•BUSCO

•The logic behind generating de-novo assemblies

•Draft assemblies

•Hi-C technique

Day 4: Genomics – Population genomics

•Single Nucleotide Polymorphism (SNP)

•SNP calling

•Possible biases and required filtering

•Introduction to GWAS

•Population Genetics analyses

•Forward individual-based simulations (SLiM)

Day 5: Interaction with the trainers

•We encourage participants to use their own data on the last day of the workshop and to interact with the trainers for their suggestions.

7.Teachers

01 Guillem Ylla

Guillem Ylla completed his PhD in Biomedicine at the Institute of Evolutionary Biology, CSIC - Pompeu Fabra University (Barcelona, Spain), followed by postdoctoral positions at the University of Florida (Gainesville, US) and Harvard University (Cambridge, US). Currently, he is the leader of the Laboratory of Bioinformatics and Genome Biology at the Faculty of Biochemistry, Biophysics, and Biotechnology at Jagiellonian University in Krakow (Poland). 

Dr. Ylla is broadly trained in Biotechnology, with expertise in Bioinformatics and experience in applying computational tools to the study of evolution and development. He teaches the course "AT4BR - Advanced Toolkit for Bioinformatics Research" at Jagiellonian University.

02 Tomasz Gaczorek

Tomasz Gaczorek completed his PhD in the Genomics and Experimental Evolution Group at Jagiellonian University in Krakow (Poland). Currently, Dr. Gaczorek is a postdoctoral fellow in the Laboratory of Bioinformatics and Genome Biology and assists Dr. Ylla with the course 'AT4BR - Advanced Toolkit for Bioinformatics Research.

03 Evgenii Baiakhmetov

Evgenii Baiakhmetov completed his PhD in Biology at Jagiellonian University in Krakow (Poland). The main research expertise of Dr. Baiakhmetov focuses on applying genomic data and bioinformatics tools in studies on hybridisation and speciation, phylogenetic reconstructions, as well as high-throughput omics data analyses. Dr. Baiakhmetov will coordinate the workshop from the XTBG side. 

8.Registration

This workshop requires participants to have a certain relevant knowledge base and experience.

(1) Be familiar with Linux + Bash + R (entry-level). 

(2) Laptops to access server. Computational resources (Ubuntu Server) will be provided by the trainers.

Registration deadline:

15:00 on February 5, 2025

URL: https://www.wjx.cn/vm/wOHZLry.aspx 

or Please  scan the QR code

9. Contact

If you have any questions about the workshop, please feel free to contact

Zhao Yiran

Zhaoyiran@xtbg.ac.cn

10. Host

Community Ecology and Conservation group,
Xishuangbanna Tropical Botanic Garden (XTBG),
Chinese Academy of Sciences (CAS)