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  Events - November 2013

2013 EMBO Practical Course - Bioinformatics and statistics for large-scale data

17 Nov 2013 - 22 Nov 2013 - Shenzhen, China

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2013 EMBO Practical Course Bioinformatics and statistics for large-scale data 

17–22 November 2013 | Yantian District, Shenzhen, China 

This international advanced course will provide training on bioinformatics and statistics methods for genomic research. It will give insight into how biological knowledge can be generated from high-throughput sequencing (DNASeq, RNAseq, ChIPseq) experiments and will illustrate how to analyze such data. The course covers both the underlying statistical and algorithmic concepts, and the practice of how to automate and code such analyses using the scripting language R. 

The course will be a mix of lectures and handson training. Practicals will consist of computer exrcises that will enable the participants to apply statistical methods to the analysis of data under the guidance of the lecturers and teaching assistants. The EMBO Practical course will also teach the basics of the R/Bioconductor environment for statistical-bioinformatic data analysis. 

The course is aimed at PhD students, postdocs and interested faculty. The teaching language will be English. Basic experience in computer programming (writing scripts) is required. 


• DNA variant calling 
• differential expression 
• quality control 
• statistical significance tests and multiple testing, pathway enrichment analyses 
• clustering and classification (machine learning) 
• working with genome annotation 
 • using R and Bioconductor 

Day one
18:00 Arrival and Registration (Yolanda Zheng)
19:00 Welcome Dinner & Poster Session

Day two
8:40 Registration (Yolanda Zheng)
8:50 Introduction (W. Huber, Doris Yang, Yolanda Zheng)
9:00 Lecture: RNA-Seq, ChiP-Seq, DNA-Seq intro: what are the data analytic challenges? (G. Rustici, W. Huber)
10:00 Coffee Break
10:30 Lecture: Introduction to R and Bioconductor (M. Morgan)
11:30 Tutorial: Working with sequence data, part I (M. Morgan, W. Huber, G. Rustici)
12:30 Lunch
14:00 Practical Session: Working with sequence data. part II (M. Morgan W. Huber, G. Rustici) 16:00 Practical Session: Important concepts and idioms of the R language (Gang Chen)
17:15 Wrap-up, Question and answers
17:30 Tour of BGI
18:30 Dinner & Back to hotel

Day three
 9:00 Lecture: RNA-Seq & differential expression part I (W. Huber)
10:00 Coffee Break
10:30 Lecture: ChIP-Seq (G. Rustici)
11:30 Lecture: Leveraging Annotation and Data Integration (M. Morgan)
12:30 Lunch
14:00 Practical Session: Differential expression with DESeq and DEXSeq
16:45 Wrap-up, Question and answers
17:00 Poster Session
18:30 Dinner & Back to hotel

Day four
09:00 Lecture: Ranges-based computations (M. Morgan)
10:00 Coffee Break
10:30 Lecture: Elements of Statistics: t-test and linear model (W. Huber)
11:30 Lecture: TBC (G. Rustici)
12:30 Lunch
14:00 Practical Session: ChIP-Seq, Ranges, Annotation
16:45 Wrap-up, Question and answers
 17:00 Flashlight talks by participants (4 x 7 min)
 17:30 Dinner & Back to hotel

Day five
09:00 Lecture: RNA-Seq & differential expression part II (W. Huber)
10:00 Coffee Break
10:30 Lecture: TBC (provisional title: Gene set enrichment methods; M. Morgan)
11:30 Lecture: TBC (provisional title: Pathway analyses; G. Rustici)
12:30 Lunch
14:00 Lecture: DNA-variant calling (including plant and animal; Xin Liu)
15:00 Coffee Break
15:30 Practical Session: DNA-variant calling (Xin Liu)
16:45 Wrap-up, Question and answers
17:00 Flashlight talks by participants (4 x 7 min)
17:30 Dinner & Back to hotel

Day six
09:00 Lecture: High-Quality Data Visualisation (Huber/Rustici)
10:00 Coffee Break
10:30 Lecture: TBC (provisional title: Methods for reproducible research; M. Morgan)
11:30 Lecture: Basics of Machine Learning (Gang Chen)
12:30 Lunch
14:00 Practical Session: Machine Learning (Gang Chen)
17:00 Wrap and Departure

Wolfgang Huber EMBL Germany
Simon Anders EMBL Germany
Martin Morgan Fred Hutchinson Cancer Research Center USA
Gabriella Rustici EMBL-EBL UK
Doris Yang BGI College Shenzhen, China
Xin Liu BGI Shenzhen, China
Gang Chen BGI Shenzhen, China

Registration Fee:
Academic: € 400 / RMB 3400 / $520
Students: € 300 / RMB 2550 / $390
Industry: € 500 / RMB 4250 / $650

Register by: 20 September 2013

Yolanda Zheng
External Training Department,
BGI College
Tel :+86 -755-25273851
Beishan Industrial Zone,
Yantian District,
Shenzhen, 518083, China.

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