EMBO Practical Course Bioinformatics and statistics for large-scale data - China
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Date:
Sunday 17 November 2013Application deadline:
Friday 20 September 2013Registration closed
Overview
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 (DNA-Seq, RNA-seq, ChIP-seq) 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 hands-on training. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of data under the guidance of the lecturers and teaching assistants. The 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.
Specific topic areas include:
- 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
Additional information
Travel Grants
A limited number of travel grants are available for eligible participants who are selected to attend EMBO Practical Courses. The aim of these grants is to facilitate the participation of those coming from labs located in countries in need of scientific strengthening.
These grants are designed to cover travel (Apex / Economy) to attend the practical course. (Visa costs, accommodation and subsistence will not be covered by these funds).
Priority is given to participants working in labs in: Croatia, Czech Republic, Cyprus, Estonia, Greece, Hungary, Israel, Poland, Portugal, Slovakia, Slovenia, and Turkey.
Travel grants may also be provided to participants working in labs in the following: Africa, Asia (excluding Japan, Singapore, and Korea) South and Central America, Albania, Armenia, Azerbaijan, Bulgaria, Belarus, Bosnia and Herzegovina, Bulgaria, Georgia, Kazakhstan, Kosovo, Kyrgyzstan, Lithuania, Macedonia, Malta, Moldova, Montenegro, Romania, Russia, Serbia, and Ukraine.
Further details regarding this course can be found here: http://events.embo.org/13-large-scale-data/index.html
Programme
| Time | Topic | Trainer |
|---|---|---|
| Sunday 17 November | ||
| 18:00 | Arrival and registration | |
| 19:00 | Welcome Dinner & Poster Session | |
| Monday 18 November | ||
| 08:40 | Registration | |
| 08:50 | Course overview | Wolfgang Huber, Doris Yang, Yolanda Zheng |
| 09:00 | Lecture: RNA-Seq, ChiP-Seq, DNA-Seq intro: what are the data analytic challenges? | Gabriella Rustici, Wolfgang Huber |
| 10:00 | Coffee break | |
| 10:30 | Lecture: Introduction to R | Wolfgang Huber |
| 11:30 | Lecture: Introduction to Bioconductor | Martin Morgan |
| 12:30 | Lunch | |
| 14:00 | Practical Session: Basics of R | Bo Wen |
| 17:00 | Flashlight talks by participants (4 x 7 min) | |
| 17:30 | Dinner | |
| Tuesday 19 November | ||
| 09:00 | Lecture: RNA-Seq & differential expression part I | Wolfgang Huber |
| 10:00 | Coffee break | |
| 10:30 | Lecture: ChIP-Seq | Gabriella Rustici |
| 11:30 | Lecture: Leveraging Annotation and Data Integration | Martin Morgan |
| 12:30 | Lunch | |
| 14:00 | Practical session: Differential expression with DESeq and DEXSeq | |
| 17:00 | Flashlight talks by participants (4 x 7 min) | |
| 17:30 | Dinner | |
| Wednesday 20 November | ||
| 09:00 | Lecture: Ranges-based computations | Martin Morgan |
| 10:00 | Coffee break | |
| 10:30 | Lecture: Elements of Statistics: t-test and linear model | Wolfgang Huber |
| 11;30 | tbc | Gabriella Rustici |
| 12:30 | Lunch | |
| 14:00 | Practical Session: ChIP-Seq, Ranges, Annotation | |
| 17:00 | Flashlight talks by participants (4 x 7 min) | |
| 17:30 | Dinner | |
| Thursday 21 November | ||
| 09:00 | Lecture: RNA-Seq & differential expression part II | Wolfgang Huber |
| 10:00 | Coffee break | |
| 10:30 | Lecture: Gene set enrichment methods (tbc) | Martin Morgan |
| 11:30 | Lecture: Pathway analysis (tbc) | Gabriella Rustici |
| 12:30 | Lunch | |
| 14:00 | Lecture: DNA-variant calling including plant and ani | Xin Liu |
| 15:00 | Coffee break | |
| 15:30 | Practical Session: DNA-variant calling | Xin Liu |
| 17:00 | Flashlight talks by participants (4 x 7 min) | |
| 17:30 | Dinner | |
| Friday 22 November | ||
| 09:00 | Lecture: High-Quality Data Visualisation | Gabriella Rustici, Wolfgang Huber |
| 10:00 | Coffee break | Martin Morgan |
| 10:30 | Lecture: Methods for reproducible research (tbc) | |
| 11:30 | Lecture: Basics of Machine Learning | Gang Chen |
| 12:30 | Lunch | |
| 14:00 | Practical session: Basics of Machine Learning | |
| 17:00 | Wrap up and departure | |
How to apply
| Registration Fee: | |||
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Academic Students Industry |
€ 400 € 300 € 500 |
RMB 3.400 RMB 2.550 RMB 4.250 |
$520 $390 $650 |
Registration deadline: 20 September
Participants will be notified regarding acceptance by 7 October.
Registration fee includes:
- accommodation (16 Nov to 22 Nov)
- Access to all scientific sessions
- abstract book
- 10 coffee breaks
- welcome dinner
- all breakfasts and lunches
- gala dinner
The course language is English therefore the ability to understand and communicate in English is required. Experience with computer programming or scripting and basic knowledge of R is required.
Please pay the registration fee only when you have received a “Letter of Acceptance" on 7 October.
Registration fee should be paid before the deadline 31st October.
PAYMENT
Wire Transfer
(please include very word even "blank" and it should be the same as below per Chinese bank requirement)
******Domestic******
开 户 行：中国工商银行深圳保税区支行
开户名称： 深圳市华大基因学院
账 号：4000 0255 0920 0144 415
汇款时请务必标明"您的姓名"
******Foreign*******
Account name: BGI College
Office address: Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083 China
Beneficiary's bank: INDUSTRIAL AND COMMERCIAL BANK OF CHINA, SHENZHEN BRANCH YANTIAN DISTRICT BRANCH
Office address: No.99, Finance Road Yantian town, Yantian district, Shenzhen, China.
IBAN (International Bank Account Number): 4000 0255 0920 0144 415
SWIFT code (BIC): ICBKCNBJSZN
Note: Please send us an email: training@service.genomics.cn after paying with the following information:
- Account holder (if different to participant)
- Participant's name
- Organization/Affiliation
- Amount
- Date
Credit Card
Payment can be made at the registration desk on the first day of the Practical Course using Visa or Master Card. Accommodation will still be guaranteed.
Application deadline
20 September 2013
Organisers
Yolanda Zheng - BGI College, China
Wolfgang Huber
Grace Ji - BGI College, China
Trainers
Yolanda Zheng - BGI College, China
Doris Yang - BGI College, China
Gang Chen - BGI College, China
Bo Wen - BGI College, China
Xin Liu - EMBL-EBI, UK