2013 Advanced Genomics-Bioinformatics Workshop
ILRI campus, Nairobi
Dates: October 7th - 18th, 2013
Venue: Bioscience eastern and central Africa – International Livestock Research
Institute Hub (BecA-ILRI Hub)
Workshop Facilitators:
Dr. Appolinaire Djikeng (ILRI/BecA Hub, Nairobi, Kenya)
Dr. Etienne de Villiers (Wellcome Trust, Kilifi, Kenya)
Dr. Mark Wamalwa (ILRI/BecA Hub, Nairobi, Kenya)
Ms. Joyce Njuguna (ILRI/BecA Hub, Nairobi, Kenya)
Mr. Alan Orth (ILRI/BT, Nairobi, Kenya)
Dr. Blaise Alako (EBI, UK)
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WORKSHOP PROGRAM
MONDAY (7) OCTOBER 2013:
8:30 - 8:30 Arrival and Registration
8:30 – 9:00 Welcome remarks and outline of the workshop objectives
Appolinaire Djikeng (Director, BecA-ILRI Hub, Nairobi, Kenya)
LECTURE SESSION 1: LINUX
9:00-9:30 Lecture: Basics of Bioinformatics
9:30-10:30 Lecture: Introduction to LINUX
10:30-11:00 TEA/COFFEE BREAK
11:00-12:30 Lab session: Command line LINUX
12:30-2:00 LUNCH BREAK
2:00-3:00
More about Linux: managing data with the OS built-in tools
3:00-3:30
TEA/COFFEE BREAK
3:30-4:30
Lab session: Command line LINUX - continued
4:30-5:30
Participants Presentations: Current and future projects with a possibility
for collaboration with BecA / Poster presentations display.
TUESDAY (8) OCTOBER 2013
9:00-09:45 Lecture: Unix Shell Programming
9:45-10:30 Tutorial: Applying Unix
10:30-11:00 TEA/COFFEE BREAK
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11:00-12:30 Lab session: Applying Unix
12:30-2:00 LUNCH BREAK
LECTURE SESSION 2: PERL PROGRAMMING
2:00-3:00
Perl programming: introduction, syntax, and simple data types
3:00-3:30
TEA/COFFEE BREAK
3:30-5:30
Data structures - scalar data, Lists, Arrays and Files (+Eclipse) I/O
Hands-on session
5:30 - 7:30 COCKTAIL
WEDNESDAY (9) OCTOBER 2013
9:00-10:00 Loops and Pattern matching (regular expressions)
Hands-on session
10:00-11:00 Hashes (Associative arrays) and Subroutines
Hands-on session
11:00-11:30 TEA/COFFEE BREAK
11:30-12:15 References and complex data structures
Hands-on session
12:15-1:00 Lecture: Subroutines and Modules
Hands-on session
1:00-2:00
LUNCH BREAK
2:00-3:00
BioPerl
Hands-on session
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3:30-4:00
TEA/COFFEE BREAK
LECTURE SESSION 3: EMBnet’s NGS ANALYSIS SUITE
3:30-4:30
Lecture: Introduction to EMBnet’s NGS analysis suite
4:30-5:30
Tutorial: Hands-on Training on EMBnet’s NGS analysis suite
THURSDAY (10) OCTOBER 2013
LECTURE SESSION 4: BASIC BIOINFORMATICS
9:00-09:45 Lecture: Bioinformatics resources for data management (Etienne de
Villiers)
9:45-10:30: Sequence analysis using EMBOSS tools
10:30-11:00 TEA/COFFEE BREAK
11:00-12:30 Lab session: Nucleotide and protein sequence analysis
 Sequence analysis using EMBOSS tools
12:30-2:00 LUNCH BREAK
2:00-3:00
Lecture: Database search using NCBI BLAST
3:00-3:30
TEA/COFFEE BREAK
3:30-5:00
Lab session: Hands-on BLAST Command Line Applications
5:00-5:30
Open discussion on emerging technologies, education and capacity
building: Challenges and Perspectives
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FRIDAY (11) OCTOBER 2013
LECTURE SESSION 5: CLC BIO
Program of the day to be provided by Oliver Preseig
SATURDAY (12) AND SUNDAY (13) OCTOBER 2013
Continued hands-on practice on Linux, Perl and other basic bioinformatics tools learnt
in the past week.
MONDAY (14) OCTOBER 2013
LECTURE SESSION 6: GENOMICS AND NGS TECHNOLOGIES
9:00 - 9:30 Lecture: Introduction to Genomics and applications to Infectious Diseases
(Sequencing, transcriptomics, proteomics, systems bio, etc)
9:30 - 10:30 Lecture: Overview of Sequencing Technologies, Sanger sequencing and
(NGS).
10:30 - 11:00 TEA/COFFEE BREAK
10:30 - 11:30 Lecture: Transcriptomics (RNA-SEQ) using Next Generation Sequencing
(NGS) Technologies
Algorithms behind assembly of short reads (Velvet and AbySS) and
mapping short reads to the genome (Bowtie and BWA etc).
11:30 - 12:30 Lab session: NGS-Data analysis and computation
Topics:
NGS Quality control
Assembly, Annotation.
Comparative Genomic Analysis
12:30 - 2:00 LUNCH BREAK
2:00 – 3:30 Lab session – NGS-Data analysis and computation -Continued
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3:30 - 4:00 TEA/COFFEE BREAK
4:00 - 5:00 Lab session – Working with the output: Introduction to Sam tools and IGV
Visualize your RNA-seq output
TUESDAY (15) OCTOBER 2013:
LECTURE SESSION 7: INTEGRATED DATA SETS
8:30-09:15 Lecture: Statistical Analysis of RNA-seq data.
-Normalizing your data.
-Introduction to Basic Statistics to determine differentially
-expressed genes (Cuffdiff)
- Correlation and clustering of data ( looking at heatmaps )
- Using MeV to analyze RNA-seq data
9:15-10:00 Lab session: Statistical Analysis of RNA-seq data
10:00 - 10:30 TEA/COFFEE BREAK
10:30 – 11:15 Lecture: A Systems Biology Approach to Study Infectious Diseases,
Genomes and Microbiomes.
11:15 - 12:30 Lab session – Systems Biology Approaches for Studying
Genomes and Microbiomes
Topics: 16S rDNA data analysis, WGS‐assembly of genomes and data
analysis, RNA Seq Analysis, Metagenomics and Microbiome
Analysis–Tools and Approaches.
12:30 - 2:00 LUNCH BREAK
2:00 – 3:00
3:00 -3:30
Lab session – Systems Biology Approaches for Studying Genomes and
Microbiome continued
TEA/COFFEE BREAK
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3:30 - 5:00 Lab session: Introduction to CLOUD Computing and using tools in CLOUD
WENESDAY (16) OCTOBER 2013
LECTURE SESSION 8: METAGENOMICS AND METAGENOME ANALYSIS.
9:00-9:30
Metagenomics data analysis current state-of-the-art WGS analysis
workflows (from annotation to comparative analysis)
9:30 - 12:30 Lab session – Using Solr/Lucene for Large-Scale Metagenomics Data
Retrieval and Analysis. Large-scale Metagenomics Analysis using JCVI
Metagenomics Reports (METAREP)
Hands on Session.
12:30 - 2:00 LUNCH BREAK
2:00 - 3:30 Lab session: Introduction to MEGAN metagenomics analysis software
3:30 -4:00
TEA/COFFEE BREAK
4:00 -5:00
5:00 -5:30
Lecture: Introduction to EBI and ENSEMBLE resources (Blaise Alako)
Demo: ENSEMBL database (Blaise Alako)
THURSDAY (17) OCTOBER 2013
9:00-10:00 EBI – metagenomics portal for analysis and archiving (Blaise Alako)
10:00-10:30 COFFEE BREAK
10:30-11:30 Lab session: EBI – metagenomics portal (Blaise Alako)
LECTURE SESSION 9: MULTIPLE SEQUENCE ANALYSIS AND PHYLOGENETICS
11:30-12:30 Multiple Sequence Alignment (MSA) and phylogenetic methods
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12:30-2:00 LUNCH BREAK
2:00-3:30
Lab session: Hands-on Session MSA and phylogenetic tree construction
3:30-4:00
TEA/COFFEE BREAK
4:00 - 5:00
Lab session:
FRIDAY (18) OCTOBER 2013
LECTURE SESSION 10: BAYESIAN PHYLOGENETIC ANALYSIS
9:00-10:00 Lecture: Introduction to Bayesian phylogenetic analysis
Topics: Markov chain Monte Carlo sampling
Comparison of MrBayes and BEAST
Strict molecular clocks and relaxed molecular clocks
Calibrating estimates of rates and divergence times
10:00-10:30 TEA/COFFEE BREAK
10:30-12:30 Lab session: Phylogenetic analysis using BEAST
Creating and manipulating input files
Interpreting BEAST output
12:30 - 2:00 LUNCH BREAK
2:00 - 3:00 Lab session: Phylogenetic analysis using BEAST continued
3:00 - 3:30 TEA/COFFEE BREAK
3:30 - 4:00 Final Lab wrap-up session
Closing Keynote: Engaging African Scientists in the Genomics Revolution
4:00 - 4:30 Closing Remarks and Certificates: Appolinaire Djikeng.
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