2013 Advanced Genomics-Bioinformatics Workshop ILRI campus, Nairobi

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2013 Advance
d

Genomics
-
Bioinformatics Workshop

ILRI campus, Nairobi



Dates
:
October

7
th

-

18
th
,
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 (
Wel
l
come 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)




pwd
2

WORKSHOP PROGRAM


MONDAY

(
7)
OCTOBER

201
3
:



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
-
12:3
0

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:
3
0

Lab session
: Command line LINUX

-

continued


4
:3
0
-
5:30

Participants Presentations: Current and future projects with a possibil
ity
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

3


11:00
-
12:30

Lab session
: Applying Unix



12:30
-
2:00


LUNCH BREAK


LECTURE SESSION 2:
PE
RL 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
-
10:0
0

Loops and Pattern
matching (regular expressions)



Hands
-
on session




10
:
0
0
-
11:0
0

Hashes (Associative arrays) and Subroutines



Hands
-
on session


11:00
-
11:3
0

TEA/COFFEE BREAK


11:30
-
12:15

References and complex data structures



Hands
-
on sessio
n


12:15
-
1:0
0

Lecture
:
Subroutines and Modules



Hands
-
on session


1:0
0
-
2:00


LUNCH BREAK


2:00
-
3:00

BioPerl



Hands
-
on session


4

3:30
-
4:0
0


TEA/COFFEE BREAK


LECTURE SESSION 3: EMB
net’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


LECT
URE SESSION 4
:
BASIC BIOINFORMATICS


9:00
-
09:45


Lecture
:

Bioinformatics r
esources f
or data management
(
Etienne de
Vill
i
er
s)


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





5

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
, P
erl

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


Algo
rithms behind assembly of short reads
(Velvet and AbySS
) and
mapping short reads to the genome (Bowtie and
BWA

etc
).


11:30
-

12
:3
0

Lab session:
NGS
-
Data analysis and computation



Topics:



NGS Quality control


Assembly, Annotation.





Comparative Genomic
Analysis


12:30
-

2
:
0
0


LUNCH BREAK



2:00


3
:30

Lab session



NGS
-
Data analysis and computation
-
Continued



6

3:30
-

4:0
0

TEA/COFFEE BREAK


4:0
0
-

5
:0
0

Lab session



Working with the output: Introduction to Sam tools and IGV






Visualize your RNA
-
seq output






TUESDAY
(
15
)

OCTOBER
201
3
:


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


10:0
0
-

10:3
0



TEA/COFFEE BREAK


10:30


11:15
Lecture
:
A

Systems Biology Approac
h to Study Infectious Diseases,





Genomes and Microbiomes.


11:15
-

12:3
0

Lab session



Systems Biology Appr
oaches for Studying





Genomes and Microbiomes




Topics:

16S rDNA data analysis, W
GS‐assembly of
genomes and data





analysis, RNA Seq Analys
is, Metagenomics and Microbiome






Analysis

Tools and Approaches.



12:30
-

2
:00

LUNCH BREAK



2:00


3:00

Lab session



Systems Biology Approaches for Studying Genom
es and






Microbiome

continued


3:00
-
3:30

TEA/COFFEE BREAK


7

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
Metagen
omics Reports (METAREP)





Hands on Session
.


12:30
-

2
:
0
0

LUNCH BREAK



2
:
0
0
-

3:
3
0

Lab session
:

Introduction to MEGAN metagenomics analysis software


3:30
-
4:
00

TEA/COFFEE BREAK




4:0
0
-
5:0
0

Lecture
:

Introduction to EBI and ENSEMBLE
resources (
Blaise Alako
)

5
:0
0
-
5:3
0

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
-
11:3
0

Lab session
:

EBI


metagenomics

portal

(
Blaise Alako
)


LECTURE SESSION 9:

MULTIPLE SEQUENCE ANALYSIS AND PHYLOGENETICS


11
:3
0
-
12
:3
0

Multiple Sequence Alignment (MSA) and phylogenetic methods

8


12:30
-
2
:00

LUNCH BREAK


2:00
-
3:30

Lab session
:

Hands
-
on Session MSA and
phylogenetic tree construction




3
:3
0
-
4:0
0


TEA/COFFEE BREAK


4:00
-

5
:00


Lab session
:



FRIDAY

(
18
)
OCTOBER
2013


LECTURE SESSION 10
:

BAYESIAN PHYLOGENETIC ANALYSIS


9:00
-
10:0
0

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
-
10:3
0
TEA/COFFEE BREAK


10:3
0
-
12:30

L
ab 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
.