Introduction to Molecular Biology
and Bioinformatics
May 2016
|
Time |
Activity |
Location |
Trainers/resource persons |
|
Day 1: Monday 9th May |
|||
|
0730 |
Bus leaves Pride Inn for
ILRI |
Pride
Inn |
|
|
0800-0815 |
Registration |
N’Dama Lounge |
Val Aloo,
Marvin Wasonga |
|
0815-0830 |
Workshop Opening · Introducing the participants and trainers |
N’Dama Lounge |
Appolinaire Djikeng,
Wellington Ekaya |
|
0830-0930 |
Introduction to the course ·
Overview
of BecA-ILRI Hub and the ABCF Program ·
Housekeeping
issues ·
Objectives
and expectations ·
Workshop
outline ·
Inqaba
Introduction |
N’Dama Lounge |
Wellington Ekaya Francesca Stomeo Fabrice Wane/Jose Geda |
|
0930-1000 |
Pre-workshop test |
N’Dama Lounge |
Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Joyce Njuguna, Dedan Githae, Maureiq
Ojwang, Collins Mutai,
Leah Kago |
|
1000-1015 |
Tea/coffee/ Group photo |
N’Dama Lounge |
|
|
1015-1115 |
Seminar · Laboratory Health and Safety |
N’Dama Lounge |
Ephy Khaemba |
|
1115-1145 |
Lab · Laboratory Health and Safety |
Lab 4 |
Ephy Khaemba |
|
1145-1245 |
Lab ·
Pipetting
skills ·
Introduction
to lab equipment |
Lab 4 |
Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Collins Mutai, Leah Kago |
|
1245-1330 |
Lunch |
Poolside |
|
|
1330-1500 |
Seminar ·
Molecular
biology and DNA structure (30’) ·
Genomic
DNA extraction (30’) ·
Agarose gel
electrophoresis (30’) |
N’Dama Lounge |
Francesca Stomeo Roger Pelle Tina Kyalo |
|
1500-1600 |
Seminar ·
The
benefits of tropical forage genetic resources to African agriculture (30’) ·
Seminar
Importance and History of Phytophthora (30’) |
N’Dama Lounge |
Sita Ghimire/Collins Mutai/Leah Kago Jean Ristaino |
|
1600-1700 |
Seminar · Phytophthora Isolation and Morphology (60’) |
N’Dama Lounge |
Jean Ristaino |
|
1700-1730 |
Tea/coffee |
N’Dama Lounge |
|
|
1830 |
Bus leaves ILRI for Pride
Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 2: Tuesday 10th
May |
|||
|
0745 |
Bus leaves Pride
Inn for ILRI |
Pride
Inn |
|
|
0830-0900 |
Outline of Day 2 activities and
Q&A |
N’Dama Lounge |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Collins Mutai,
Leah Kago |
|
0900-0930 |
Seminar · Lucid keys for species identification (30’) |
N’Dama Lounge |
Jean Ristaino |
|
0930-1030 |
Lab · Morphology Lab- unknowns (60’) |
Lab 4 |
Jean Ristaino
(leading) Francesca Stomeo, Tina Kyalo, Roger Pelle, Pauline Asami, Eunice Machuka, Collins Mutai, Leah Kago (assistance) |
|
1030-1045 |
Tea/coffee |
Tent outside Lab 4 |
|
|
1045-1300 |
Lab · DNA Extractions – fresh, dried
material (plant) (165’) |
Lab 4 |
Jean Ristaino Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Collins Mutai, Leah Kago |
|
1300-1400 |
Lunch |
Poolside |
|
|
1400-1600 |
Lab · DNA purification (animal tissue) (120’) |
Lab 4 |
Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Collins Mutai, Leah Kago |
|
1600-1630 |
Seminar · Spectrophotometry of nucleic acids (30’) |
N’Dama Lounge |
Pauline Asami |
|
1630-1700 |
Review of Day 2 activities and
Quiz (30’) |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Collins Mutai,
Leah Kago |
|
1700-1730 |
Tea/coffee |
N’Dama Lounge |
|
|
1830 |
Bus leaves ILRI for Pride
Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 3: Wednesday 11th
May |
|||
|
0745 |
Bus leaves Pride
Inn for ILRI |
Pride
Inn |
|
|
0830-0900 |
Outline of Day 3 activities and
Q&A |
N’Dama Lounge |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Collins Mutai,
Leah Kago |
|
9000-9030 |
Seminar · NanoDrop spectrophotometry of DNA (30’) |
N’Dama Lounge |
Fabrice Wane/Jose Geda |
|
9030-1030 |
Lab (60’) ·
New NanoDrop System ·
Preparation
of 1% agarose gels ·
Gel
electrophoresis of DNA (1% gel) |
Lab 4 |
Fabrice Wane/Jose Geda Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Mutai Collins, Leah Kago |
|
1030-1045 |
Tea/coffee |
N’Dama Lounge |
|
|
1045-1145 |
Seminar (60’) · Introduction to PCR: theory and principle |
N’Dama Lounge |
Roger Pelle |
|
1145-1300 |
Lab (75’) ·
PCR set up
using Bioneer master mix ·
1.8% agarose gel electrophoresis (pre-run) |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Collins Mutai,
Leah Kago |
|
1300-1400 |
Lunch |
Poolside |
|
|
1400-1500 |
Seminar (60’) ·
Restriction
analysis of DNA ·
PCR-RFLP ·
LAMP PCR
and primer design |
N’Dama Lounge |
Jean Ristaino |
|
1500-1530 |
Lab (30’) · LAMP PCR Assays |
Lab 4 |
Jean Ristaino Francesca Stomeo, Tina Kyalo, Roger Pelle, Pauline Asami, Eunice Machuka, Collins Mutai, Leah Kago (assistance) |
|
1530-1630 |
Lab (60’) · PCR identification – Rapid PCR Assay |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Collins Mutai,
Leah Kago |
|
1630-1700 |
Review of Day 3 activities and
Quiz |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Collins Mutai,
Leah Kago |
|
17h00 - 17h30 |
Tea/coffee |
Tent outside Lab 4 |
|
|
1830 |
Bus leaves ILRI for Pride
Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 4: Thursday 12th
May |
|||
|
0745 |
Bus leaves Pride
Inn for ILRI |
Pride
Inn |
|
|
0830-0900 |
Outline of Day 4 activities and
Q&A |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Mutai
Collins, Leah Kago |
|
0900-1030 |
Lab (90’) ·
Gel
electrophoresis of PCR products ·
Purification
of PCR product using column |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Mutai
Collins, Leah Kago |
|
1030-1045 |
Tea/coffee |
Tent outside the Lab |
|
|
1045-1200 |
Lab (75’) ·
NanoDrop
spectrophotometry of purified PCR products · Submit
PCR products to SegoliP Unit for DNA sequencing ·
Restriction
digest of PCR products |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Leah Kago,
Collins Mutai |
|
1200-1300 |
Seminar (60’) · PCR optimisation and Standard PCR primer
design |
N’Dama Lounge |
Roger Pelle |
|
1300-1400 |
Lunch |
Poolside |
|
|
1400-1630 |
Lab (150’) ·
Preparation
of agarose gels (2%) ·
PCR set
up: optimisation by Mg titration ·
PCR run ·
Gel
electrophoresis of restriction digest of PCR products |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Mutai
Collins, Leah Kago |
|
1630-1700 |
Review of Day 4 activities and
Quiz |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Mutai
Collins, Leah Kago |
|
17h00 - 17h30 |
Tea/coffee |
Tent outside Lab |
|
|
1800 |
Bus leaves ILRI for Pride Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 5: Friday 13th
May |
|||
|
0745 |
Bus leaves Pride Inn for
ILRI |
Pride Inn |
|
|
0830-0900 |
Outline of Day 5 activities and
Q&A |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka |
|
0900-0930 |
Lab (30’) · PCR set up: optimisation by gradient
annealing temperature |
Lab 4 |
Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Leah Kago, Collins Mutai |
|
0930-1000 |
Lab (30’) · Set up LAMP PCR (repeat) |
Lab 4 |
Jean Ristaino Francesca Stomeo, Tina Kyalo, Roger Pelle, Pauline Asami, Eunice Machuka, Mutai Collins, Leah Kago
(assistance) |
|
1000-1030 |
Lab (30’) · Preparation of agarose
gels (2%) |
Lab 4 |
Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Mutai Collins, Leah kago |
|
1030-1045 |
Tea/coffee |
Tent outside the Lab |
|
|
1100-1200 |
Seminar (60’) ·
Restriction
digest analysis ·
Concentration/purification
of DNA by precipitation |
N’Dama Lounge |
Eunice Machuka |
|
1200-1300 |
Lab (60’) ·
LAMP PCR
analysis and gel electrophoresis ·
Concentration/purification
of DNA by ethanol precipitation |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Leah Kago,
Mutai Collins |
|
1300-1400 |
Lunch |
Poolside |
|
|
1400-1630 |
Seminar (practical) (150’) · Data analysis and interpretation |
N’Dama Lounge |
Jean Ristaino |
|
1630-1700 |
Review Day 5 activities and
Quiz |
Lab 4 |
Jean Ristaino,
Francesca Stomeo, Tina Kyalo,
Roger Pelle, Pauline Asami,
Eunice Machuka, Mutai
Collins, Leah Kago |
|
17h00 - 17h30 |
Tea/coffee |
Tent outside Lab 4 |
|
|
1730-2000 |
Barbeque dinner |
Poolside |
Marvin/David |
|
2000 |
Bus leaves ILRI for Pride
Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 6: Saturday 14th
May |
|||
|
0745 |
Bus leaves Pride Inn for
ILRI |
Pride Inn |
|
|
0830-0900 |
Outline of Day 6 activities and
Q&A |
Lab 4 |
Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
0900-1030 |
Lab (90’) ·
Preparation
of agarose gels (1.8%) ·
Gel
electrophoresis of precipitated PCR products ·
Repeat lab
work as required |
Lab 4 |
Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1030-1045 |
Tea/coffee |
Tent outside lab 4 |
|
|
1045-1230 |
Lab (105’) · Download and installation of CLC for
Bioinformatics |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae |
|
1230-1330 |
Lunch |
Poolside |
|
|
1500 |
Bus leaves ILRI for Pride Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 7: Sunday 15th
May |
|||
|
All day |
Day of rest. Participants are
free to tour Nairobi or go shopping at their own discretion. |
||
|
|
|
|
|
|
Day 8: Monday 16th
May |
|||
|
0745 |
Bus leaves Pride Inn |
Pride Inn |
|
|
0830-0900 |
Outline of Day 8 activities and
Q&A |
Lab 4 |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
0900-0945 |
Seminar ·
Principle
of DNA sequencing (30’) ·
Principle
of NGS Technologies and Illumina MiSeq |
JVC |
Roger Pelle Francesca Stomeo |
|
0945-1030 |
Lab · Suppliers Exhibition |
Outside |
All |
|
1030-1045 |
Tea/coffee |
Tent outside lab 4 |
|
|
1045-1300 |
Seminar: Introduction to
bioinformatics ·
What is
bioinformatics? ·
Scope of
bioinformatics ·
History of
bioinformatics ·
Applications
of bioinformatics |
JVC |
Joyce Njuguna |
|
1300-1400 |
Lunch |
Poolside |
|
|
1400-1530 |
Lab tour (90’) · The BecA-ILRI Hub (90’) |
Lab 4, BecA-ILRI Hub and Brachiaria field |
Julius Osaso
and team |
|
1530-1600 |
Tea/coffee |
Tent outside Lab 4 |
|
|
1600-1645 |
Seminar (45’) · Introduction to the Participant Action Plan
Approach (PAPA) |
JVC |
Wellington Ekaya
and Val Aloo |
|
1645-1730 |
Review of Day 8 activities and
Quiz |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1800 |
Bus leaves ILRI for Pride Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 9: Tuesday 17th
May |
|||
|
0745 |
Bus leaves Pride Inn for
ILRI |
Pride Inn |
|
|
0830-0900 |
Introductions and Outline of
Day 9 activities |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
0900-1030 |
Seminar: ·
Introduction
to CLC Main Workbench ·
Sequence
trace file editing ·
Sequence
assembly |
JVC |
Dedan Githae |
|
1030-1045 |
Tea/coffee |
JVC |
|
|
1145-1245 |
Practical ·
Importing
data into CLC ·
Quality
control of data ·
BLAST |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1245-1345 |
Lunch |
Poolside |
|
|
1345-1530 |
Practical · Sequence assembly and resolving conflicts |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1530-1545 |
Tea/coffee |
JVC |
|
|
1545-1730 |
Practical · Sequence assembly - continued |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1730-1800 |
Review Day 9 activities and
Quiz |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1800 |
Bus leaves ILRI for Pride
Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 10: Wednesday 18th
May |
|||
|
0745 |
Bus leaves Pride Inn for
ILRI |
Pride Inn |
|
|
0830-0900 |
Outline of Day 10 activities
and Q&A |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
0900-1030 |
Seminar · DNA Barcoding |
JVC |
Joyce Njuguna |
|
1030-1045 |
Tea/coffee |
JVC |
|
|
1045-1245 |
Practical · DNA Barcoding |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1245-1345 |
Lunch |
Poolside |
|
|
1345-1530 |
Seminar ·
Biological
databases ·
BLAST |
JVC |
Maureiq Ojwang |
|
1530-1545 |
Tea/coffee |
JVC |
|
|
1545-1730 |
Practical · BLAST and result interpretation |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1730-1800 |
Review Day 10 activities and
Quiz |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1800 |
Bus leaves ILRI for Pride
Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 11: Thursday 19th
May |
|||
|
0745 |
Bus leaves Pride Inn for
ILRI |
Pride Inn |
|
|
0830-0900 |
Outline of Day 11 activities
and Q&A |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
0900-0945 |
Seminar ·
Nucleotide
sequence analysis and editing o
Sequence
transcription o
Reverse
complement o
Trimming o
Open
reading frames and translation o
Restriction
enzyme analysis |
JVC |
Dedan Githae |
|
0945-1030 |
Practical ·
Nucleotide
sequence analysis and editing ·
Restriction
enzyme analysis |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1030-1045 |
Tea/coffee |
JVC |
|
|
1045-1130 |
Seminar · Multiple sequence alignments |
JVC |
Maureiq Ojwang |
|
1130-1245 |
Practical · Multiple sequence alignments |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1245-1345 |
Lunch |
Poolside |
|
|
1345-1530 |
Seminar · Phylogenetics |
JVC |
Joyce Njuguna |
|
1530-1545 |
Tea/coffee |
JVC |
|
|
1645-1730 |
Practical · Phylogenetics |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1730-1800 |
Review Day 11 activities and
Quiz |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1800 |
Bus leaves ILRI for Pride
Inn |
ILRI Reception |
|
|
|
|
|
|
|
Day 12: Friday 20th
May |
|||
|
0745 |
Bus leaves Pride Inn for
ILRI |
Pride Inn |
|
|
0830-0900 |
Outline of Day 12 activities
and Q&A |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
0900-1000 |
Seminar ·
Online
bioinformatics resources o
Further
sequence manipulation o
Physiochemical
properties o
Motifs and
domains o
Cellular
localization o
Secondary
structure |
JVC |
Dedan Githae/Joyce Njuguna |
|
1000-1030 |
Practical · Further sequence analysis |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1030-1045 |
Tea/coffee |
Tent outside the Lab |
|
|
1100-1230 |
Practical · Online bioinformatics resources |
JVC |
Joyce Njuguna,
Dedan Githae, Maureiq Ojwang |
|
1230-1330 |
Lunch |
Poolside |
|
|
1330-1400 |
Review Day 12 activities and
Quiz |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka |
|
1400-1500 |
Review of whole week, and
general discussion |
JVC |
Maureiq Ojwang, Joyce Njuguna, Dedan Githae, Francesca Stomeo,
Tina Kyalo, Roger Pelle,
Pauline Asami, Eunice Machuka,
Leah Kago, Mutai Collins |
|
1500-1530 |
Participant Action Plan
Approach (PAPA) |
JVC |
Wellington Ekaya |
|
1530-1545 |
Tea/coffee |
JVC |
|
|
1545-1645 |
Post-workshop evaluations |
JVC |
Wellington Ekaya,
Roger Pelle, Francesca Stomeo |
|
1645-1730 |
Closing ceremony |
JVC |
Appolinaire Djikeng |
|
1730-1930 |
Dinner for all participants |
(TBD) |
Val, Marvin, David |
|
1930 |
Bus leaves Venue for Pride Inn |
|
|
