| ParaFrap II -- Bioinformatics Workshop -- 3-8 July 2017, Montpellier FR | ||||||
| Monday | Tuesday | Wednesday | Thursday | Friday | Saturday | |
| 3 July 2017 | 4 July 2017 | 5 July 2017 | 6 July 2017 | 7 July 2017 | 8 July 2017 | |
| 9 | Overview and Introductions | Genome Browser Exercises -
II (Group Exercise) |
RNA-seq Mapping
Exercise - II (Group Exercise) |
Functional Genomics Exercises | Intro to Regular Expressions | Group Project Presentations |
| Bastien, Baumgarten, Harb, MacPherson, Roos, Warrenfeltz |
Analysis & interpretation of RNA-seq evidence GBrowse Image |
Interpreting RNA-seq mapping results |
Transcriptomics, Proteomics | Cameron MacPherson | all students
Survey |
|
| Pattern recognition, colocation |
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| 10 | Who are you? What do you do? | Roos et al | Harb et al | Warrenfeltz et al | ||
| Turbo-Intros by all students 1-2 slides, 2-3 min max |
Sequence analysis Exercises Regular Expressions More Regular Expressions Warrenfeltz et al |
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| Tea / Coffee | ||||||
| 11 | Tea / Coffee | Tea / Coffee | Tea / Coffee | Tea / Coffee | Pathway Exercises Metabolism & Pathways |
Tea / Coffee |
| Results of RNA-seq analysis |
SNP Mapping Exercise - I Variant calling (Galaxy) (Group Exercise) |
Host response datasets |
Metabolic Pathways |
all students | ||
| all students | Harb | Warrenfeltz et al | Harb et al | |||
| 12 | Seminar/Discussion (over lunch) | Seminar/Discussion (over lunch) | Seminar/Discussion (over lunch) | Seminar/Discussion (over lunch) | Lunchtime Discussion | |
| Designing & mining pathogen genome databases |
Genomic-scale analysis of
trans- criptional reg'n in kinetolastida |
Epigenomic control in Plasmodium |
Dissecting structure /
function relationships in the kinetoplastida |
Intro to complex queries,
data integration & group projects |
||
| Lunch & Farewell | ||||||
| 13 | David Roos, Univ Pennsylvania | Nicolai Siegel, Univ W�rzburg | Sebastian Baumgarten, Inst Pasteu | Eva Gluenz, Oxford University | all instructors | |
| Lunchbox | Lunchbox | Lunchbox | Lunchbox | Lunchbox | ||
| 14 | Intro to EuPathDB databases | RNA-seq
Mapping Exercise - I (Group Exercise) TopHat Cufflinks Galaxy Project iPlant Collaborative |
Free time / Group activity? | Intro to SNPs &
Population Biology |
Group Projects (Group Exercise) |
|
| Omar Harb | Mapping RNAseq data (Galaxy) | David Roos | all students, all instructors | |||
| Gene Page Exercises | Warrenfeltz et al | SNP mapping Exercise - II (Group Exercise) |
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| 15 |
Finding genes, interpreting gene pages; Intro to search strategies |
Interpreting variant calling results |
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| Warrenfeltz et al | Harb et al | |||||
| 16 | Tea / Coffee | Tea / Coffee | Tea / Coffee | Tea / Coffee | ||
| Intro to Phylogeny & Orthology | ||||||
| David Roos | ||||||
| 17 | Genome Browser Exercises - I | Orthology Exercises | Population Biology Exercises | |||
| Evidence tracks, alignments, comparative genomics |
Phyletic pattern queries | SNPs, Population genetics | ||||
| MacPherson et al | Roos et al | Roos et al | ||||
| 18 | ||||||
| 19 | Welcome Dinner Le Chat Perche 10 et 12 rue du College |
Dinner (on your own) | Dinner (on your own) | Dinner (on your own) | Closing Dinner / Party | |
| 20 | ||||||
