ParaFrap Bioinformatics Course, Montpellier, 5-9 January 2015
	Monday	Tuesday	Wednesday	Thursday	Friday
	1/5/15	1/6/15	1/7/15	1/8/15	1/9/15
8 am
	Students arriving Sunday
	or Monday morning  < 8:30am
9 am	Workshop Welcome, Overview	Browser Exercises - II	Mapping Exercises - II	Lecture	Lecture
	Bastien, Harb,	Interpreting RNAseq data Hi-Res image	Interpretating mapping results	Pattern recognition, Regular	Designing (pathogen) genome
	Warrenfeltz, MacPherson, Roos	Roos, et al	Harb, et al	expressions	databases
				Harb	Roos
10 am	Student presentations			Sequence Exercises	Data Integration Exercises - I
	Who are you, and what			Motif Searches, Genomic Colocation	Complex queries
	are your interests?				all instructors
	5-10 min each			Harb, et al
11 am	Tea/Coffee	Tea/Coffee	Tea/Coffee	Tea/Coffee	Tea/Coffee
		Report on results, discuss		Additional Regular Expression Help Links to Regular Expression Resources About InterPro RegEx Lecture	Meme Output
		all students
12 noon
	Lunch	Lunch	Lunch	Lunch	Lunch
1 pm
	Lecture	Mapping Exercises - I	Lecture	Lecture	Research Lecture
	Introduction to Genome Infor-	Mapping RNAseq data	Gx Technologies & Applications	Population genetics datasets	Bioinformatics of
2 pm	matics & EuPathDB databases	Warrenfeltz, et al	Jose Juan Lopez-Rubio	Roos	organismal diversity
	Harb				Toni Gabaldon
	Gene Page Exercises		Functional Genomics - I	Genetics Exercises	Data Integration Exercises - II
	GeneIDGeneID, BLAST, Text searches		Transcriptomics & Proteomics	SNPs, Population genetics	Group projects
3 pm	Warrenfeltz, et al		Warrenfeltz, et al	MacPherson, et al	all instructors
		Lecture	Transcriptomics Exercises
		Phylogeny & Orthology	Proteomics Exercises
4 pm		Roos
	Tea/Coffee	Tea/Coffee	Tea/Coffee	Tea/Coffee	Tea/Coffee
5 pm	Browser Exercises - I	Orthology Exercises		Pathway Exercises
	Alignments, Comparative	Phyletic pattern queries		Metabolism & Pathways
	Genomics	Harb, et al		Warrenfeltz, et al
	MacPherson, et al		Functional Genomics - II
6 pm			Host response datasets		Report on results, discuss
			Harb, et al		all students
7 pm
	Dinner	Dinner	Dinner	Dinner	Closing Dinner
8 pm	Research Lecture	Research Lecture	Research Lecture	Research Lecture
	Biology & genomics of	Plasmodium gene regulation	Identification and roles of transposons	Functional genetic screens	Students departing Saturday
	host-pathogen interactions	and population diversity	in the trypanosomatid genomes
	David Roos	Artur Scherf	Fred Bringaud	David Horn