Review of rabbit genomic resources where to find them and how to use them NCBI

Review of rabbit genomic resources where to find them

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Review of rabbit genomic resources, where to find them and how to use them (NCBI, UCSC, ENSEMBL, BROAD). Databases: hands on training will focus on one of the most asked questions: "how do I find the gene of interest?" "what should I do if I don't find the gene of interest?" Short introduction to BioMart that will be used in the afternoon for practicing 12:15-13:00 Alignments: Blast, local, global, multiple: Federica di Palma Basic web based alignments tools such as BLAST-N, X, P and BLAT. Databases of transcription factors and mammalian constraint for traits with mutations in regulatory regions. Multiple genome alignments, scientific uses and tools Afternoon: 14:00-18:00: Federica Di Palma 14:00-16:00 Practical training 16:00-16:30 Coffee break 16:30-18:00 Practical training
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Tuesday, October 23 Morning: 8:30-13:00 Pier Luigi Martelli ( and Giuseppina Schiavo for practical training ) 8:30-10:30 An introductory lecture on the basics and logics of programming (without referring to a particular language, and introducing flowcharts and pseudocoding). This will be the only part that would not require computers for the student 10:30-11:00 Coffee break 11:00-13:00 A very basic practical introduction to Linux, with students trying the commands on their terminals Afternoon: 13:00-19:00 14:00-16:00 Introduction to R: Bernardo Clavijo 16:00-16:30 Coffee break 16:30-19:00 Perl language, explaining the basic statements, variables and so on and letting time to the students to have some simple practice step-by-step on the computers: Pier-Luigi Martelli (and Giuseppina for practical training)
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Wednesday, October 24 Morning : 8:30-13:00 8:30-9:00 A historical perspective to transcriptome analysis by using microarrays and RNA-Seq. Tom Freeman 9:00-9:30 DNA chips for transcriptome analysis: application to the Rabbit species. Véronique Duranthon 9:30-11:00 Bio-statistical analysis. Andréa Rau Introduction to differential analysis of microarray expression data Brief discussion of the fundamentals of experimental design Statistical analysis to identify differentially expressed genes from single-channel Agilent microarrays: data pre-processing and normalization, models and tests for differential expression, correction for multiple testing Gene ontology enrichment analysis for microarray data 11:00-11:15 Coffee break 11:15-13:00 Practical session. Andrea Rau Differential analysis of Agilent microarray expression data from rabbit using the Limma Bioconductor package Afternoon: 14:00-18:00. Tom Freeman 14:00-14:30 Network analysis of transcriptomics data. Introduction to networks and their application to biological research Basic principles of the application of networks to analysis of high dimensional data 14:30-15:45 Practical 1: Network analysis of transcriptomics analysis using BioLayout Express 3D Input formats and graph navigation Visual preferences Graph clustering and analysis 15:45-16:00 Coffee break 16:00-18:00 Practical 2: Network analysis of transcriptomics analysis Worked example 'Expression atlas of the domestic pig'
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Thursday, October 25 Morning: 8h30-13:00 8:30-10:30 Introduction to computational analysis of NGS data (Type of data, quality control, read mapping): Jordi Estellé 10:30-11:00 Coffee break 11:00-13:00
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