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H.Bioinfo 2018 Workshops


Thursday, November 15th, 2018

Theme:           Workshops

Lecture Location: Central Computer Lab, Main Library Building AUTH 

Morning workshop  

Chair: Michalis Aivaliotis

09:00-14:00 Proteomics & Bioinformatics Hands-on Workshop: From raw MS-data to knowledge
09:00-09:15 Michalis Aivaliotis

  • Introduction to proteomics
    • Brief history of MS-based proteomics
    • State-of-the-art quantitative MS-based proteomics approaches

09:15-11:00 G. Orfanoudaki, K. Psatha, M. Aivaliotis

  • Bioinformatics I – MS-Raw data processing
    • Proteome Identification, Quantitation and Characterization
    • Available bioinformatics platforms for MS-data processing
    • Quality control and filtering of proteomics data

11:30-14:00 N. Fikas, G. Orfanoudaki, A. Malousi, K. Psatha, M. Aivaliotis

  • Bioinformatics II – Meta-data analysis and visualization
    • Comparative proteomics analysis
    • Functional proteome annotation
    • GO terms and pathways enrichment analysis
    • Protein-protein interaction networks
    • Visualization of proteomics data

Important Notes:

  • Number of maximum participants: 30.
  • A digital textbook and references will be provided to all participants in advance.
  • The organizers will provide computers with all the required bioinformatics tools and demo data.

Evening workshop

Chair: Andigoni Malousi, Lab. of Biological Chemistry, Medical School, AUTh

15:00-20:00 Advanced RNASeq and ChIPSeq data analysis – Hands-on Workshop
15:00-15:30 Andigoni Malousi, Stefania Maniatsi

  • Introduction to sequencing technologies
    • From Sanger to Nanopores: Advances in sequencing technologies
    • Public data repositories and data formats
    • Basic processing steps and bioinformatics tools

15:30-16:00  Andigoni Malousi, AUTh IT expert

  • Prerequisites
    • Introduction to the AUTh’s cluster environment
    • Basic bash commands
    • Working environment setup

16:00-18:00 Andigoni Malousi, Stefania Maniatsi

  • RNA-Seq data analysis workflow
    • Fetching raw RNA-Seq data from public repositories
    • Quality control and mapping to reference genome
    • Quantification and differential gene expression
    • Visualisation and downstream analysis (fusion genes, gene set enrichment)

16:00-18:00 Andigoni Malousi, Stefania Maniatsi

  • ChIP-Seq data analysis workflow
    • Quality control and trimming of raw reads
    • Mapping to reference genome
    • Peak calling
    • Visualisation and peak annotation

Important Notes:

  • Number of maximum participants 30.
  • Basic knowledge of command-line environments/bash scripting is highly desirable.
  • We require students to self-study the online course http://linuxsurvival.com before start.
  • The organizers will provide computers with all the required bioinformatics tools.
Publication ID hbio- #0006-2018
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