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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: Pantelis Topalis

14:00-20:00 Advanced RNASeq and ChIPSeq data analysis – Hands-on Workshop
15:00-15:30 Pantelis Topalis

  • Introduction to sequencing technologies
    • First Generation Sequencing (Maxam-Gilbert, Sanger methods)
    • Second Generation Sequencing (Pyrosequencing, Ion-Torrent, Illumina)
    • Third Generation Sequencing (Oxford Nanopore, PacBio)

15:30-18:00 P. Ioannidis, P. Topalis

  • RNA-Seq Data Analysis
    • Quality control of raw reads – Mapping to reference genome – Differential gene expression
    • De novo transcriptome assembly

18:00-20:00 P. Topalis, P. Ioannidis

  • ChIP-Seq Data Analysis
    • ChIPSeq Irreproducible Discovery Rate (IDR) pipeline
    • ENCODE pipeline

Important Notes:

  1. Number of maximum participants 30.
  2. Participants MUST have a basic knowledge of linux command line / bash scripting.
  3. We require students to self-study the online course http://linuxsurvival.com before start.
  4. The organizers will provide computers with all the required bioinformatics tools and demo data.
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