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.
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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
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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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H.bioinfo 