wiki:Courses/ComputationalMolecularBiologyResearch2016

Version 22 (modified by Pieter Neerincx, 8 years ago) (diff)

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Computational Molecular Biology Research

Table of Contents

  1. Course Overview
  2. Rating
  3. Projects
    1. Methods/tools for detection of fusion gene transcripts in RNA sequencing
    2. Single cell RNA sequencing quantification
    3. Improved detection of regulatory transcription factor binding sites in …
  4. Course Schedule
    1. Venue
    2. Regular events
    3. Week 1
    4. Weeks 2-5
    5. Week 6
    6. Contact

Course Overview

This research course demonstrates the in silico data analysis used for genetics research at the RUG and UMCG. The emphasis of the research topics is on finding better methods for the analysis of high throughput data generated using technologies like Next Generation Sequencing (both DNA and RNA), Gene expression arrays, Genome wide association studies (GWAS), etc.

In the first week the research topics will be introduced and a minimal introduction for scripting in Bash and R will be provided. At the end of the first week the students will choose a research project to work on under supervision of a PhD-student or Postdoc. In weeks 2-5 the in silico experiments are performed. The 6th and last week is reserved for writing a report, preparing a presentation and presenting the results to the other in the department.

Rating

Students will be rated as follows:

  • 50% Code + data produced during practical work
  • 30% Report
  • 20% Presentation

Projects

    Methods/tools for detection of fusion gene transcripts in RNA sequencing

    1. Analysis of trans-spliced transcripts in RNA seq data - Lennart / Birgit / Analyse team

    Single cell RNA sequencing quantification

    1. Single cell RNA seq quantification - Gerben / Pieter van der Vlies / Iris? [waar komt de data vandaan?]

    Improved detection of regulatory transcription factor binding sites in non-coding DNA by merging sequence (context) with in vivo DNA accessibility data

    1. Improved DNA Motif finding - Iris / Pieter

    Course Schedule

    Venue

    Course will be organized at or near the UMCG Genetics department, which is located on the 5th floor of the European Research Institute for the Biology of Aging - ERIBA building plus the complete 5th and partial 6th floor of the adjacent Dentistry building. The address for both buildings is 

    Antonius Deusinglaan 1
9713 AV Groningen
    Building Room Name
    3226 302 ERIBA building, meeting room, 3rd floor, in the corner and next to auditorium
    3226 314 ERIBA building, auditorium, 3rd floor
    3211 519 Dentistry building, meeting room without a name opposite the secretary, 5th floor, opposite the secretary and near elevators
    3211 501 Dentistry building, meeting room 1, 5th floor, end of corridor
    3211 flex desks Dentistry building, 5th floor
    3226 flex desks ERIBA building, 5th floor

    Regular events

    Day Time What Where
    Mondays 09:15 - 09:30 Course SCRUM in weeks 2-6 TBA instant meeting room 3211 5th floor
    Mondays 12:00 - 13:00 Research meeting (ADCB groups) 3226-314 ERIBA auditorium
    Tuesdays 08:45 - 10:00 Research meeting (Entire Genetics dept.) 3226-314 ERIBA Auditorium
    Tuesdays 10:15 - 10:30 Course SCRUM in weeks 2-6 TBA instant meeting room 3211 5th floor
    Wednesdays 09:15 - 09:30 Course SCRUM in weeks 2-6 TBA instant meeting room 3211 5th floor
    Thursdays 09:15 - 09:30 Course SCRUM in weeks 2-6 TBA instant meeting room 3211 5th floor
    Thursdays 12:00 - 13:00 Literature club (Wijmenga/Weersma/Franke groups) 3226-314 ERIBA auditorium
    Fridays 09:15 - 09:30 Course SCRUM in weeks 2-6 TBA instant meeting room 3211 5th floor

    Week 1

    Monday 01-02-2016

    When What Where
    09:15 - 09:45 Course kick off (Pieter Neerincx) 3211-501 Room "1"
    09:45 - 10:00 Break
    10:00 - 10:45 Lecture: Next Generation Sequencing (Morris Swertz) 3211-501 Room "1"
    10:45 - 11:00 Break
    11:00 - 11:45 Project intro: (Birgit Sikkema-Raddatz / Lennart Johansson)3211-501 Room "1"
    11:45 - 12:00 Break
    12:00 - 13:00 Research lunch meeting (ADCB groups) 3226-314 ERIBA Auditorium
    13:00 - 13:45 Bash scripting intro part I (Lennart Johansson) 3211-501 Room "1"
    13:45 - 14:00 Break
    14:00 - 17:00 Bash scripting tutorials 3211-501 Room "1"

    Tuesday 02-02-2016

    When What Where
    08:45 - 09:45 Research meeting (Entire genetics dept.) 3226-314 ERIBA Auditorium
    09:45 - 10:00 Break
    10:00 - 10:45 Lecture: Experimental Design (Lude Franke) 3211-501 Room "1"
    10:45 - 11:00 Break
    11:00 - 11:45 Lecture: GWAS (Lude Franke) 3211-501 Room "1"
    12:00 - 13:00 Lunch break
    13:00 - 13:45 Bash scripting intro part II (Lennart Johansson) 3211-501 Room "1"
    13:45 - 14:00 Break
    14:00 - 17:00 Bash scripting tutorials 3211-501 Room "1"

    Wednesday 03-02-2016

    When What Where
    09:00 - 12:00 R-turorial part I (Annique Claringbould) 3211-501 Room "1"
    12:00 - 13:00 Lunch break
    13:00 - 17:00 R-turorial part II (Annique Claringbould) 3211-501 Room "1"

    Thursday 04-02-2016

    When What Where
    09:00 - 09:45 Project intro: Quantification for RNA seq (Niek de Klein) 3211-501 Room "1"
    09:45 - 10:00 Break
    10:00 - 10:45 Project intro: mtDNA analysis (Pieter Neerincx) 3211-501 Room "1"
    10:45 - 11:00 Break
    11:00 - 11:45 Project intro: DNA Motif finding (Iris Jonkers) 3211-501 Room "1"
    12:00 - 13:00 Lunch break
    13:00 - 13:45 Lecture: Gene Expression (Lude Franke) 3211-501 Room "1"
    13:45 - 14:00 Break
    14:00 - 14:45 Lecture: Integrating Datasets (Lude Franke) 3211-501 Room "1"
    14:45 - 15:00 Break
    15:00 - 15:45 Lecture: Data visualization (Lude Franke) 3211-501 Room "1"
    15:45 - 16:00 Break
    16:00 - 16:45 Project intro: Single cell RNA seq (Pieter van der Vlies) 3211-501 Room "1"

    Friday 05-02-2016

    When What Where
    09:00 - 09:45 Project intro: RNA editing (Yang Li) 3211-501 Room "1"
    09:45 - 10:00 Deadline: choose project. 3211-501 Room "1"
    10:00 - 12:00 Getting familiar with your project:
    Search literature,
    Design experiment and
    write (validation) plan     		flex desks
    12:00 - 13:00 Lunch break
    13:00 - 17:00 Getting familiar with your project:
    Search literature,
    Design experiment and
    write (validation) plan     		flex desks

    Weeks 2-5

    Monday 08-02-2016

    When What Where
    09:15 - 09:30 Scrum TBA
    09:30 - 12:00 Finish experimental design / (validation) plan flex desks
    12:00 - 13:00 Research lunch meeting (Wijmenga/Weersma/Franke/Swertz groups) 3226-314 ERIBA Auditorium
    12:00 - 17:00 Finish experimental design / (validation) plan flex desks
    17:00 Deadline: have experimental design / (validation) plan approved by your supervisor(s) TBA

    From Tuesday 09-02-2016 onwards

    • Regular meetings
    • Execute your experiment / plan

    Week 6

    From Monday 07-03-2016 onwards

    • Regular meetings
    • Write report and prepare presentation.

    Thursday 10-03-2015

    When What Where
    13:00 - 13:30 Project Presentation I TBA
    13:30 - 14:00 Project Presentation II TBA
    14:00 - 14:15 Break
    14:15 - 14:45 Project Presentation III TBA
    14:45 - 15:15 Project Presentation IV TBA
    15:15 - 15:30 Break
    15:30 - 16:00 Project Presentation V TBA
    16:00 - 16:30 Project Presentation VI TBA
    16:30 - 17:00 Wrap up (Pieter) TBA

    Friday 11-03-2015

    When What Where
    17:00 Report submission deadline Your project supervisor's mailbox

    Contact

    Morris Swertz coordinator m.a.swertz AT rug DOT nl
    Pieter Neerincx daily supervision pieter.neerincx AT gmail DOT com