wiki:Courses/ComputationalMolecularBiologyResearch2016

Version 29 (modified by Pieter Neerincx, 9 years ago) (diff)

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Computational Molecular Biology Research

Table of Contents

  1. Course Overview
  2. Projects
  3. Experimental design a.k.a validation plan
  4. Report and presentation
  5. Rating
  6. Course Schedule
    1. Venue
    2. Regular events
    3. Week 1
    4. Weeks 2-5
    5. Week 6
  7. 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, which will be supervised by 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 others in the department.

Projects

  1. Increasing diagnostic yield of fast diagnostics using NGS
    1. Supervisors
    2. Introduction
    3. Project 1
  2. Benchmarking RNAseq gene expression quantification tools
    1. Supervisors
    2. Introduction
    3. Project 2
    4. Refs
  3. Analysis of trans-spliced transcripts in RNA seq data
    1. Supervisors
    2. Introduction
    3. Project 3
    4. Refs
  4. Single cell RNA seq quantification
    1. Supervisors
    2. Introduction
    3. Project 4
    4. Refs
  5. Improved DNA Motif finding
    1. Supervisors
    2. Introduction
    3. Project 5
  6. Detection of RNA-editing sites in human RNA-sequencing data
    1. Supervisors
    2. Introduction
    3. Project 6

Experimental design a.k.a validation plan

At the start of a project the students have to draft a plan outlining their experimental design. This should contain the following:

  • Short intro explaining the goal the experiment: why are you going to perform this experiment?
  • Material and methods: how are you going to do this experiment?
  • Validation criteria:
    • Quality: how are you going to determine which analysis / software package yields the best results?
    • Other criteria may be important as well depending the application.
      For example for fast diagnostics the analysis speed may be an important factor in addition to reliability of the results.
  • Schedule for the remaining 5 weeks of the project.

Report and presentation

The report produced at the end of the project consists of the original experimental design / validation plan supplemented with:

  • Results
  • Conclusion and discussion: the conclusion should logically follow from combining the results with the previously defined validation criteria.

The key findings of the project will be presented in slots of 30 minutes per project:

  • 20 minutes for presentating
  • 10 minutes for answering questions

Rating

Students will be rated as follows:

  • 35% Code + data produced during practical work
  • 35% Report
  • 30% Presentation

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 -s42a Dentistry building, basement
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/Swertz 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 3 Analysis of trans-spliced transcripts in RNA seq data (Marten) 3211-s42a
13:30 - 14:00 Project 2 Benchmarking RNAseq gene expression quantification tools (Jasper) 3211-s42a
14:00 - 14:15 Break
14:15 - 14:45 Project 1 Increasing diagnostic yield of fast diagnostics using NGS (Matthijs) 3211-s42a
14:45 - 15:15 Project 4 3211-s42a
15:15 - 15:30 Break
15:30 - 16:00 Project 5 3211-s42a
16:00 - 16:30 Project 6 3211-s42a
16:30 - 17:00 Wrap up (Pieter) 3211-s42a

Friday 11-03-2015

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

Contact

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