wiki:Courses/ComputationalMolecularBiologyResearch2016

Version 4 (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. Increasing diagnostic yield of fast whole genome diagnostics for new …
    2. Improved quantification for RNA sequencing
    3. Detection of fusion gene transcripts in RNA sequencing
    4. Single cell RNA sequencing quantification
  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

Increasing diagnostic yield of fast whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU)

  1. Improved variant calling for MtDNA? - Pieter / Freerk

Improved quantification for RNA sequencing

  1. Improved quantification for RNA sequencing? - Niek / Freerk

Detection of fusion gene transcripts in RNA sequencing

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

Single cell RNA sequencing quantification

  1. Single cell RNA seq quantification ? - Gerben

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, 5th floor, opposite the secretary
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 (Wijmenga/Weersma/Franke 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 01-02-2015

When What Where
09:15 - 09:45 Course kick off (Pieter Neerincx) TBA
09:45 - 10:00 Break
10:00 - 10:45 Lecture: Next Generation Sequencing (Morris Swertz) TBA
10:45 - 11:00 Break
11:00 - 11:45 Project intro (Birgit Sikkema-Raddatz / Lennart Johansson) TBA
11:45 - 12:00 Break
12:00 - 13:00 Research lunch meeting (Wijmenga/Weersma/Franke groups) 3226-314 ERIBA Auditorium
13:00 - 13:45 Project intro or lecture TBA
13:45 - 14:00 Break
14:00 - 14:45 Project intro or lecture TBA
14:45 - 15:00 Break
15:00 - 15:45 Project intro or lecture TBA

Tuesday 02-02-2015

When What Where
08:45 - 10:00 Research meeting (Entire genetics dept.) 3226-314 ERIBA Auditorium
10:00 - 10:15 Break
10:15 - 11:00 Project introduction: Transcriptome analysis to elucidate human fatty liver disease development (Biljana Atanasovska) 3211-608 GCC room
11:00 - 11:15 Break
11:15 - 12:00 Project introduction: Non-invasive early detection of (pre-)diabetes (Andries Smit & Martijn Dijkstra) 3211-608 GCC room
12:00 - 13:00 Lunch break
13:00 - 13:45 R scripting intro (Martijn Dijkstra) 3211-608 GCC room
13:45 - 14:00 Break
14:00 - 17:00 R tutorials 3211-608 GCC room

Wednesday 03-02-2015

When What Where
09:30 - 10:15 Lecture: Experimental Design (Lude Franke) 3211-608 GCC room
10:15 - 10:30 Break
10:30 - 11:15 Lecture: GWAS (Lude Franke) 3211-608 GCC room
11:15 - 11:30 Break
11:30 - 12:15 Project introduction: Microbiome anaylses (Floris Imhann) 3211-608 GCC room
12:15 - 13:00 Lunch break
13:00 - 13:45 R scripting intro (Martijn Dijkstra) 3211-608 GCC room
13:45 - 14:00 Break
14:00 - 17:00 R scripting tutorials 3211-608 GCC room
18:00 Deadline: Preferences for project mailed to course coordinator Morris Swertz

Thursday 04-02-2015

When What Where
09:30 - 10:15 Lecture: Gene Expression (Lude Franke) 3211-608 GCC room
10:15 - 10:30 Break
10:30 - 11:15 Lecture: Integrating Datasets (Lude Franke) 3211-608 GCC room
11:15 - 11:30 Break
11:30 - 12:15 Lecture: Data visualization (Lude Franke) 3211-608 GCC room
12:15 - 13:00 Lunch break
13:00 - 13:45 Bash scripting intro (Lennart Johansson) 3211-608 GCC room
13:45 - 14:00 Break
14:00 - 17:00 Bash scripting tutorials 3211-608 GCC room

Friday 05-02-2015

When What Where
09:30 - 10:15 Bash scripting intro (Lennart Johansson) 3211-608 GCC room
10:15 - 10:30 Break
10:30 - 12:15 Bash scripting tutorials 3211-608 GCC room
12:15 - 13:00 Lunch break
13:00 - 17:00 Getting familiar with your project: search literature
Start designing experiment / writing (validation) plan 		3211-608 GCC room

Weeks 2-5

Monday 08-02-2015

When What Where
09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke groups) 3226-302 ERIBA meeting room
10:30 - 10:45 Break
10:45 - 12:00 Finish experimental design / (validation) plan 3211-608 GCC room
12:00 - 13:00 Literature discussion 3226-302 ERIBA meeting room
12:00 - 17:00 Finish experimental design / (validation) plan 3211-608 GCC room
17:00 Deadline: have experimental design / (validation) plan approved by your supervisors 3211-608 GCC room

From Tuesday 09-02-2015 onwards

  • Regular meetings
  • Execute your experiment / plan

Week 6

  • Regular meetings
  • Write report and prepare presentation.

Thursday 12-03-2015

When What Where
13:00 - 13:30 Presentation Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs (Selle) 3211-S42A
13:30 - 14:00 Presentation Improved variant calling for large insertions (Glenn) 3211-S42A
14:00 - 14:15 Break
14:15 - 14:45 Presentation Optimizing decision trees to differentiate between healthy and diseased using parameter optimization (Sandra) 3211-S42A
14:45 - 15:15 Presentation Improved variant calling for MtDNA (Falke) 3211-S42A
15:15 - 15:30 Break
15:30 - 16:00 Presentation Improved variant interpretation by combining gene networks with phenotype networks (Tessa) 3211-S42A
16:00 - 16:30 Presentation Analyzing Whole Genome Shotgun Microbiomome data (Rogier) 3211-S42A
16:30 - 17:00 Wrap up (Morris Swertz) 3211-S42A

Friday 13-03-2015

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

Contact

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