= Computational Molecular Biology Research =

[[TOC()]]

== 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 beginning of the second week the students will choose a research project to work on under supervision of a PhD-student or Postdoc.

== Rating ==
Students will be rated as follows:
 * 50% 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. [wiki:Courses/ComputationalMolecularBiologyResearch/P1 Improved variant calling for CNVs] - Pieter / Freerk
2. [wiki:Courses/ComputationalMolecularBiologyResearch/P1 Improved variant calling for large insertions] - Pieter / Freerk
3. [wiki:Courses/ComputationalMolecularBiologyResearch/P1 Improved variant calling for sex chromosomes] - Pieter / Freerk
4. [wiki:Courses/ComputationalMolecularBiologyResearch/P1 Improved variant calling for MtDNA] - Pieter / Freerk
5. [wiki:Courses/ComputationalMolecularBiologyResearch/P1 Improved variant calling of medium sized InDels] - Pieter / Freerk
6. [wiki:Courses/ComputationalMolecularBiologyResearch/P6 Improved variant interpretation by combining gene networks with phenotype networks] - Juha / Joeri

=== Transcriptome analysis to elucidate human fatty liver disease development ===
7. [wiki:Courses/ComputationalMolecularBiologyResearch/P7 Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs] - Bibi / Jing

=== Changes in the gut microbiome ===
8. [wiki:Courses/ComputationalMolecularBiologyResearch/P8 Analyzing Whole Genome Shotgun data] - Floris / Arnau / Marc Jan

=== Non-invasive early detection of (pre-)diabetes using Advanced Glycemic Endproduct detection ===
9. [wiki:Courses/ComputationalMolecularBiologyResearch/P9 Optimizing decision trees to differentiate between healthy and diseased using parameter optimization] - Martijn / Patrick / Andries / Bernadette

== 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 [[BR]]
{{{
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 || 608 ||''Dentistry'' building, GCC room, 6th floor, at the end of the corridor ||
|| 3211 || flex desks ||''Dentistry'' building, 5th floor ||
|| 3226 || flex desks ||''ERIBA'' building, 5th floor ||

=== Regular events ===

|| **Day** || **Time** || **What** || **Where** ||
||Mondays  ||09:15 - 10:30 ||Research meeting (!Wijmenga/Weersma/Franke groups) ||3226-302 ERIBA meeting room ||
||Mondays  ||10:45 - 11:00 ||Course SCRUM in weeks 2-6 ||2311-608 GCC room ||
||Mondays  ||12:00 - 13:00 ||Literature discussion ||3226-302 ERIBA meeting room ||
||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 ||2311-608 GCC room ||
||Wednesdays ||09:30 - 09:45 ||Course SCRUM in weeks 2-6 ||2311-608 GCC room ||
||Thursdays ||09:30 - 09:45 ||Course SCRUM in weeks 2-6 ||2311-608 GCC room ||
||Fridays ||09:30 - 09:45 ||Course SCRUM in weeks 2-6 ||2311-608 GCC room ||

=== Week 1 ===

**Monday 02-02-2015**

|| **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 - 11:00 ||Course kick off (Morris Swertz) ||2311-608 GCC room ||
||11:00 - 12:00 ||Lecture: Next Generation Sequencing (Morris Swertz) ||2311-608 GCC room ||
||12:00 - 13:00 ||Lunch break || ||
||13:00 - 13:45 ||Project introduction: Whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (Cleo van Diemen) ||2311-608 GCC room ||
||13:45 - 14:00 ||Break || ||
||14:00 - 14:45 ||Project introduction: Improved variant calling (Freerk van Dijk) ||2311-608 GCC room ||
||14:45 - 15:00 ||Break || ||
||15:00 - 15:45 ||Project introduction: Improved variant interpretation (Juha Karjalainen) ||2311-608 GCC room ||

** Tuesday 03-02-2015 **

|| **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) ||2311-608 GCC room ||
||11:00 - 11:15 ||Break || ||
||11:15 - 12:00 ||Project introduction: Non-invasive early detection of (pre-)diabetes (Andries Smit & Martijn Dijkstra) ||2311-608 GCC room  ||
||12:00 - 13:00 ||Lunch break || ||
||13:00 - 13:45 ||R scripting intro (Martijn Dijkstra) ||2311-608 GCC room ||
||13:45 - 14:00 ||Break || ||
||14:00 - 17:00 ||R tutorials ||2311-608 GCC room ||

** Wednesday 04-02-2015 **

|| **When** || **What** || **Where** ||
||09:30 - 10:15 ||Lecture: Experimental Design (Lude Franke) ||2311-608 GCC room ||
||10:15 - 10:30 ||Break || ||
||10:30 - 11:15 ||Lecture: GWAS (Lude Franke) ||2311-608 GCC room ||
||11:15 - 11:30 ||Break || ||
||11:30 - 12:15 ||Project introduction: Microbiome anaylses (Floris Imhann) ||2311-608 GCC room ||
||12:15 - 13:00 ||Lunch break ||
||13:00 - 13:45 ||R scripting intro (Martijn Dijkstra) ||2311-608 GCC room ||
||13:45 - 14:00 ||Break || ||
||14:00 - 17:00 ||R scripting tutorials ||2311-608 GCC room ||
|| 18:00 ||Deadline: Preferences for project mailed to course coordinator Morris Swertz || ||

** Thursday 05-02-2015 **

|| **When** || **What** || **Where** ||
||09:30 - 10:15 ||Lecture: Gene Expression (Lude Franke) ||2311-608 GCC room ||
||10:15 - 10:30 ||Break || ||
||10:30 - 11:15 ||Lecture: Integrating Datasets (Lude Franke) ||2311-608 GCC room ||
||11:15 - 11:30 ||Break || ||
||11:30 - 12:15 ||Lecture: Data visualization (Lude Franke) ||2311-608 GCC room ||
||12:15 - 13:00 ||Lunch break ||
||13:00 - 13:45 ||Bash scripting intro (Lennart Johansson) ||2311-608 GCC room ||
||13:45 - 14:00 ||Break || ||
||14:00 - 17:00 ||[wiki:Courses/BASH Bash scripting tutorials] ||2311-608 GCC room ||

** Friday 06-02-2015 **

|| **When** || **What** || **Where** ||
||09:30 - 10:15 ||Bash scripting intro (Lennart Johansson) ||2311-608 GCC room ||
||10:15 - 10:30 ||Break || ||
||10:30 - 12:15 ||Bash scripting tutorials ||2311-608 GCC room ||
||12:15 - 13:00 ||Lunch break ||
||13:00 - 17:00 ||Getting familiar with your project: search literature [[BR]] Start designing experiment / writing (validation) plan ||2311-608 GCC room ||

=== Weeks 2-5 ===

** Monday 09-02-2015 **

|| **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 ||2311-608 GCC room ||
||12:00 - 13:00 ||Literature discussion ||3226-302 ERIBA meeting room ||
||12:00 - 17:00 ||Finish experimental design / (validation) plan ||2311-608 GCC room ||
|| 17:00 ||Deadline: have experimental design / (validation) plan approved by your supervisors ||2311-608 GCC room ||

**From Tuesday 10-02-2015 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) ||T.B.A. ||
||13:30 - 14:00 ||Presentation Improved variant calling for large insertions (Glenn) ||T.B.A. ||
||14:00 - 14:15 ||Break || ||
||14:15 - 14:45 ||Presentation Analyzing Whole Genome Shotgun Microbiomome data (Rogier) ||T.B.A. ||
||14:45 - 15:15 ||Presentation Improved variant calling for MtDNA (Falke) ||T.B.A. ||
||15:15 - 15:30 ||Break || ||
||15:30 - 16:00 ||Presentation Improved variant interpretation by combining gene networks with phenotype networks (Tessa) ||T.B.A. ||
||16:00 - 16:30 ||Presentation Optimizing decision trees to differentiate between healthy and diseased using parameter optimization (Sandra) ||T.B.A. ||
||16:30 - 17:00 ||Wrap up (Morris Swertz) ||T.B.A. ||

** 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 ||
||Martijn Dijkstra ||daily supervision ||m.dijkstra.work AT gmail DOT com ||
||Elisa Hoekstra ||daily supervision ||e.j.hoekstra AT umcg DOT nl ||