= Computational Molecular Biology Research =

[[TOC()]]

== Course Overview ==

== Projects ==

* Increasing diagnostic yield of fast whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU):
 A. Improved variant calling of CNVs or large insertions or sex chromosome specific variants (choose one) - Pieter / Freerk
 B. Improved variant calling of medium sized !InDels - Pieter / Freerk
 C. Improved variant interpretation by combining gene networks with phenotype networks - Juha / Joeri

* Transcriptome analysis to elucidate human fatty liver disease development:
 D. Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs - Bibi / Jing

* Interaction of microbe and host genomes in IBD???:
 E. Microbiome anaylses - Floris / Arnau / Marc Jan

* Non-invasive early detection of (pre-)diabetes using Advanced Glycemic Endproduct detection:
 F. Optimizing decision trees to differentiate between healthy and diseased using parameter optimisation - Martijn

* Towards better treatment of cancer patients: Identifying new tumor (sub) types:
 G. By re-analysing DNA aberrations in 16,000 tumor samples - Lude?


== 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  ||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 ||

=== 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 - 11:15 ||Course kick off (Morris Swertz) ||2311-608 GCC room ||
||11:15 - 12:00 ||Lunch break ||
||12:00 - 13:00 ||Literature discussion ||3226-302 ERIBA meeting room ||
||13:00 - 13:15 ||Break || ||
||13:15 - 14:15 ||Project introduction: 5GpM - whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU) (?) ||2311-608 GCC room ||
||14:15 - 14:45 ||Break || ||
||14:45 - 15:45 ||Project introduction: Improved variant calling (Freerk van Dijk) ||2311-608 GCC room ||
||15:45 - 16:00 ||Break || ||
||16:00 - 16:45 ||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 (Anries Smit & Martijn Dijkstra) ||2311-608 GCC room  ||
||12:00 - 13:00 ||Lunch break || ||
||13:00 - 13:45 ||Project introduction: Microbiome anaylses (Floris Imhann) ||2311-608 GCC room  ||
||13:45 - 14:00 ||Break || ||
||14:00 - 14:45 ||Project introduction: ? (?) ||2311-608 GCC room ||
||14:45 - 15:00 ||Break || ||
||15:00 - 16:00 ||Discuss options, ask questions and choose project ||2311-608 GCC room  ||

** Wednesday 04-02-2015 **

|| **When** || **What** || **Where** ||
||09:30 - 10:15 ||Experimental Design (Lude) ||2311-608 GCC room ||
||10:15 - 10:30 ||Break || ||
||10:30 - 11:15 ||GWAS (Lude) ||2311-608 GCC room ||
||11:15 - 11:30 ||Break || ||
||11:30 - 12:15 ||NGS (Morris) ||2311-608 GCC room ||
||12:15 - 13:00 ||Lunch break ||
||13:00 - 13:45 ||R and bash scripting intro (Martijn Dijkstra) ||2311-608 GCC room ||
||13:45 - 14:00 ||Break || ||
||14:00 - 17:00 ||R and bash scripting tutorials ||2311-608 GCC room ||
17:00 Preferences for project mailed to course coordinator

** Thursday 05-02-2015 **

|| **When** || **What** || **Where** ||
||09:30 - 10:15 ||Gene Expression (Lude) ||2311-608 GCC room ||
||10:15 - 10:30 ||Break || ||
||10:30 - 11:15 ||Integrating Datasets (Lude) ||2311-608 GCC room ||
||11:15 - 11:30 ||Break || ||
||11:30 - 12:15 ||Data visualization (Lude) ||2311-608 GCC room ||
||12:15 - 13:00 ||Lunch break ||
||13:00 - 13:45 ||R and bash scripting intro (Martijn Dijkstra) ||2311-608 GCC room ||
||13:45 - 14:00 ||Break || ||
||14:00 - 17:00 ||R and bash scripting tutorials ||2311-608 GCC room ||

** Friday 06-02-2015 **

|| **When** || **What** || **Where** ||
||19:30 - 10:15 ||R and bash scripting intro (...) ||2311-608 GCC room ||
||10:15 - 10:30 ||Break || ||
||10:30 - 12:15 ||R and bash scripting tutorials ||2311-608 GCC room ||
||12:15 - 13:00 ||Lunch break ||
||13:00 - ..... ||Getting familiar with your project: search literature and read more. ||2311-608 GCC room ||
||..... - 17:00 ||Designing experiment / writing (validation) plan ||2311-608 GCC room ||

=== Weeks 2-5 ===

** Monday 09-02-2015 **

|| **When** || **What** || **Where** ||
|| all day except for regular meetings ||Finish experimental design / (validation) plan ||2311-608 GCC room ||
||16:00 - 17:00 ||Discuss final version of design / plan with supervisor and have it approved by the end of the day ||2311-608 GCC room ||

* 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 project 1 ||T.B.A. ||
||13:30 - 14:00 ||Presentation project 2 ||T.B.A. ||
||14:00 - 14:15 ||Break || ||
||14:15 - 14:45 ||Presentation project 3 ||T.B.A. ||
||14:45 - 15:15 ||Presentation project 4 ||T.B.A. ||
||15:15 - 15:30 ||Break || ||
||15:30 - 16:00 ||Presentation project 5 ||T.B.A. ||
||16:00 - 16:30 ||Presentation project 6 ||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 ||

Rating:
50% Practical work
30% Report
20% Presentation