= !ComputationalMolecularBiologyResearch =

[[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 - Jing / Bibi

* 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 ==

===================================================================================================
 Week 1
===================================================================================================

///// Monday 02-02-2015 /////

09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke groups) ERIBA 3rd floor corner room next to Auditorium
10:30 - 10:45 Break
10:45 - 11:15 Course introduction / kick off
11:15 - 12:00 Lunch break
12:00 - 13:00 Literature discussion
13:00 - 13:15 Break
13:15 - 14:15 Lecture project 1
14:15 - 14:45 Break
14:45 - 15:45 Lecture project 2
15:45 - 16:00 Break
16:00 - 16:45 Lecture project 3

///// Tuesday 03-02-2015 /////

08:45 - 10:00 Research meeting (Entire genetics dept.) ERIBA 3rd floor Auditorium
10:00 - 10:15 Break
10:15 - 11:00 Lecture project 4
11:00 - 11:15 Break
11:15 - 12:00 Lecture project 5
12:00 - 13:00 Lunch break
13:00 - 13:45 Lecture project 6
13:45 - 14:00 Break
14:00 - 14:45 Lecture project 7
14:45 - 15:00 Break
15:00 - 16:00 Discuss options, ask questions and choose project.

///// Wednesday 04-02-2015 /////

09:30 - 10:15 Experimental Design (Lude)
10:15 - 10:30 Break
10:30 - 11:15 GWAS (Lude)
11:15 - 11:30 Break
11:30 - 12:15 NGS (?)

Afternoon:
* Getting familiar with the topic: search literature and read read read.

///// Thursday 05-02-2015 /////

09:30 - 10:15 Gene Expression (Lude)
10:15 - 10:30 Break
10:30 - 11:15 Integrating Datasets (Lude)
11:15 - 11:30 Break
11:30 - 12:15 Data visualization (Lude)

Afternoon:
* Getting familiar with the topic: search literature and read more.
* Learning to script depending on project either R or Bash or...

///// Friday 06-02-2015 /////

* Getting familiar with the topic: search literature and read more.
* Learning to script depending on project either R or Bash or...
* Start designing experiment / writing (validation) plan

===================================================================================================
 Week 2-5
===================================================================================================

///// Monday 09-02-2015 /////

* Regular meetings
* Finish experimental design / (validation) plan.
  Discuss design with supervisor and have approved experimental design ready by the end of the day.

///// Regular events /////

Mondays  09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke groups) @ ERIBA 3rd floor corner room next to Auditorium.
Mondays  12:00 - 13:00 Literature discussion @ ERIBA 3rd floor corner room next to Auditorium.
Tuesdays 08:45 - 10:00 Research meeting (Entire genetics dept.) @ ERIBA 3rd floor Auditorium.
Other    09:00 - 17:00 Perform experiments and continue to learn scripting.

===================================================================================================
 Week 6
===================================================================================================

Mondays  09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke groups) @ ERIBA 3rd floor corner room next to Auditorium.
Mondays  12:00 - 13:00 Literature discussion @ ERIBA 3rd floor corner room next to Auditorium.
Tuesdays 08:45 - 10:00 Research meeting (Entire genetics dept.) @ ERIBA 3rd floor Auditorium.

Full days: Write report and prepare presentation.

///// Thursday 12-03-2015 /////

13:00 - 13:30 Presentation project 1
13:30 - 14:00 Presentation project 2
14:00 - 14:15 Break
14:15 - 14:45 Presentation project 3
14:45 - 15:15 Presentation project 4
15:15 - 15:30 Break
15:30 - 16:00 Presentation project 5
16:00 - 16:30 Presentation project 6
16:30 - 17:00 Wrap up by Morris

///// Friday 13-03-2015 /////

17:00 Report submission deadline