= 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 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. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P1 Improved variant calling for MtDNA] - Pieter / Freerk

=== Improved quantification for RNA sequencing ===
2. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P2 Improved quantification for RNA sequencing] - Niek / Freerk

=== Detection of fusion gene transcripts in RNA sequencing ===
3. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P3 Analysis of trans-spliced transcripts in RNA seq data] - Lennart / Birgit

=== Single cell RNA sequencing quantification ===
4. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P4 Single cell RNA seq quantification ] - Gerben

=== Improved detection of transcription factor binding sites by merging sequence (context) with in vivo DNA accessibility data ===
5. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P5 Improved DNA Motif finding] - Iris / Pieter

== 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 || 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 ||Bash scripting intro part I (Lennart Johansson) ||TBA ||
||13:45 - 14:00 ||Break || ||
||14:00 - 17:00 ||[wiki:Courses/BASH Bash scripting tutorials] ||TBA ||

** Tuesday 02-02-2015 **

|| **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 ||Project intro or lecture ||TBA ||
||10:45 - 11:00 ||Break || ||
||11:00 - 11:45 ||Project intro or lecture ||TBA ||
||12:00 - 13:00 ||Lunch break || ||
||13:00 - 13:45 ||Bash scripting intro part II (Lennart Johansson) ||TBA ||
||13:45 - 14:00 ||Break || ||
||14:00 - 17:00 ||[wiki:Courses/BASH Bash scripting tutorials] ||TBA ||

** Wednesday 03-02-2015 **

|| **When** || **What** || **Where** ||
||09:00 - 12:00 ||R-turorial part I (Annique Claringbould) ||TBA ||
||12:00 - 13:00 ||Lunch break ||
||13:00 - 13:45 ||Improved DNA Motif finding (Iris Jonkers) ||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 ||
||15:45 - 16:00 ||Break || ||
||16:00 - 16:45 ||Project intro or lecture ||TBA ||

** Thursday 04-02-2015 **

|| **When** || **What** || **Where** ||
||09:00 - 12:00 ||R-turorial part II (Annique Claringbould) ||TBA ||
||12:00 - 13:00 ||Lunch break ||
||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 ||
|| 16:00        ||Last chance to discuss projects and ask questions || || 
|| 18:00        ||Deadline: Preferences for project mailed to course coordinator Pieter Neerincx || ||

** Friday 05-02-2015 **

|| **When** || **What** || **Where** ||
||09:15 - 09:30 ||Scrum ||TBA ||
||09:30 - 12:00 ||Getting familiar with your project: search literature [[BR]] Design experiment and write (validation) plan ||TBA ||
||12:00 - 13:00 ||Lunch break ||
||13:00 - 17:00 ||Getting familiar with your project: search literature [[BR]] Design experiment and write (validation) plan ||TBA ||

=== 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 ||