= 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 using MtDNA for new borns on the Neonatal Intensive Care Unit (NICU) === 1. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P1 Improved variant calling for MtDNA] - Pieter / Gerben === Improved quantification for RNA sequencing - what combination of methods should we use? === 2. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P2 Improved quantification for RNA sequencing] - Niek / Freerk === Methods/tools for detection of fusion gene transcripts in RNA sequencing === 3. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P3 Analysis of trans-spliced transcripts in RNA seq data] - Lennart / Birgit / Analyse team === Single cell RNA sequencing quantification === 4. [wiki:Courses/ComputationalMolecularBiologyResearch2016/P4 Single cell RNA seq quantification ] - Gerben / Pieter van der Vlies / Iris? [waar komt de data vandaan?] === Improved detection of regulatory transcription factor binding sites in non-coding DNA 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, meeting room without a name opposite the secretary, 5th floor, opposite the secretary and near elevators || || 3211 || 501 ||''Dentistry'' building, meeting room ''1'', 5th floor, end of corridor || || 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 01-02-2016 ** || **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 02-02-2016 ** || **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 ||Lecture: Experimental Design (Lude Franke) ||TBA || ||10:45 - 11:00 ||Break || || ||11:00 - 11:45 ||Lecture: GWAS (Lude Franke) ||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 03-02-2016 ** || **When** || **What** || **Where** || ||09:00 - 12:00 ||R-turorial part I (Annique Claringbould) ||TBA || ||12:00 - 13:00 ||Lunch break || || ||13:00 - 17:00 ||R-turorial part II (Annique Claringbould) ||TBA || ** Thursday 04-02-2016 ** || **When** || **What** || **Where** || ||09:00 - 09:45 ||Project intro: Quantification for RNA seq (Niek de Klein) ||TBA || ||09:45 - 10:00 ||Break || || ||10:00 - 10:45 ||Project intro: mtDNA analysis (Pieter Neerincx) ||TBA || ||10:45 - 11:00 ||Break || || ||11:00 - 11:45 ||Project intro: DNA Motif finding (Iris Jonkers) ||TBA || ||12:00 - 13:00 ||Lunch break || || ||13:00 - 13:45 ||Lecture: Gene Expression (Lude Franke) ||TBA || ||13:45 - 14:00 ||Break || || ||14:00 - 14:45 ||Lecture: Integrating Datasets (Lude Franke) ||TBA || ||14:45 - 15:00 ||Break || || ||15:00 - 15:45 ||Lecture: Data visualization (Lude Franke) ||TBA || ||15:45 - 16:00 ||Break || || ||16:00 - 16:45 ||Project intro: Single cell RNA seq (Pieter van der Vlies) ||TBA || || 18:00 ||Deadline: Preferences for project mailed to course coordinator Pieter Neerincx || || ** Friday 05-02-2016 ** || **When** || **What** || **Where** || ||09:15 - 09:30 ||Scrum ||TBA || ||09:30 - 12:00 ||Getting familiar with your project: [[BR]]Search literature, [[BR]] Design experiment and [[BR]] write (validation) plan || flex desks || ||12:00 - 13:00 ||Lunch break || || ||13:00 - 17:00 ||Getting familiar with your project: [[BR]]Search literature, [[BR]] Design experiment and [[BR]] write (validation) plan || flex desks || === Weeks 2-5 === ** Monday 08-02-2016 ** || **When** || **What** || **Where** || ||09:15 - 09:30 ||Scrum ||TBA || ||09:30 - 12:00 ||Finish experimental design / (validation) plan ||flex desks || ||12:00 - 13:00 ||Research lunch meeting (!Wijmenga/Weersma/Franke groups) ||3226-314 ERIBA Auditorium || ||12:00 - 17:00 ||Finish experimental design / (validation) plan ||flex desks || || 17:00 ||Deadline: have experimental design / (validation) plan approved by your supervisor(s) ||TBA || ** From Tuesday 09-02-2016 onwards ** * Regular meetings * Execute your experiment / plan === Week 6 === ** From Monday 07-03-2016 onwards ** * Regular meetings * Write report and prepare presentation. ** Thursday 10-03-2015 ** || **When** || **What** || **Where** || ||13:00 - 13:30 ||Project Presentation I ||TBA || ||13:30 - 14:00 ||Project Presentation II ||TBA || ||14:00 - 14:15 ||Break || || ||14:15 - 14:45 ||Project Presentation III ||TBA || ||14:45 - 15:15 ||Project Presentation IV ||TBA || ||15:15 - 15:30 ||Break || || ||15:30 - 16:00 ||Project Presentation V ||TBA || ||16:00 - 16:30 ||Project Presentation VI ||TBA || ||16:30 - 17:00 ||Wrap up (Morris/Pieter) ||TBA || ** Friday 11-03-2015 ** || **When** || **What** || **Where** || || 17:00 ||Report submission deadline || Your project supervisor's mailbox || === Contact === ||Morris Swertz ||coordinator ||m.a.swertz AT rug DOT nl || ||Pieter Neerincx ||daily supervision ||pieter.neerincx AT gmail DOT com ||