= 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, which will be supervised by 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 others in the department. == Projects == [[TOC(Courses/ComputationalMolecularBiologyResearch2016/*, inline, noheading)]] == Experimental design a.k.a validation plan == At the start of a project the students have to draft a plan outlining their experimental design. This should contain the following: * Short intro explaining the goal the experiment: why are you going to perform this experiment? * Material and methods: how are you going to do this experiment? * Validation criteria: * Quality: how are you going to determine which analysis / software package yields the best results? * Other criteria may be important as well depending the application. [[BR]] For example for fast diagnostics the analysis speed may be an important factor in addition to reliability of the results. * Schedule for the remaining 5 weeks of the project. == Report and presentation == The report produced at the end of the project consists of the original experimental design / validation plan supplemented with: * Results * Conclusion and discussion: the conclusion should logically follow from combining the results with the previously defined validation criteria. The key findings of the project will be presented in slots of 30 minutes per project: * 20 minutes for presentating * 10 minutes for answering questions == Rating == Students will be rated as follows: * 35% Code + data produced during practical work * 35% Report * 30% Presentation == 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 || -s42a ||''Dentistry'' building, basement || || 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 (ADCB 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/Swertz 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) ||3211-501 Room "1" || ||09:45 - 10:00 ||Break || || ||10:00 - 10:45 ||Lecture: Next Generation Sequencing (Morris Swertz) ||3211-501 Room "1" || ||10:45 - 11:00 ||Break || || ||11:00 - 11:45 ||Project intro: (Birgit Sikkema-Raddatz / Lennart Johansson)||3211-501 Room "1" || ||11:45 - 12:00 ||Break || || ||12:00 - 13:00 ||Research lunch meeting (ADCB groups) ||3226-314 ERIBA Auditorium || ||13:00 - 13:45 ||Bash scripting intro part I (Lennart Johansson) ||3211-501 Room "1" || ||13:45 - 14:00 ||Break || || ||14:00 - 17:00 ||[wiki:Courses/BASH Bash scripting tutorials] ||3211-501 Room "1" || ** 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) ||3211-501 Room "1" || ||10:45 - 11:00 ||Break || || ||11:00 - 11:45 ||Lecture: GWAS (Lude Franke) ||3211-501 Room "1" || ||12:00 - 13:00 ||Lunch break || || ||13:00 - 13:45 ||Bash scripting intro part II (Lennart Johansson) ||3211-501 Room "1" || ||13:45 - 14:00 ||Break || || ||14:00 - 17:00 ||[wiki:Courses/BASH Bash scripting tutorials] ||3211-501 Room "1" || ** Wednesday 03-02-2016 ** || **When** || **What** || **Where** || ||09:00 - 12:00 ||R-turorial part I (Annique Claringbould) ||3211-501 Room "1" || ||12:00 - 13:00 ||Lunch break || || ||13:00 - 17:00 ||R-turorial part II (Annique Claringbould) ||3211-501 Room "1" || ** Thursday 04-02-2016 ** || **When** || **What** || **Where** || ||09:00 - 09:45 ||Project intro: Quantification for RNA seq (Niek de Klein) ||3211-501 Room "1" || ||09:45 - 10:00 ||Break || || ||10:00 - 10:45 ||Project intro: mtDNA analysis (Pieter Neerincx) ||3211-501 Room "1" || ||10:45 - 11:00 ||Break || || ||11:00 - 11:45 ||Project intro: DNA Motif finding (Iris Jonkers) ||3211-501 Room "1" || ||12:00 - 13:00 ||Lunch break || || ||13:00 - 13:45 ||Lecture: Gene Expression (Lude Franke) ||3211-501 Room "1" || ||13:45 - 14:00 ||Break || || ||14:00 - 14:45 ||Lecture: Integrating Datasets (Lude Franke) ||3211-501 Room "1" || ||14:45 - 15:00 ||Break || || ||15:00 - 15:45 ||Lecture: Data visualization (Lude Franke) ||3211-501 Room "1" || ||15:45 - 16:00 ||Break || || ||16:00 - 16:45 ||Project intro: Single cell RNA seq (Pieter van der Vlies) ||3211-501 Room "1" || ** Friday 05-02-2016 ** || **When** || **What** || **Where** || ||09:00 - 09:45 ||Project intro: RNA editing (Yang Li) ||3211-501 Room "1" || ||09:45 - 10:00 ||Deadline: choose project. ||3211-501 Room "1" || ||10:00 - 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/Swertz 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 3 [wiki:ComputationalMolecularBiologyResearch2016/P3#Analysisoftrans-splicedtranscriptsinRNAseqdata Analysis of trans-spliced transcripts in RNA seq data] (Marten) ||3211-s42a || ||13:30 - 14:00 ||Project 2 [wiki:ComputationalMolecularBiologyResearch2016/P2#BenchmarkingRNAseqgeneexpressionquantificationtools Benchmarking RNAseq gene expression quantification tools] (Jasper) ||3211-s42a || ||14:00 - 14:15 ||Break || || ||14:15 - 14:45 ||Project 1 [wiki:ComputationalMolecularBiologyResearch2016/P1#IncreasingdiagnosticyieldoffastdiagnosticsusingNGS Increasing diagnostic yield of fast diagnostics using NGS] (Matthijs) ||3211-s42a || ||14:45 - 15:15 ||Project 4 [wiki:ComputationalMolecularBiologyResearch2016/P4#SinglecellRNAseqquantification Single cell RNA seq quantification] (Floris) ||3211-s42a || ||15:15 - 15:30 ||Break || || ||15:30 - 16:00 ||Project 5 [wiki:ComputationalMolecularBiologyResearch2016/P5#ImprovedDNAMotiffinding Improved DNA Motif finding] (Laura) ||3211-s42a || ||16:00 - 16:30 ||Project 6 [wiki:ComputationalMolecularBiologyResearch2016/P6#DetectionofRNA-editingsitesinhumanRNA-sequencingdata Detection of RNA-editing sites in human RNA-sequencing data] (Bram) ||3211-s42a || ||16:30 - 17:00 ||Wrap up (Pieter) ||3211-s42a || ** Friday 11-03-2015 ** || **When** || **What** || **Where** || || 17:00 ||Report submission deadline || Your project supervisor's mailbox || == Contact == ||Morris Swertz ||m.a.swertz AT rug DOT nl || ||Pieter Neerincx ||pieter.neerincx AT gmail DOT com ||