Changes between Initial Version and Version 1 of Courses/ComputationalMolecularBiologyResearch2016


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Timestamp:
2016-01-19T14:01:09+01:00 (9 years ago)
Author:
Pieter Neerincx
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  • Courses/ComputationalMolecularBiologyResearch2016

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     1= Computational Molecular Biology Research =
     2
     3[[TOC()]]
     4
     5== Course Overview ==
     6
     7This research course demonstrates the in silico data analysis used for genetics research at the RUG and UMCG.
     8The 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.
     9
     10In 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.
     11
     12== Rating ==
     13Students will be rated as follows:
     14 * 50% Practical work
     15 * 30% Report
     16 * 20% Presentation
     17
     18== Projects ==
     19
     20=== Increasing diagnostic yield of fast whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU) ===
     211. [wiki:Courses/ComputationalMolecularBiologyResearch/P1 Improved variant calling for MtDNA] - Pieter / Freerk
     22
     23=== Increasing diagnostic yield of fast whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU) ===
     242. [wiki:Courses/ComputationalMolecularBiologyResearch/P2 Improved quantification] - Niek / Freerk
     25
     266. [wiki:Courses/ComputationalMolecularBiologyResearch/P6 Improved variant interpretation by combining gene networks with phenotype networks] - Juha / Joeri
     27
     28=== Transcriptome analysis to elucidate human fatty liver disease development ===
     297. [wiki:Courses/ComputationalMolecularBiologyResearch/P7 Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs] - Bibi / Jing
     30
     31=== Changes in the gut microbiome ===
     328. [wiki:Courses/ComputationalMolecularBiologyResearch/P8 Analyzing Whole Genome Shotgun data] - Floris / Arnau / Marc Jan
     33
     34=== Non-invasive early detection of (pre-)diabetes using Advanced Glycemic Endproduct detection ===
     359. [wiki:Courses/ComputationalMolecularBiologyResearch/P9 Optimizing decision trees to differentiate between healthy and diseased using parameter optimization] - Martijn / Patrick / Andries / Bernadette
     36
     37== Course Schedule ==
     38
     39=== Venue ===
     40
     41Course 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]]
     42{{{
     43Antonius Deusinglaan 1
     449713 AV Groningen
     45}}}
     46
     47|| **Building** || **Room** || **Name** ||
     48|| 3226 || 302 ||''ERIBA'' building, meeting room, 3rd floor, in the corner and next to auditorium ||
     49|| 3226 || 314 ||''ERIBA'' building, auditorium, 3rd floor ||
     50|| 3211 || 608 ||''Dentistry'' building, GCC room, 6th floor, at the end of the corridor ||
     51|| 3211 || flex desks ||''Dentistry'' building, 5th floor ||
     52|| 3226 || flex desks ||''ERIBA'' building, 5th floor ||
     53
     54=== Regular events ===
     55
     56|| **Day** || **Time** || **What** || **Where** ||
     57||Mondays  ||09:15 - 10:30 ||Research meeting (!Wijmenga/Weersma/Franke groups) ||3226-302 ERIBA meeting room ||
     58||Mondays  ||10:45 - 11:00 ||Course SCRUM in weeks 2-6 ||3211-608 GCC room ||
     59||Mondays  ||12:00 - 13:00 ||Literature discussion ||3226-302 ERIBA meeting room ||
     60||Tuesdays ||08:45 - 10:00 ||Research meeting (Entire genetics dept.) ||3226-314 ERIBA Auditorium ||
     61||Tuesdays ||10:15 - 10:30 ||Course SCRUM in weeks 2-6 ||3211-608 GCC room ||
     62||Wednesdays ||09:30 - 09:45 ||Course SCRUM in weeks 2-6 ||3211-608 GCC room ||
     63||Thursdays ||09:30 - 09:45 ||Course SCRUM in weeks 2-6 ||3211-608 GCC room ||
     64||Fridays ||09:30 - 09:45 ||Course SCRUM in weeks 2-6 ||3211-608 GCC room ||
     65
     66=== Week 1 ===
     67
     68**Monday 02-02-2015**
     69
     70|| **When** || **What** || **Where** ||
     71||09:15 - 10:30 ||Research meeting (!Wijmenga/Weersma/Franke groups) ||3226-302 ERIBA meeting room ||
     72||10:30 - 10:45 ||Break || ||
     73||10:45 - 11:00 ||Course kick off (Morris Swertz) ||3211-608 GCC room ||
     74||11:00 - 12:00 ||Lecture: Next Generation Sequencing (Morris Swertz) ||3211-608 GCC room ||
     75||12:00 - 13:00 ||Lunch break || ||
     76||13:00 - 13:45 ||Project introduction: Whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (Cleo van Diemen) ||3211-608 GCC room ||
     77||13:45 - 14:00 ||Break || ||
     78||14:00 - 14:45 ||Project introduction: Improved variant calling (Freerk van Dijk) ||3211-608 GCC room ||
     79||14:45 - 15:00 ||Break || ||
     80||15:00 - 15:45 ||Project introduction: Improved variant interpretation (Juha Karjalainen) ||3211-608 GCC room ||
     81
     82** Tuesday 03-02-2015 **
     83
     84|| **When** || **What** || **Where** ||
     85||08:45 - 10:00 ||Research meeting (Entire genetics dept.) ||3226-314 ERIBA Auditorium ||
     86||10:00 - 10:15 ||Break || ||
     87||10:15 - 11:00 ||Project introduction: Transcriptome analysis to elucidate human fatty liver disease development (Biljana Atanasovska) ||3211-608 GCC room ||
     88||11:00 - 11:15 ||Break || ||
     89||11:15 - 12:00 ||Project introduction: Non-invasive early detection of (pre-)diabetes (Andries Smit & Martijn Dijkstra) ||3211-608 GCC room  ||
     90||12:00 - 13:00 ||Lunch break || ||
     91||13:00 - 13:45 ||R scripting intro (Martijn Dijkstra) ||3211-608 GCC room ||
     92||13:45 - 14:00 ||Break || ||
     93||14:00 - 17:00 ||R tutorials ||3211-608 GCC room ||
     94
     95** Wednesday 04-02-2015 **
     96
     97|| **When** || **What** || **Where** ||
     98||09:30 - 10:15 ||Lecture: Experimental Design (Lude Franke) ||3211-608 GCC room ||
     99||10:15 - 10:30 ||Break || ||
     100||10:30 - 11:15 ||Lecture: GWAS (Lude Franke) ||3211-608 GCC room ||
     101||11:15 - 11:30 ||Break || ||
     102||11:30 - 12:15 ||Project introduction: Microbiome anaylses (Floris Imhann) ||3211-608 GCC room ||
     103||12:15 - 13:00 ||Lunch break ||
     104||13:00 - 13:45 ||R scripting intro (Martijn Dijkstra) ||3211-608 GCC room ||
     105||13:45 - 14:00 ||Break || ||
     106||14:00 - 17:00 ||R scripting tutorials ||3211-608 GCC room ||
     107|| 18:00 ||Deadline: Preferences for project mailed to course coordinator Morris Swertz || ||
     108
     109** Thursday 05-02-2015 **
     110
     111|| **When** || **What** || **Where** ||
     112||09:30 - 10:15 ||Lecture: Gene Expression (Lude Franke) ||3211-608 GCC room ||
     113||10:15 - 10:30 ||Break || ||
     114||10:30 - 11:15 ||Lecture: Integrating Datasets (Lude Franke) ||3211-608 GCC room ||
     115||11:15 - 11:30 ||Break || ||
     116||11:30 - 12:15 ||Lecture: Data visualization (Lude Franke) ||3211-608 GCC room ||
     117||12:15 - 13:00 ||Lunch break ||
     118||13:00 - 13:45 ||Bash scripting intro (Lennart Johansson) ||3211-608 GCC room ||
     119||13:45 - 14:00 ||Break || ||
     120||14:00 - 17:00 ||[wiki:Courses/BASH Bash scripting tutorials] ||3211-608 GCC room ||
     121
     122** Friday 06-02-2015 **
     123
     124|| **When** || **What** || **Where** ||
     125||09:30 - 10:15 ||Bash scripting intro (Lennart Johansson) ||3211-608 GCC room ||
     126||10:15 - 10:30 ||Break || ||
     127||10:30 - 12:15 ||Bash scripting tutorials ||3211-608 GCC room ||
     128||12:15 - 13:00 ||Lunch break ||
     129||13:00 - 17:00 ||Getting familiar with your project: search literature [[BR]] Start designing experiment / writing (validation) plan ||3211-608 GCC room ||
     130
     131=== Weeks 2-5 ===
     132
     133** Monday 09-02-2015 **
     134
     135|| **When** || **What** || **Where** ||
     136||09:15 - 10:30 ||Research meeting (!Wijmenga/Weersma/Franke groups) ||3226-302 ERIBA meeting room ||
     137||10:30 - 10:45 ||Break || ||
     138||10:45 - 12:00 ||Finish experimental design / (validation) plan ||3211-608 GCC room ||
     139||12:00 - 13:00 ||Literature discussion ||3226-302 ERIBA meeting room ||
     140||12:00 - 17:00 ||Finish experimental design / (validation) plan ||3211-608 GCC room ||
     141|| 17:00 ||Deadline: have experimental design / (validation) plan approved by your supervisors ||3211-608 GCC room ||
     142
     143**From Tuesday 10-02-2015 onwards **
     144
     145* Regular meetings
     146* Execute your experiment / plan
     147
     148=== Week 6 ===
     149
     150* Regular meetings
     151* Write report and prepare presentation.
     152
     153** Thursday 12-03-2015 **
     154
     155|| **When** || **What** || **Where** ||
     156||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 ||
     157||13:30 - 14:00 ||Presentation Improved variant calling for large insertions (Glenn) ||3211-S42A ||
     158||14:00 - 14:15 ||Break || ||
     159||14:15 - 14:45 ||Presentation Optimizing decision trees to differentiate between healthy and diseased using parameter optimization (Sandra) ||3211-S42A ||
     160||14:45 - 15:15 ||Presentation Improved variant calling for MtDNA (Falke) ||3211-S42A ||
     161||15:15 - 15:30 ||Break || ||
     162||15:30 - 16:00 ||Presentation Improved variant interpretation by combining gene networks with phenotype networks (Tessa) ||3211-S42A ||
     163||16:00 - 16:30 ||Presentation Analyzing Whole Genome Shotgun Microbiomome data (Rogier) ||3211-S42A ||
     164||16:30 - 17:00 ||Wrap up (Morris Swertz) ||3211-S42A ||
     165
     166** Friday 13-03-2015 **
     167
     168|| **When** || **What** || **Where** ||
     169||17:00 ||Report submission deadline || Your project supervisor's email inbox ||
     170
     171=== Contact ===
     172
     173||Morris Swertz ||coordinator ||m.a.swertz AT rug DOT nl ||
     174||Pieter Neerincx ||daily supervision ||pieter.neerincx AT gmail DOT com ||
     175||Martijn Dijkstra ||daily supervision ||m.dijkstra.work AT gmail DOT com ||
     176||Elisa Hoekstra ||daily supervision ||e.j.hoekstra AT umcg DOT nl ||
     177
     178