Changes between Initial Version and Version 1 of Courses/ComputationalMolecularBiologyResearch2015


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Timestamp:
2015-01-28T14:37:04+01:00 (11 years ago)
Author:
Pieter Neerincx
Comment:

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  • Courses/ComputationalMolecularBiologyResearch2015

    v1 v1  
     1= !ComputationalMolecularBiologyResearch =
     2
     3[[TOC()]]
     4
     5== Course Overview ==
     6
     7== Projects ==
     8
     9* Increasing diagnostic yield of fast whole genome diagnostics for new borns on the Neonatal Intensive Care Unit (NICU):
     10 A. Improved variant calling of CNVs or large insertions or sex chromosome specific variants (choose one) - Pieter / Freerk
     11 B. Improved variant calling of medium sized !InDels - Pieter / Freerk
     12 C. Improved variant interpretation by combining gene networks with phenotype networks - Juha / Joeri
     13
     14* Transcriptome analysis to elucidate human fatty liver disease development:
     15 D. Improving Ribo-zero RNA seq data analysis to detect non-coding RNAs in addition to coding RNAs - Jing / Bibi
     16
     17* Interaction of microbe and host genomes in IBD???:
     18 E. Microbiome anaylses - Floris / Arnau? / Marc Jan?
     19
     20* Non-invasive early detection of (pre-)diabetes using Advanced Glycemic Endproduct detection:
     21 F. Optimizing decision trees to differentiate between healthy and diseased using parameter optimisation - Martijn
     22
     23* Towards better treatment of cancer patients: Identifying new tumor (sub) types:
     24 G. By re-analysing DNA aberrations in 16,000 tumor samples - Lude?
     25
     26
     27== Course Schedule ==
     28
     29===================================================================================================
     30 Week 1
     31===================================================================================================
     32
     33///// Monday 02-02-2015 /////
     34
     3509:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke groups) ERIBA 3rd floor corner room next to Auditorium
     3610:30 - 10:45 Break
     3710:45 - 11:15 Course introduction / kick off
     3811:15 - 12:00 Lunch break
     3912:00 - 13:00 Literature discussion
     4013:00 - 13:15 Break
     4113:15 - 14:15 Lecture project 1
     4214:15 - 14:45 Break
     4314:45 - 15:45 Lecture project 2
     4415:45 - 16:00 Break
     4516:00 - 16:45 Lecture project 3
     46
     47///// Tuesday 03-02-2015 /////
     48
     4908:45 - 10:00 Research meeting (Entire genetics dept.) ERIBA 3rd floor Auditorium
     5010:00 - 10:15 Break
     5110:15 - 11:00 Lecture project 4
     5211:00 - 11:15 Break
     5311:15 - 12:00 Lecture project 5
     5412:00 - 13:00 Lunch break
     5513:00 - 13:45 Lecture project 6
     5613:45 - 14:00 Break
     5714:00 - 14:45 Lecture project 7
     5814:45 - 15:00 Break
     5915:00 - 16:00 Discuss options, ask questions and choose project.
     60
     61///// Wednesday 04-02-2015 /////
     62
     6309:30 - 10:15 Experimental Design (Lude)
     6410:15 - 10:30 Break
     6510:30 - 11:15 GWAS (Lude)
     6611:15 - 11:30 Break
     6711:30 - 12:15 NGS (?)
     68
     69Afternoon:
     70* Getting familiar with the topic: search literature and read read read.
     71
     72///// Thursday 05-02-2015 /////
     73
     7409:30 - 10:15 Gene Expression (Lude)
     7510:15 - 10:30 Break
     7610:30 - 11:15 Integrating Datasets (Lude)
     7711:15 - 11:30 Break
     7811:30 - 12:15 Data visualization (Lude)
     79
     80Afternoon:
     81* Getting familiar with the topic: search literature and read more.
     82* Learning to script depending on project either R or Bash or...
     83
     84///// Friday 06-02-2015 /////
     85
     86* Getting familiar with the topic: search literature and read more.
     87* Learning to script depending on project either R or Bash or...
     88* Start designing experiment / writing (validation) plan
     89
     90===================================================================================================
     91 Week 2-5
     92===================================================================================================
     93
     94///// Monday 09-02-2015 /////
     95
     96* Regular meetings
     97* Finish experimental design / (validation) plan.
     98  Discuss design with supervisor and have approved experimental design ready by the end of the day.
     99
     100///// Regular events /////
     101
     102Mondays  09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke groups) @ ERIBA 3rd floor corner room next to Auditorium.
     103Mondays  12:00 - 13:00 Literature discussion @ ERIBA 3rd floor corner room next to Auditorium.
     104Tuesdays 08:45 - 10:00 Research meeting (Entire genetics dept.) @ ERIBA 3rd floor Auditorium.
     105Other    09:00 - 17:00 Perform experiments and continue to learn scripting.
     106
     107===================================================================================================
     108 Week 6
     109===================================================================================================
     110
     111Mondays  09:15 - 10:30 Research meeting (Wijmenga/Weersma/Franke groups) @ ERIBA 3rd floor corner room next to Auditorium.
     112Mondays  12:00 - 13:00 Literature discussion @ ERIBA 3rd floor corner room next to Auditorium.
     113Tuesdays 08:45 - 10:00 Research meeting (Entire genetics dept.) @ ERIBA 3rd floor Auditorium.
     114
     115Full days: Write report and prepare presentation.
     116
     117///// Thursday 12-03-2015 /////
     118
     11913:00 - 13:30 Presentation project 1
     12013:30 - 14:00 Presentation project 2
     12114:00 - 14:15 Break
     12214:15 - 14:45 Presentation project 3
     12314:45 - 15:15 Presentation project 4
     12415:15 - 15:30 Break
     12515:30 - 16:00 Presentation project 5
     12616:00 - 16:30 Presentation project 6
     12716:30 - 17:00 Wrap up by Morris
     128
     129///// Friday 13-03-2015 /////
     130
     13117:00 Report submission deadline