Changes between Version 25 and Version 26 of Courses/ComputationalMolecularBiologyResearch2016


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Timestamp:
2016-01-30T12:43:39+01:00 (9 years ago)
Author:
Pieter Neerincx
Comment:

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  • Courses/ComputationalMolecularBiologyResearch2016

    v25 v26  
    88The 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.
    99
    10 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.
    11 
    12 == Rating ==
    13 Students will be rated as follows:
    14  * 50% Code + data produced during practical work
    15  * 30% Report
    16  * 20% Presentation
     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, 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.
    1711
    1812== Projects ==
    1913
    2014[[TOC(Courses/ComputationalMolecularBiologyResearch2016/*, inline, noheading)]]
     15
     16== Experimental design a.k.a  validation plan ==
     17
     18At the start of a project the students have to draft a plan outlining their experimental design. This should contain the following:
     19 * Short intro explaining the goal the experiment: why are you going to perform this experiment?
     20 * Material and methods: how are you going to do this experiment?
     21 * Validation criteria:
     22   * Quality: how are you going to determine which analysis / software package yields the best results?
     23   * 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.
     24 * Schedule for the remaining 5 weeks of the project.
     25
     26== Report and presentation ==
     27
     28The report produced at the end of the project consists of the original experimental design / validation plan supplemented with:
     29 * Results
     30 * Conclusion and discussion: the conclusion should logically follow from combining the results with the previously defined validation criteria.
     31
     32The key findings of the project will be presented in slots of 30 minutes per project:
     33 * 20 minutes for presentating
     34 * 10 minutes for answering questions
     35
     36== Rating ==
     37Students will be rated as follows:
     38 * 35% Code + data produced during practical work
     39 * 35% Report
     40 * 30% Presentation
    2141
    2242== Course Schedule ==
    … …  
    153173|| 17:00    ||Report submission deadline || Your project supervisor's mailbox ||
    154174
    155 === Contact ===
     175== Contact ==
    156176
    157 ||Morris Swertz ||coordinator ||m.a.swertz AT rug DOT nl ||
    158 ||Pieter Neerincx ||daily supervision ||pieter.neerincx AT gmail DOT com ||
     177||Morris Swertz   ||m.a.swertz AT rug DOT nl        ||
     178||Pieter Neerincx ||pieter.neerincx AT gmail DOT com ||
    159179
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