====== Practical Course: Bioinformatics Applications in Genome Research ======
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|392177 | Dörr | Summer semester 2017 | Block 13.03.2017-24.03.2017 - 9:30-17:30 Uhr in V6-116 |[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=89694283|ekvv]] |


===== Content =====
In this course, practical applications and issues in concrete problem statements and handling real data sets will be addressed. The following topics are intended: assembly, scaffolding, annotation, gene prediction, comparative analysis, etc.  

Theoretical knowledge of the students shall be supplemented by practical aspects such as setting up and running existing tools, implementing small own tools, pre- and postprocessing, and critical interpretation of results. A continuously enriched visualization of the data and the obtained results will also guide through the course. 


  * Requires participation in the lecture "Algorithms in Genome Research". 
  * Beside regular and active participation in the course, each student gives a short (15min) presentation and presents their results shall to other participants. 

===== Overview =====

| **Date**   | **Topic**               | **Presentation** | **Solution (for next day)**|
| Mon, 13.3. | Shell                   | Dany: //Introduction to Python// | Tilman |
| Tue, 14.3. | Assembly                | Christian: //Genome Assembly, de Brujin Graphs// | Christian|
| Wed, 15.3. | Finishing               | Philipp: //BWA// | Jens |
| Thu, 16.3. | Genome rearrangements I | Franzi: //Rearrangement distances//, Dany: //Workflow management: snakemake//| Marcel |
| Fri, 17.3. | Genome rearrangements II| Tilman: //Circos tutorial// | Philipp |
| Mon, 20.3. | Gene Prediction         | Ago: //Gene Prediction (software: Glimmer, Prodigal)// | Ago |
| Tue, 21.3. | Hidden Markov Models (HMMs)| Marcel: //HMMs// | Franzi |
| Wed, 22.3. | Position-Specific Scoring Matrices (PSSMs)| Jens: //PSSMs// | Tilman|
| Thu, 23.3. | Metagenomics            | Philipp: //Metagenomics// | -- |
| Fri, 24.3. | Finishing the Circos plot  | -- | -- |


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