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— teaching:2017summer:bioappgere [2020/02/14 09:07] (current)
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 +====== 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]] |
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 +
 +===== 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. ​
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 +
 +  * 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  | -- | -- |
 +
 +
 +----
 +Back to [[:​teaching|Teaching]]