Pro-/Seminar: Computational Approaches in Microbial Community Research (Winter Term 2017/2018)

This is a block pro-/seminar covering topics related to microbial community research. The topics include de novo genome assembly, resolution of the community structure, and functional annotation.

Tutor: Cedric Laczny

Dates:

Registration * from October 17th, 2017 to October 24th, 2017 HERE
Kick-off meeting [optional] January 15th, 2018 – 2 p.m. (s.t.) – E2.1, room 206
Deadline for feedback ** [optional] January 29th, 2018
Deadline to (de-)register in HISPOS OR de-register from seminar * February 5th, 2018
Presentations February 28th, 2018
Summary submission deadline March 7th, 2018

* If you want to de-register from the seminar, please send the tutor an email irrespectively whether you (de)registered in HISPOS or not.

** If you would like to get feedback about your slides, e.g. to improve your presentation before the talk, send your slides to the tutor before the feedback deadline. We strongly encourage you to take this opportunity. Before sending in the slides, check out our presentations guidelines (presentation guidelines, presentation guidelines checklist). Please note: The more complete the submitted presentation the more helpful the feedback can be. Please try to avoid submitting half-finished slides.

Hint Your slides will make up a substantial part of the final grade. Reading and paying attention to the provided presentation guidelines (see above) will help you to get an impression of which aspects are relevant for the evaluation. Disregarding many of the points listed in the guidelines may negatively affect your grade.

Place and Time:

  • E2.1, room 206, 9 a.m. (s.t.)

Requirements for participation:

  • Proseminar: at least in 3rd semester, Bioinformatics I

Certificate requirements:

  • Successful presentation:
    • Talk: 30 minutes (proseminar); 40 minutes (seminar)
    • Questions from the audience after the presentation
  • Attendance to all presentations
  • Submitting a summary (can have an impact on the final grade):
    • Short description of the presented topic(s)
    • Ca. 2 pages of text, i.e. excluding title (page), references, figures, tables etc.
    • No figures or tables required
    • Main structure: title page, main text, references

Final grade:

  • Based on the given presentation (see “Certificate requirements”)
  • May be influenced by the submitted summary

Topics

Nr. Presentation Topic Participant
1 Seminar metaSPAdes: a new versatile metagenomic assembler N/A
2 Pro/Seminar MinPath: A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes N/A
3 Seminar Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations Moomal A.
4 Seminar Centrifuge: rapid and sensitive classification of metagenomic sequences Maximilian G.
5 Seminar VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data Esha C.
6 Pro/Seminar MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples N/A
7 Seminar Improving Min Hash via the containment index with applications to metagenomic analysis N/A
8 Seminar Bracken: estimating species abundance in metagenomics data N/A