APPLS

Applied Python Programming for Life Scientists

This course is intended for life scientists without any prior knowledge about bioinformatics/programming. The objective is to provide a sufficient amount of knowledge about Python to solve small problems by writing simple scripts. Feel free to re-use our slides and please report any mistakes that you discover. We are planning to provide an updated version in the future.

The last part contains examples from my published research:

Pucker, B., Holtgräwe, D., Rosleff Sörensen, T., Stracke, R., Viehöver, P., and Weisshaar, B. (2016). A de novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PloS‑ONE 11:e0164321. doi:10.1371/journal.pone.0164321.

Pucker, B., Holtgräwe, D., & Weisshaar, B. (2017). Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes, 10, 667. doi:10.1186/s13104-017-2985-y.

Haak, M., Vinke, S., Keller, W., Droste, J., Rückert, C., Kalinowski, J., & Pucker, B. (2018). High Quality de Novo Transcriptome Assembly of Croton tiglium. Frontiers in Molecular Biosciences, 5. doi:10.3389/fmolb.2018.00062.

Pucker, B. and Brockington, S.F. (2018). Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5360-z.

Pucker, B., Holtgraewe, D., Stadermann, K. B., Frey, K., Huettel, B., Reinhardt, R., & Weisshaar, B. (2019). A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set. PLOS ONE: e0216233. doi: 10.1371/journal.pone.0216233.

Additional courses are listed here:

https://www.cebitec.uni-bielefeld.de/~bpucker#teaching

and here:

https://www.cebitec.uni-bielefeld.de/~hschilbe