=====Software tools in Bioinformatics=====
Olga Zolotareva and Konstantinos Tzanakis\\
Seminar: Monday 10:00-12:00\\
Classroom: U10-146
====Content====
In this seminar, students will choose, study and present one of the recent bioinformatic software tools published in peer-reviewed journals. The students are encouraged to suggest topics and tools of their interest or choose one of the following topics (shortlists of tools and a review article for topics will be provided):
* Biclustering
* Read Alignment
* SNP Calling
* Gene Expression Quantification
* Gene Prioritization
* Noise filtering and Baseline Correction
* Peak detection
* Peak alignment
* Metabolite identification
* Metabolomics data pre-treatment (normalization, scaling, transformation)
| **Topic** | **Review** | **Recommended tools** |
| - Noise filtering and Baseline Correction \\ - Peak detection \\ - Metabolite identification\\ - Metabolomics data pre-treatment\\ (normalization, scaling, transformation) | [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358739/| Piasecka et al., 2019]] \\ [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5550549/| Spicer et al., 2017]] \\ [[https://journals.usamvcluj.ro/index.php/zootehnie/article/view/11536/9357| Lazar et al., 2015]] | OpenMs, XCMS, Workflow4Metabolomics, MeltDB, MetAlign |
| Peak alignment | [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-375| Lange et al., 2008]] | XCMS, OpenMs, MZmine |
| De novo transcriptome assembly | [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511074/| Hölzer & Marz, 2019]] | Trinity, SPAdes |
| Read Mapping | [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425171/| Canzar & Salzberg, 2015]] \\ [[https://www.annualreviews.org/doi/full/10.1146/annurev-genom-090413-025358| Reinert et al., 2015]] | bwa, bowtie2, HISAT, STAR, GMAP |
| Single Nucleotide Variant Calling | [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852328/| Xu 2018]] | VarScan2, Strelka, MuTect, DeepVariant |
| Expression Quantification and\\ differential expression analysis | [[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005457| Lowe et al., 2017]] \\ [[https://academic.oup.com/bfg/article/14/2/130/257370/| Finotello & Di Camillo, 2016]] | kallisto, limma-voom, DESeq2, EdgeR |
| Biclustering | [[https://www.ncbi.nlm.nih.gov/pubmed/26160444| Pontes et al., 2015]] | QUBIC, DeBi, COALESCE, FABIA |
| Gene prioritization | [[https://www.ncbi.nlm.nih.gov/pubmed/31494632| Zolotareva & Kleine 2019]] | Endeavour, PhenoRank, pBrit |
| | | |
The participants will give oral presentations (20-45 min’s, optimally about 25 min's) and prepare short summaries (5 to 10 pages) based on original research papers. In their reports, students must (i) briefly explain the problem solved by a selected tool (ii) describe the algorithm(s) implemented in this tool (iii) explain the choice of the tool among its analogs. At the end of the course, the students will peer-review their essays and revise them based on the received feedback.
====Goals of the seminar====
In this seminar students will develop skills necessary for:
* independent reading and understanding of scientific texts (in English)
* composition of a short written report (as a practice for the bachelor thesis)
* oral presentation
* peer-reviewing
====Plan====
| **Title** | **Date** |
| {{ :teaching:2019winter:software_tools_in_bioinformatics1.pdf |Preliminaries, topic selection}} (Kostas) | 07.10.2019 |
| {{ :teaching:2019winter:software_tools_in_bioinformatics2.pdf |Example presentation}} (Olga) | 14.10.2019 |
| {{ :teaching:2019winter:software_tools_in_bioinformatics3.pdf |Best Practices for Scientific Writing}} (Kostas) | 21.10.2019 |
| //(preparing presentations)// | 28.10.2019 |
| Jonas Waas - De novo transcriptome assembly, SPAdes | 04.11.2019 |
| Aya Bezine - Single Nucleotide Variant Calling, VarScan2 | 11.11.2019 |
| Fabian Kolesch - Biclustering, QUBIC | 18.11.2019 |
| //(preparing reports)// | 25.11.2019 |
| //(preparing reports)// | 02.12.2019 |
| Lukas Schulte - Expression quantification and DE analysis,DeSeq2 | 16.12.2019 |
| **Submitting reports (1st version)** | 20.12.2019 |
| Submitting reviews of essays | 13.01.2020 |
| Submitting revised essays | 20.01.2020 |