Overview

Teaching: 120 min
Exercises: 30 min

Questions

• many for sure

Objectives

• does this work?

Introduction to the module

In this module you will learn how to analyse bacteriophage sequences with computational approaches. The theoretical part will be covered in the mornings and include a series of questions. Document the questions and answers in a lab book. These will also be considered in your final evaluation. The evaluation will be composed of:

• Performance in the dry lab, lab journal (60%)
• Presentation of the final project (40%)

To write a good lab book be attentive to:

• Write in the lab book every day, documenting your tasks;
• Structure it in cronological order, so that each section corresponds to a different day.

To keep up with a good organization, in your practical experiments, use a logical order for naming your folders. For instance: 0_download, 1_quality_evaluation, 2_assembly. Always name them in your lab book, so that you can find your files while reading the lab book in the future.

Lab Book

Documenting your work is crucial in Computational Biology/Bioinformatics. This way you can make sure your work is reproducible, you can transfer text to other documents, such as reports or papers and you can send it to collegues, so that they can access your work.

You are required to write a Lab Book in markdown for this module, which will count as part of your evaluation. If you want, you can start a GITHub repository for the course and write your lab book there. References:

• https://commonmark.org/help/
• https://www.markdownguide.org/basic-syntax/

You should divide the lab book into sections (days) and add subsections for different tasks. Each subsection should have a meaningful title, e. g. “Documenting module Viromics-Bioinformatics”, “Downloading phage sequences”, “Evaluating sequence quality”. Any relevant information should be included, such as websites used in searches, folders where you can find files, tool names and versions and bibliographic references. An example can be seen in the link: https://github.com/waltercostamb/course_viral-microbiology/blob/main/tutorials/lab-book.pdf. Start your lab book today and write on it whenever necessary during the module. In the last day, send a copy to your advisor.

The paper “Ten Simple Rules for a Computational Biologist’s Laboratory Notebook”, by Santiago Schnell of 2015 offers interesting insights: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004385 Most relevant are rules 4, 6 and 10. Keeping a hard copy of your lab book is not necessary, however make sure you have it backed up.

Supplementary reference

• “Ten Simple Rules for Reproducible Computational Research”, by Geir Sandve and collaborators, 2013: https://app.dimensions.ai/details/publication/pub.1022987921

Access to draco

Draco is a high-performance cluster created and maintained by the Universitätsrechenzentrum. It is available for members of Thuringian Universities. To log in, you can use ssh:

ssh <fsuid>@login1.draco.uni-jena.de

Key Points