The Summer School on Human Health and Environment by the Baltic Sea in Seili is organised by the Nordic network BalticSeaBioMed, comprised of the Universities of Eastern Finland, Southern Denmark, Turku, Vilnius, Åbo Akademi University and Karolinska Institutet.
BalticSeaBioMed builds on the highly successful work of our founding network, NordBioMedNet, and makes an important innovative leap to bring state-of-the-art biomedical methodology into global health research. Here, we apply funding for a new Master's level intensive course to teach with new digi-pedagogical tools and focus on a new theme: the environmental impact of human behaviour. As an example and an educational “case study”, we will examine the effect of human use of pharmaceuticals and certain other harmful factors or changes on the Baltic Sea, and study them with modern biomedical omics technologies and large-scale data analysis using advanced computational methods. Our goal is to train the students in the skills and competencies required to solve complex problems of global health by using the challenges closer to us; the populations and well-being around the Baltic Sea as an example.
For the official program, see https://ki.instructure.com/courses/24319
Students will apply their previous knowledge to identify relevant and realistic topics/problems in the field of Biomedicine.
Students will work in groups and each group is guided by a junior mentor.
Based on the course material and guidance during the summer school, each group will develop and present a virtual preclinical research project to solve the selected problems.
The final report/assignment will be prepared individually after the summer school.
Please get familiar with the following material and platforms:
The Ethics of Biomedicine
This online course will prepare you for the Ethics session in the summer school:
https://ki.eu-west.catalog.canvaslms.com/browse/oer/courses/the-ethichs-of-biomedicine-2023
Group work
Here you will learn about getting most from the group work: https://rise.articulate.com/share/YOSU8I4BZjkJZK4_KUlIjcvBVzBMvs1x
Please, download and fill in the Group Contract with your group members.
Python, R and friends:
A short introduction to programming and how to prepare yourself and
your computer for the computational exercises at the Summer School https://rise.articulate.com/share/Y-vw0ZckATqKqyh4u44c8p9YN-UEtr8r
Protein interaction
Please take this online course: https://www.ebi.ac.uk/training/online/courses/protein-interactions-and-their-importance/
Introduction to biomacromolecular structure
Please take this online course: https://www.ebi.ac.uk/training/online/courses/biomacromolecular-structures/
Introduction to AlphaFold2 for predicting 3D structures for proteinse
Please take the introductory part of this online course: https://www.ebi.ac.uk/training/online/courses/alphafold/an-introductory-guide-to-its-strengths-and-limitations/. The course is comprehensive but only the introduction is compulsory and, thereafter, please Test your knowledge.
Install Cytoscape and PyMOL
Cytoscape: Please make sure that you have the latest version of Cytoscape installed. Then start Cytoscape and update the current apps if necessary by checking the App Updates icon in the right-most corner of the manubar.
The exercises require you to have certain Cytoscape apps installed. Go to the Cytoscape App Store in your web browser and search for stringApp, select the app and press the Install button to install it. Similarly, make sure you have the yFiles Layout Algorithms and clusterMaker2 apps installed before switching back to Cytoscape.
If you are not already familiar with the STRING database, we highly recommend that you go through the short STRING exercises to learn about the underlying data before working with it in these exercises.
Please also get familiar with the R programming language by attending the Introduction in R on DataCamp.
We expect you to have a working Jupyter environment with Python and R kernels.
PyMOL:
PyMOL is a molecular visualization program for studying and preparing figures of macromolecular 3D structures.
Please download and install PyMOL2.6 on your laptop: Instructions how to download and install PyMOl. You will get the license file for the program later during the course.