Seminar 2 - motif discovery (Deadline: 17.02.2025 23:59)
The paper reading guidelines can be found here
Submit your three paper questions below:
Seminar 3 - splicing models (Deadline: 24.02.2025 23:59)
The paper reading guidelines can be found here
Submit your three (in total!) paper questions below:
Seminar 5 - interpreting ML models (Deadline: 10.03.2025 23:59)
The paper reading guidelines can be found here
Submit your three (in total!) book questions below:
Homework 1 (Deadline: 29.03.2025 23:59)
1. Download the code and data archive from here
2. Upload .zip archive to HPC via scp HW1.zip [user_name]@rocket.hpc.ut.ee:/gpfs/helios/home/[user_name]/
3. Log into HPC ssh [user_name]@rocket.hpc.ut.ee
4. Unzip the archive unzip HW1.zip
5. Read further instructions cat HW1/setup.md
Submit the completed jupyter notebook below:
Seminar 6 - chromatin accessibility part 1 (Deadline: 17.03.2025 23:59)
The paper reading guidelines can be found here
Submit your three paper questions below:
Seminar 7 - chromatin accessibility part 2 (Deadline: 24.03.2025 23:59)
The paper reading guidelines can be found here
Submit your three paper questions below:
Seminar 8 - gene expression part 1(Deadline: 31.03.2025 23:59)
The paper reading guidelines can be found here
Submit your three (in total!) paper questions below:
Seminar 9 - gene expression part 2 (Deadline: 7.04.2025 23:59)
The paper reading guidelines can be found here
Submit your three (in total!) paper questions below:
Seminar 10 - gene expression part 3 (Deadline: 14.04.2025 23:59)
Fill up the models (Basenji2, Enformer, Borzoi) comparison sheet
Submit the photo (if you did it by hand) or text file here:
Seminar 11 - limitations part 1 (Deadline: 28.04.2025 23:59)
The paper reading guidelines can be found here
Submit your three (in total!) paper questions below:
Homework 2 (Deadline: 10.05.2025 23:59)
1. Download the code and data archive from here
2. Upload .zip archive to HPC via scp HW2.zip [user_name]@rocket.hpc.ut.ee:/gpfs/helios/home/[user_name]/
3. Log into HPC ssh [user_name]@rocket.hpc.ut.ee
4. Unzip the archive unzip HW2.zip
5. Read further instructions cat HW2/setup.md
Submit the completed jupyter notebook below:
Seminar 12 - Genomic foundational models part 1(Deadline: 5.05.2025 23:59)
The paper reading guidelines can be found here
Submit your three paper questions below:
Seminar 13 - Genomic foundational models part 2(Deadline: 12.05.2025 23:59)
The paper reading guidelines can be found here
Submit your three paper questions below:
Seminar 14 - Summary (Deadline: 19.05.2025 23:59)
This is the final seminar, so this time please answer a couple of questions. They can be found here
Submit your answers below: