Type:
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Lecture (4 SWS) + Exercise (2 SWS)
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Ects:
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8.0
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Lecturer
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Burkhard Rost (lecture)
tba (exercise)
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Rotation:
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Tuesday, 12:30 - 14:00
Thursday, 12:30 - 14:00
Thursday, (exercise), 14:00 - 15:00
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Place:
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Lecture: Virtual (Potential for in-person Q&A)
Exercise: Virtual
Exam: tba
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Language:
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English
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Announcements:
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The latest news are always on top!
First lecture on Thursday in the second lecture week!
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Exam
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Communication
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For this course, we will use Moodle. You will be automatically registered.
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Content
This lecture continues the 'Protein Prediction I' lecture. The attendance of this lecture however is not a mandatory requirement for 'Protein Prediction II'. Topics will include (but not be limited to):
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Predicting protein function using sequence: sequence alignments, multiple sequence alignments, motifs, domain assignment, annotation transfer by homology, ab initio predictions.
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Predicting protein function using structure: structural alignments, structural motifs, annotation transfer via structure similarity.
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From structure prediction to function prediction: comparative modeling; prediction of: secondary structure, hydrophilicity profiles, solvent accessibility, transmembrane segments, disordered regions, contact maps, functional residues; template free modeling.
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Machine learning.
Slides
Exercise
Slides
To successfully complete the exercise each group needs to fulfill the following requirements:
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Give a presentation regarding their project that focuses either on the biological background, current state-of-the-art methods, or the provided data set.
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Give a final presentation about their approach; e.g. architecture and performance.
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Actively participate in the exercise. This primarily means attending all students' presentations and participating in the corresponding Q&A sessions.
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Submit a working solution at the end of the semester. It should be able to make informed predictions based on new data and perform better than a random or very naive solution.
Presentations in general:
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Attendance is mandatory for all students (not just the groups presenting) whenever there is a presentation by students.
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For sessions without students' presentations, attendance is not mandatory.
Working in a group:
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The workload within each group should be evenly split.
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Not every student has to speak during their group's presentation (e.g. some could work on the presentations, the rest on the programming task).
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If students in your group refuse to "carry their weight" or you are the only one doing any work, feel free to contact us (better early than late).