SCP7079337 - BIOLOGICAL DATA 2022-2023

Topic outline

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  BIOLOGICAL DATA - Damiano Piovesan & Silvio Tosatto

  Welcome to the E-learning site of the course! In these pages you will find all up-to-date information regarding the course. Please follow the links below for information regarding program, slides and course materials.

  NB: Hybrid teaching mode will be guaranteed in the first semester to international students waiting for a student visa. Lectures will be streamed, recorded and made available for offline use. The recorded lectures will be uploaded (see below) and remain available for at least three weeks from the day of recording.

  
  

  Midterm 2
  Link available below. Submission deadline 16 January 2023 - 2:30 pm - New deadline 20 January 2023 - 2:30 pm
  
  Journal club - 13/16/20 January 2023
  Please, select your favourite date from the students sheet
  
  Exam dates - 8/23 February 2023
  Students who submit the final project within the winter session (at least 10 days before the exam date), will be evaluated offline, i.e. without the need of an oral exam.
  
  
  

  • Educational offer page URL
  • Zoom lectures Zoom meeting
  • Evaluation criteria File 134.3KB documento PDF
  • Students (Google Sheet) URL
  • Midterm 2 document URL
  • Final project specifications URL
  • Mid-course survey on the effectiveness and organisation of in-person teaching Feedback
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  Slides

  The lecture slides are made available in PDF format below (as soon as they are ready).

  • L1 - Intro File 4.2MB documento PDF
  • L2 - Sequences File 2.7MB documento PDF
  • L3 - Sequences 2 File 3.3MB documento PDF
  • L4 - Sequence databases File 3.9MB documento PDF
  • L5 - Database search File 3.4MB documento PDF
  • L6 - Perspectives in Biological Data File 13.6MB documento PDF
  • L7 - Non-globular proteins File 3.9MB documento PDF
  • L8 - Disordered proteins File 4.2MB documento PDF
  • L9 - Linear motifs File 1.8MB documento PDF
  • L10 - Knowledge representation File 1.6MB documento PDF
  • L11 - Protein function File 2MB documento PDF
  • L12 - Function prediction File 7.6MB documento PDF
  • L13 - Literature File 3MB documento PDF
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  Lecture recordings

  Lecture recordings will be posted here and remain visible for up to three weeks after the lecture date.
  NB: These are large files, requiring a good Internet connection.
  NB: Lecture recordings will be accessible only by students waiting their visa that cannot attend lectures in person. While recordings of the practical sessions will be made available to all students. 
  

  • Lecture 2022/10/03 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/10/07 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/10/10 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/10/14 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Practical 2022/10/17 Kaltura Video Presentation
  • Lecture 2022/10/21 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/10/24 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/10/28 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/11/04 Kaltura Video Presentation
  • Practical 2022/11/07 Kaltura Video Presentation
  • Practical 2022/11/11 Kaltura Video Presentation
  • Lecture 2022/11/14 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/11/18 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Lecture 2022/11/21 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Practical 2022/11/25 Kaltura Video Presentation
  • Practical 2022/11/28 Kaltura Video Presentation
  • Lecture 2022/12/02 Kaltura Video Presentation

    Restricted Not available unless: You belong to VISA
  • Practical 2022/12/05 Kaltura Video Presentation
  • Practical 2022/12/16 Kaltura Video Presentation
  • Practical 2022/12/19 Kaltura Video Presentation
  • Lecture 2023/01/09 Kaltura Video Resource
  • Journal Club 2023/01/13 Kaltura Video Resource
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  JOURNAL CLUB

  Each student is asked to choose an article to present as a short (10') presentation followed by questions (5').
  
  Below are the links to three relevant journals from which papers can be chosen. Note that the journals are in decreasing order of relevance. Nature Methods is the most prestigious but only partially devoted to bioinformatics. It does recently feature several papers using advanced machine learning though. Bioinformatics is the top journal in the field and provides a good choice of methodological papers. BMC Bioinformatics papers tend to be of lesser impact and are perhaps not so thorough. Alternatively, we will provide a list of recent papers of interest.
  
  During the regular lecturing hours. We will be able to have 4-5 presentations per day. The dates have been tentatively assigned to students based on their order of signing up. Changes are possible, but please arrange them between you and record them on the Google Sheet.
  
  The student presentations should be uploaded to the folder linked below once ready.
  
  
  

  • Proposed articles URL
  • Folder for uploading student presentations URL
  • Nature Methods journal URL
  • Bioinformatics journal URL
  • BMC Bioinformatics URL
  • CASP15 articles (recommended by John Jumper) URL
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  Practicals

  Information regarding the practicals will be posted here.

  • Data (Google Drive folder) URL
  • Genome assembly (CoLab notebook) URL
  • Protein family (CoLab notebook) URL
  • Slims search (CoLab notebook) URL
  • Slims discovery (CoLab notebook) URL
  • Function (CoLab notebook) URL
  • Function exercise (Python script) URL
  • API (CoLab notebook) URL
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  References & Useful Material

  Below is a collection of useful links and references for further reading. Wikipedia pages are a way point to understand the broader topics treated in the course. Some links are provided as starting points.
  The examples shown in the practical with Jalview are also listed below. These include a multiple sequence alignment and protein structure for GPx. The Jalview software desktop version can be downloaded from www.jalview.org.

  • BOOK - Biological Sequence Analysis Probabilistic Models of Proteins and Nucleic Acids File 4.3MB documento PDF
  • Wikipedia, Bioinformatics URL
  • Wikipedia MolecularBiologyPortal URL
  • Wikipedia, DNA URL
  • Wikipedia, Proteins URL
  • Wikipedia Evolution URL
  • Sample GPx sequence alignment File 216.4KB File di testo
  • Sample GPx protein structure File 307.1KB