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CS 175 - Introduction to Bioinformatics for Genomics and Transcriptomics

Announcements

 15 October 2017 - Malacanang has suspended classes for tomorrow, 16 October 2017, in line with the planned nationwide transport strike. The lecture on DNA barcoding and the release of Problem Set 3 is thus moved to 23 October 2017. Please be guided accordingly.



10 October 2017
  • Again, kindly e-mail me your proposed topic for the mini-project requirement by 20 October, Friday. The guidelines for determining a topic are:
    • The proposed topic should involve the use of at least one of the analyses (to be) discussed in class.
    • The data to be used should be readily available.
  • The DNA barcoding lecture on Monday, 16 October, will be conducted in Room 318 of the Institute of Biology. The session will be handled by Dr. Ian Fontanilla (or his representative).
  • There are changes to the schedule of activities starting 23 October 2017. The main change of interest is that the project presentations are now scheduled on 04 December 2017 instead of 11 December 2017. Please be guided accordingly.





29 September 2017 - Some changes for the next couple of activities:
  • The lecture on DNA Barcoding will be moved to 16 October 2017.
  • Lectures on Phylogenetic Tree Reconstruction will be held on 02 and 09 October 2017. In line with this, the lecture for this coming Monday (and the next) will be held in the ERDT Room.
  • Problem Set 2 will still be released on 02 October 2017. The questions will cover Sequence Alignment and Sequence Database Searching.
Please be guided accordingly. See you this coming Monday in the ERDT Room. :)



25 September 2017 
  • Problem Set 1 Questionnaire for NON-Bio Students now up. See right hand side of the page. Deadline for submission is 09 October 2017, 11:59pm.
  • A change in the arrangements for the lecture next week, 02 October 2017, 8:00am-11:00am, on DNA Barcoding: the lecture will be held in Room 318 of the Institute of Biology building. Please be guided accordingly.



07 September 2017 - To NON-Bio Students: Here is the softcopy for your homework in Central Dogma as assigned by Dr. Fontanilla. Submit your answers on 11 September 2017, during the 2nd Biological Foundations lecture.



31 August 2017 - Lectures for non-bio students on biological foundations will be held in Room 318 of the Institute of Biology Building at 8:00am sharp. Dr. Ian Fontanilla will be presiding the class there.

For bio students, the lecture on programming foundations will still be in the ERDT Room. Please be guided accordingly.



07 August 2017 - This is the website for the CS 175 (Introduction to Bioinformatics for Genomics and Transcriptomics) class facilitated by Jan Michael Yap. Announcements and files pertinent to the class will be posted here.

    DatesTopic/ActivityMaterials
    08/07/2017Overview
    09/04/2017

    Introduction to Linux CLI and Scripting (Bio)
    DNA, RNA, and the Genome (Non-Bio)
    Central Dogma of Biology (Non-Bio)
    Linux CLI:
    Site 1
    Site 2

    Scripting:
    Site 1
    Site 2
    Site 3
    Sample Scripts
    09/11/2017

    Introduction to Programming in R (Bio)
    Molecular Evolution (Non-Bio)
    Sequencing and Measuring Gene Expression (Non-Bio)
    R:
    Ebook
    Site 1
    Site 2
    Bio:
    09/11/2017
    09/25/2017

    Non-Bio:
    09/25/2017
    10/09/2017
    PROBLEM SET 1Questionnaires:
    Bio Students

    Non-Bio Students
    09/18/2017

    Sequence Alignment Sample Data
    09/25/2017Sequence Database Searching: BLASTBLAST Guides
    10/02/2017
    10/16/2017
    PROBLEM SET 2Questionnaire
    Dataset
    10/02/2017Distance-Based Phylogenetic Tree Reconstruction  
    10/09/2017 Character-Based Phylogenetic Tree Reconstruction 
     10/23/2017 DNA Barcoding  
     10/23/2017 
    11/06/2017
    PROBLEM SET 3 Questionnaire
    10/30/2017
    Sequence Assembly  
    11/06/2017Annotations  
    11/06/2017
    11/20/2017
    PROBLEM SET 4 
     11/13/2017 Differential Gene Expression Analysis Sample R script using limma
     11/20/2017 Coexpression Analysis WGCNA Tutorial 
    11/20/2017
     12/04/2017 
    PROBLEM SET 5 
     11/20/2017 
     Pipelining
     12/04/2017  PROJECT PRESENTATIONS
    • Syllabus can be downloaded here.
    • Copy of the 2012 Code of Student Conduct can be downloaded here.