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CS 175 - Introduction to Bioinformatics for Genomics and Transcriptomics

Announcements


 22 November 2018 - Here are the Problem Set 3 results, and the corresponding class standing after factoring those in. We will have one last round of consultations on Monday, 26 November 2018, following the same schedule as done last 19 November 2018 (see the announcement below for the schedule). I will expect all groups and their group members to be present.

See you by then!



18 November 2018 - Consultations for tomorrow will start at 8:15am, and will (still) be held in Classroom 2. The schedule of consultations is as follows:

8:15am - 8:30am  Group 1
8:30am - 8:45am  Group 2
8:45am - 9:00am  Group 3
9:00am - 9:15am  Group 4
9:15am - 9:30am  Group 5
9:30am - 9:45am  Group 6

See you all tomorrow!



05 November 2018 - As mentioned during class, here is the groupings and assigned topics for the mini-project requirement for the course. Again, a reminder to get in touch with your groupmates, and to choose and nominate datasets you wish to use for the assigned topics, and e-mail them to me by Monday, 12 November, next week. 

In preparation for our hands-on tutorial on coexpression analysis next week, kindly download the required packages for coexpression network analysis by typing the following 3 commands in your RStudio console:
  • install.packages(c("matrixStats", "Hmisc", "splines", "foreach", "doParallel", "fastcluster", "dynamicTreeCut", "survival"))  
  • source("http://bioconductor.org/biocLite.R") 
  • biocLite(c("GO.db", "preprocessCore", "impute", "WGCNA")) 
Make sure you are connected to the Internet prior to executing the commands. Also, download and unzip the dataset(s) for the demo from this link

See you next week!


28 October 2018 - Here are the results for Problem Sets 1 and 2:
Meanwhile, here is the class standing as of 28 October 2018. If you have questions in any of the problem set scores or in your class standing, feel free to e-mail me.

See you all tomorrow!



20 October 2018 - We will start our session on Monday, 22 October 2018, at 7:30am, for the sequence assembly hands-on. In preparation for the session, download both frag_1.fastq.gz and frag_2.fastq.gz from this site into your computer. In addition, we will need two (2) Docker images for the demo: pgcbioinfo/spades and staphb/quast-v5.0.0. So to get them, execute the following commands in your command line:
  • docker pull pgcbioinfo/spades
  • docker pull staphb/quast-v5.0.0
See you on Monday!



08 October 2018 - Problem Set 2 questionnaire is now up. I will be uploading the slides from the DNA Barcoding topic once I receive them from Dr. Fontanilla.

UPDATE (1:05pm): Slides for DNA Barcoding now up.


01 October 2018 - The lecture for DNA Barcoding by Dr. Ian Fontanilla next Monday will be in Room 318, 3/F Institute of Biology Building. 

Also, here is the link to the manual of RaxML. Also, if you want to download and install the tool directly to your PC without Docker, go here. (Note that Linux and macOS users will have to compile and install the tool from source).

UPDATE (1:10pm): Here is the link to FigTree for visualizing the Newick tree formatted file output of RaxML.



25 September 2018 - Sorry this came in late: instead of downloading Docker to be able to use MAFFT, you may download an installer of the tool and install it directly into your computer. Here is the link to the download site.



15 September 2018 - Again, we will start our session on Monday, 17 September 2018, at 7:30am. See you by then!



08 September 2018 We will start our session on Monday, 10 September 2018, at 7:30am. We will cover topics on sequence alignment and sequence database searching by then. Also, kindly bring laptops, if possible, as we will also have a hands-on tutorial/demo after class. Also, if you can, kindly download and install Docker Community Edition in your laptop:




30 August 2018 - We will start our session on Monday, 03 September 2018, at 7:45am. See you by then!

UPDATE (02 September 2018): Kindly bring laptops by then as we will have some tutorial/demo during class.



12 August 2018 - From the Office of the Chancellor: "UP Diliman Meteorology forecasts more heavy rains today and tomorrow. As a precautionary measure, work and classes are suspended tomorrow, Aug. 13, 2018."

As such, we will have our first lecture class on 03 September 2018 and the schedule of lectures for the semester will be adjusted accordingly. 

Stay safe, and please be guided accordingly.



06 August 2018 - 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
    08/06/2018

    OverviewLinux CLI:
    Site 1
    Site 2

    Scripting:
    Site 1
    Site 2
    Site 3
    Sample Scripts

    R:
    Ebook
    Site 1
    Site 2


    Diagnostics:
    Bio Students

    Non-Bio Students
    09/10/2018Sequence Alignment Slides
    09/17/2018Sequence Database Searching: BLASTSlides
    09/17/2018
    10/01/2018
    PROBLEM SET 1Questionnaire
    Dataset
    09/24/2018Distance-Based Phylogenetic Tree Reconstruction  Slides
    09/24/2018
    10/01/2018
     Character-Based Phylogenetic Tree Reconstruction(Same as above) 
     10/01/2018 Maximum Likelihood Phylogenetic Tree Reconstruction (Same as above) 
     10/08/2018 DNA Barcoding  Slides
     10/08/2018 
    10/22/2018
    PROBLEM SET 2 Questionnaire
    10/15/2018
    Reference Guided Sequence Assembly  Slides
    10/15/2018
     10/22/2018 
    De Novo Sequence Assembly  (Same as above)
    10/22/2018
    11/05/2018
    PROBLEM SET 3 Questionnaire
    Dataset
    10/29/2018 
    11/05/2018 
    Differential Gene Expression Analysis Slides
    Datasets

    Microarray:

    Part 1
    Part 2

    RNA-seq:
    Link
    11/12/2018 Coexpression Analysis (Slides, same as above)

    WGCNA Tutorial 
    11/12/2018
    11/26/2018
    PROBLEM SET 4Questionnaire
    Dataset
    11/19/2018
     11/26/2018 
    CONSULTATIONS 
     12/03/2018  PROJECT PRESENTATIONSGuidelines
    • Syllabus can be downloaded here.
    • Copy of the 2012 Code of Student Conduct can be downloaded here.