Members‎ > ‎Jan Michael C. Yap‎ > ‎

CS 197 - Introduction to Bioinformatics for Genomics and Transcriptomics

Announcements

 06 December 2016 - Here are the results for Problem Sets 4-7. Again, if you have questions or concerns, don't hesitate to e-mail me. Also, be reminded that 16 December 2016 is the deadline for the project paper.



28 November 2016 - Guidelines for the project paper now up. See right hand side menu beside "Project Paper". Deadline for the paper is on 16 December 2016, 11:59pm

In addition, do attend the Introduction to PGC-CFB Facilities and Services for Bioinformatics Students talk on 02 December 2016, at 3:30pm at the NIMBB Conference Room. This will be a great opportunity for your to learn all about the bioinformatics facilities of the Philippine Genome Center as well as to see what opportunities you may have for local bioinformatics research.



22 November 2016 - Problem Set 7 questionnaire and dataset now up. Deadline for the Problem Set is on 02 December 2016, 11:59pm.



08 November 2016 Problem Set 6 questionnaire and datasets now up. Deadline for the Problem Set is on 18 November 2016, 11:59pm.



03 November 2016 Problem Set 5 questionnaire now up. Deadline for the Problem Set is on 11 November 2016, 11:59pm.



28 October 2016 - Here are the pertinent documents for stage 2 of the mini-project requirement:
Problem Set 5 questionnaire release for today is put on hold. Hope you have a solemn long weekend ahead.



27 October 2016 - The release of the list and the guidelines is deferred to 28 October 2016. I had to prioritize another matter yesterday and as such, I was not able to finish processing the list. Hoping for your patience and understanding. 



26 October 2016 - NO CLASSES TOMORROW, 27 OCTOBER. Again, Problem Set 1 results are now up (see the previous announcement below). Also, I'm just awaiting the Problem Set 5 questionnaire from Dr. Fontanilla which will be sent in Friday at worst, so do stand by for that. Hope you have a safe and solemn long weekend ahead. See you next week.



25 October 2016
 - (UPDATED 4:35pm) Here are the results for Problem Sets 1 - 3:
The listing by the way, is according to increasing student number. If you have any questions regarding the results, don't hesitate to e-mail me. :)



21 October 2016 - Here are the initial guidelines for the mini-projectThis details team formation and topic assignment. Do read it ASAP as some things in the guidelines that need to be done by 26 October 2016. E-mail me if you have any questions



19 October 2016 - ICYMI, NO CLASSES TOMORROW, 20 OCTOBER. The lectures for DNA barcoding would be moved next week on 25 and 27 October. Stay safe, and see you next week.



18 October 2016
Problem Set 4 questionnaire and query sequence now up. Deadline for the Problem Set is on 28 October 2016, 11:59pm.



06 October 2016 - Problem Set 3 questionnaire and query sequence now up. Deadline for the Problem Set is on 14 October 2016, 11:59pm.



26 September 2016 - Problem Set 2 questionnaire and dataset now up. Deadline for the Problem Set is on 04 October 2016, 11:59pm.



17 September 2016 - In preparation for our discussions on Tuesday, here is a website serving as an introduction to hidden Markov Models (HMM). I will be showing this nonetheless during the lectures, but it might be a good headstart for you to have a gander at it. See you on Tuesday! :)



05 September 2016 - We meet tomorrow at 9:00am in the ERDT Room.
This is to discuss the problem set (which I will be uploading tomorrow), as well as to provide the download link for the slides of the last 3 topics of the Biological Foundations lectures, as well as provide a copy of the virtual machine to the BSCS students. In line with the latter part, may I request BSCS students to kindly install VirtualBox in your own computer, and if possible, to bring a USB drive or external HDD with at least 4 GB of free space. 




02 September 2016 - Here's how to create a shared folder that can be accessed both by your host operating system and the VirtualBox virtual machine:
  1. Create a folder (e.g. "bioinfo-shared") you wish to share inside Windows/Mac OS 
  2. Open VirtualBox
  3. Right-click the Bioinfo virtual machine, then click Settings
  4. Click on Shared Folder on the left-hand side menu
  5. Click the Adds new shared folder icon (blue folder with green plus sign)
  6. In the Folder Path field, click the down arrowhead icon, then look for the folder you wish to share
  7. Check the Auto-mount box and make sure that the Read-only box is (left) unchecked
  8. Click OK on the Add Share window, then click OK on the Settings window
  9. Run the Bioinfo virtual machine
  10. Open the Terminal and then type: sudo gpasswd -a bioinfo vboxsf (NOTE: What this does is that it makes the user "bioinfo" part of the group "vboxsf")
  11. Reboot the Bioinfo virtual machine
  12. The shared folder is accessible as a (virtual) hard drive inside Bioinfo. It can be accessed either by clicking Files and then clicking on the sf_<folder name> on the left-hand side menu or via Terminal/CLI by typing: cd /media/sf_<folder name>


29 August 2016 - BS Bio students will not have classes tomorrow, 30 August. The lecture on R will start on 01 September. Please be guided accordingly.



25 August 2016 - Sample shell scripts and Python codes are now available. Check the right hand side of the site for the download links.



17 August 2016 - Business as usual tomorrow, folks (i.e. Bio students will have their class in ERDT Room, and ComSci studes will have theirs in IB Rm 319).



15 August 2016 - Comsci students will not have class tomorrow, 16 August, for their Biological Foundations lecture. Bio students will have classes as usual. Please be guided accordingly.



10 August 2016 - Reminder: ComSci students will hold class in Room 319 of the Institute of Biology building for the Biological Foundations topics, while Bio students will still be in the ERDT Room (Room 202) for the Programming Foundations

To Bio students, you can download the VirtualBox installer here. Also, kindly bring your laptop on Thursday, and if possible, a 16GB (or greater) capacity thumb drive or external HDD.



09 August 2016 - This is the website for the CS 197 (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
    08/09/2016Overview
    08/11/2016
    08/16/2016
    Introduction to Linux CLI and Scripting (Bio)
    DNA, RNA, and the Genome (Non-Bio)
    Linux CLI:
    Site 1
    Site 2

    Scripting:
    Site 1
    Site 2
    Site 3
    Sample Scripts
    08/18/2016
    08/23/2016
    Introduction to Programming in Python (Bio)
    Central Dogma of Biology (Non-Bio)
    Python:
    Site
    Ebook
    Sample Codes
    08/25/2016
     08/30/2016 
     Introduction to Programming in Python (Bio)
    Molecular Evolution (Non-Bio)

    09/01/2016
    09/06/2016
    Introduction to Programming in R (Bio)
    Sequencing and Measuring Gene Expression (Non-Bio)
    R:
    Site 1
    Site 2
    09/06/2016
    09/23/2016
    PROBLEM SET 1For Bio
    For ComSci
    09/08/2016
    09/13/2016
    Pairwise Alignment 
    09/15/2016Progressive AlignmentSample Data
    09/20/2016
    09/27/2016
    Heuristics and Statistical Techniques for Multiple Sequence Alignment 

    09/27/2016
    10/04/2016
    PROBLEM SET 2Questionnaire
    Dataset
    09/29/2016
    10/04/2016
    BLAST
    BLAST Guides
    10/06/2016
     10/14/2016 
    PROBLEM SET 3 Questionnaire
     Query Sequence 
    10/06/2016
    10/11/2016
    Distance-Based Phylogenetic Tree Reconstruction  
    10/13/2016
     10/18/2016 
     Character-Based Phylogenetic Tree Reconstruction 
     10/18/2016 
    10/28/2016
    PROBLEM SET 4  Questionnaire
     10/25/2016 DNA Barcoding  
    11/03/2016
    11/11/2016
    PROBLEM SET 5  Questionnaire 
    11/03/2016
    11/08/2016
    Annotations  
    11/08/2016
    11/18/2016
    PROBLEM SET 6 Questionnaire
    Excel Template

    Datasets:
    FL478 down-reg
    IR29 up-reg
    IR29 down-reg
    11/08/2016
     11/10/2016 
    Statistical Techniques for Gene Expression Analysis Sample R script using limma
    11/10/2016
     11/17/2016 
    Coexpression Analysis WGCNA Tutorial 
    11/22/2016
     12/02/2016 
    PROBLEM SET 7 Questionnaire
    Dataset
     11/22/2016 
     Pipelining
     12/16/2016  PROJECT PAPERGuidelines
    • Syllabus can be downloaded here.
    • Copy of the 2012 Code of Student Conduct can be downloaded here.