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CS 315 - Algorithms in Bioinformatics


 12 December 2016 - Here are the results for Problem Sets 4-6.  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.

Finally, Problem Set 6 Questionnaire now up. You will also need to download the corresponding .csv file containing the dataset for the problem set (Click on the "Dataset" link below "Questionnaire"). Deadline is on 09 December 2016, 11:59pm. Please be guided accordingly.

15 November 2016 - Problem Set 5 Questionnaire now up. You will also need to download the corresponding .csv file containing the dataset for the problem set (Click on the "Dataset" link below "Questionnaire"). Deadline is on 25 November 2016, 11:59pm. Please be guided accordingly. 

28 October 2016 - Here are the pertinent documents for stage 2 of the project requirement:
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 -  Problem Set 4 Questionnaire now up. The questionnaire contains the commands we used in our hands-on SNP calling activity yesterday. Deadline is on 12 November 2016, 11:59pm. Please be guided accordingly.

25 October 2016 - Here are the results of Problem Sets 1-3. Feel free to e-mail me if you have questions regarding the results.

21 October 2016 - Here are the initial guidelines for the project. This 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

10 October 2016 - NO CLASSES TOMORROW, 11 OCTOBER 2016. Use the time to do your problem set. We'll start the lecture on SNP Calling and Analysis next week Tuesday, 18 October, followed by hands-on exercises on 25 October. Please be guided accordingly.

04 October 2016
 - Problem Set 3 Questionnaire now up. You will also need to download the corresponding Excel file containing the information needed for you to answer the problem set. Deadline is on 21 October 2016, 11:59pm. Please be guided accordingly. 

23 September 2016 - Problem Set 2 Questionnaire now up. You will also need to download the corresponding .zip file containing the dataset for the problem set (Click on the "Dataset" link below "Questionnaire"). Deadline is on 30 September 2016, 11:59pm. Please be guided accordingly. 

17 September 2016 - The release of Problem Set 2 is moved to 23 September, Friday, at around 12:00nn. Also, we won't have any classes on Tuesday, 20 September. The lectures on genome assembly will start instead on 27 September. Use the extra time to finish your Problem Set 1. Please be guided accordingly.

08 September 2016
 - To those who are running the Bioinfo.ova virtual machine (or those who have their own Ubuntu Linux installation), kindly do the following:

  1. Open Terminal
  2. Type the following
    • sudo apt-get install clustalw
    • sudo apt-get install hmmer
    • sudo apt-get install tree-puzzle
    • sudo apt-get install tree-ppuzzle
           If you are prompted for a password, the password is "bioinfo".

The commands will install alignment and tree reconstruction tools we'll be trying out on Tuesday.

As for the slides, I am still editing them, but I'll have them ready Saturday (10 September) morning at the latest.

05 September 2016 - Until further notice, the new class venue is in Room 317 (Algorithms and Complexity Laboratory) of the UPAECH Building. Also, the deadline for Problem Set 1 is extended to 23 September 2016, Friday.  See you tomorrow! :)

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>

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

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 on Tuesdays and Thursdays, 8:30am-10:00am in Room 319 of the Institute of Biology building for the Biological Foundations topics, while Bio students will still be in the Room 310 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 315 (Algorithms in Bioinformatics) class facilitated by Jan Michael Yap. This incarnation of the course will be focused on analyses for genomic and transcriptomic bioinformatics and the methods that are used for purposes therein. Announcements and files pertinent to the class will be posted here.

DatesTopic/Activity Materials
08/16/2016Introduction to Linux CLI and Scripting (Bio)
DNA, RNA, and the Genome (Non-Bio)
Linux CLI:
Site 1
Site 2

Site 1
Site 2
Site 3
Sample Scripts
Introduction to Programming in Python (Bio)
Central Dogma of Biology and Molecular Evolution (Non-Bio)
Sample Codes
 Introduction to Programming in R (Bio)
Sequencing and Measuring Gene Expression (Non-Bio)
Site 1
Site 2
PROBLEM SET 1For Bio Students
For ComSci Students
09/06/2016Multiple Sequence AlignmentSample Data
09/13/2016Character-Based Phylogenetic Tree Reconstruction 
PROBLEM SET 2Questionnaire
09/27/2016Reference-Based Assembly

De Novo Assembly
10/04/2016Quality Control and Annotation

PROBLEM SET 3 Questionnaire
Results Table
 10/18/2016 SNP Calling
10/25/2016SNP Analysis
 PROBLEM SET 4Questionnaire 
 11/08/2016  Single and Multiple QTL Models for QTL Mapping 
 11/15/2016  Multiple Trait Mapping 
 PROBLEM SET 5Questionnaire
Chip-Based and Next Generation Transcriptomic Data Analysis  Differential Analysis Sample Codes and Tutorials:

Gene Coexpression Tutorials:
11/22/2016 Pathway Inference from Transcriptomic DataR/predictionet Tutorial 
PROBLEM SET 6Questionnaire
12/06/2016PROJECT PAPERGuidelines
  • Syllabus can be downloaded here.
  • Copy of the 2012 Code of Student Conduct can be downloaded here.