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BIO 397- Advanced Bioinformatics

Announcements

 14 May 2019 - Here are the computed gradesThank you very much for a fun and productive semester. I truly hope you gained something useful from the class, and I wish you all the best on your future endeavors! :)



02 May 2019 - Here are the results for Problem Set 4 and Problem Set 5. The Project Presentations on 08 May 2019 will start at 3:00pm and will be held in the PGC Core Facility for Bioinformatics Conference Room, 2nd Floor, PGC Building, A. Maria Regidor St. The schedule of presentations are as follows:

3:00pm - 3:25pm   Malajacan, Membreve, Nacario (Phylogenetics)
3:25pm - 3:50pm   Bandong (Sequence Assembly)
3:50pm - 4:15pm   Balaga, Ferrer (Differential Expression)
4:15pm - 4:40pm   Dela Peña, Joson (Gene Coexpression)

Please be guided accordingly. See you by then!






01 April 2019 Session on 03 April 2019, Wednesday, will start at 2:30pmIn preparation for the hands-on activities for the last 2 sessions on Transcriptomic Data Analysis, kindly download the entire Transcriptomics Exercise Kit folder via the link on the right hand side of the site. Once downloaded, make sure you are (still) connected to the Internet, fire up RStudio, then set your working directory to the folder where you downloaded the files. Once done, type 

source("tdasetup.r") 

in the RStudio console, and wait for the download and installation to finish. 

Type "y" if there are times when the console prompts you to download and install from source. If the console prompts you for updates, type "n" (at least for the purposes of speeding up installation).



19 March 2019 - Here are the results for Problem Set 2. In preparation for the hands-on for QTL mapping next week, kindly install the R/qtl package in your RStudio installation in your respective laptops. To do this, first, make sure that your laptop is connected to the Internet. Next, open RStudio, then type install.packages("qtl") in the RStudio Console, then press Enter. To test if the package installation is successful, type library("qtl"), then press Enter. At worst, all you should be getting is a warning (something like "package 'qtl' was built under R version 3.5.2"). In addition to installing the package, download to your laptop the Sample Data link provided in the right hand side table. Finally, we'll meet once again in Classroom 2 for the remainder of the semester (unless otherwise specified). 



11 March 2019 - For our hands-on session on SNP calling on 13 March 2019, we meet at the 2nd Floor Lecture Room of the Philippine Genome Center, at 2:30pm. Please be guided accordingly.






26 February 2019 - For our session tomorrow, 27 February 2019, we meet at the 2nd Floor Lecture Room of the Philippine Genome Center, at 3:00pm. Please be guided accordingly.



12 February 2019 - Kindly download the data set for tomorrow's hands-on demo (click on "Sample Data" link on right hand side of the website).



29 January 2019 - To facilitate our activities for tomorrow's session, kindly download and install the following files:



21 January 2019 - Again, our regular class venue is Classroom 2 (Room 203) located at the 2nd Floor of the UP Alumni Engineers Centennial Hall. Also, for those who have not done so yet, kindly e-mail me a screenshot of the specifications of your laptop preferably on or before tomorrow (22 January 2019) 5:00pm to help me know what tools I need to download and to configure them accordingly. See you on Wednesday!



16 January 2019 - This is the website for the BIO 397 (Advanced Bioinformatics) class facilitated by Jan Michael Yap. Announcements and files pertinent to the class will be posted here.


DatesTopic/Activity Materials
01/16/2019Overview
01/23/2019Introduction to Linux CLI and ScriptingLinux CLI:
Site 1
Site 2

Scripting:
Site 1
Site 2
Site 3
Sample Scripts
 01/30/2019 
 Introduction to Programming in RR:
Ebook
Site 1
Site 2
02/06/2019
02/13/2019
Phylogenetic AnalysisSlides
Sample Data 
02/13/2019
02/27/2019
PROBLEM SET 1Questionnaire
02/20/2019
02/27/2019
Sequence Assembly
Slides
Sample Data
02/27/2019
 03/13/2019 
PROBLEM SET 2Questionnaire

Datasets:
Forward Reads
Reverse Reads
03/06/2019
 03/13/2019 
SNP Calling
Slides
03/13/2019
03/27/2019
 PROBLEM SET 3Questionnaire
 03/20/2019 UP PGC Bioinformatics Symposium  
 03/27/2019  QTL MappingSlides
R/qtl Tutorials
Sample Data
03/27/2019
04/10/2019
 PROBLEM SET 4Questionnaire
Dataset
04/03/2019
04/10/2019
Transcriptomic Data Analysis Slides
Exercise Kit 

Differential Analysis Sample Codes and Tutorials:

Microarray:
Part 1
Part 2

RNA-seq:
Link

Gene Coexpression Tutorials:
WGCNA
04/10/2019
 04/24/2019 
PROBLEM SET 5Questionnaire
Datasets
05/08/2019PROJECT PRESENTATIONSGuidelines
  • Syllabus can be downloaded here.
  • Copy of the 2012 Code of Student Conduct can be downloaded here.