Announcements 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:
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. |
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