COVID-19:
The current COVID-19 pandemic is an evolving and unpredictable situation that is limiting travel worldwide. Part of our planning for the 2022 Philippines programs includes adhering to ever changing requirements set by participating academic institutions and governmental agencies of the US and the Republic of the Philippines as these respond to the pandemic. The safety of students and staff is paramount in this process. We are exploring alternatives to face to face instruction should it be determined that international travel will not be possible.
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Hosted by Silliman University
The ‘Omics and Bioinformatics workshop is part of the training component of the Philippines PIRE Project. Participants will receive an introduction to the skills and knowledge needed to confidently develop a project using genomics or transcriptomics.
Participants of this workshop will:
- Become familiar with how natural processes interact with and affect the genome, transcriptome, and proteome.
- Understand the major influences that shape patterns of genetic variation.
- Learn which major sequencing platforms are used and how they work, guidelines for collecting and preserving specimens for genomic or transcriptomic work, and how to build the libraries used to employ next-generation sequencing.
- Gain a working knowledge of UNIX command line tools such as creating, viewing, and modifying files and directories and using regular expressions to search, alter, and output specific data from within a file.
- Navigate and work within a high performance computing cluster.
- Use a pipeline to process a data set from raw sequences through assembly, mapping, and variant calling.
- Examine and analyze genomics and transcriptomics data using command line, spreadsheets, and GUI-based programs including FastQC, MultiQC, PGDSpider, BayeScan, BayPass, Genepop, and R.
The workshop is held at the Mariano & Lina Lao Activity Center Computer Lab, Silliman University High School, Dumaguete, Negros Oriental, Republic of the Philippines.
The workshop is a ten day course, held from Monday to Friday, from 9:00 am to 5:00 pm, that covers the following subjects:
Fundamentals of Molecular Evolution
These lectures cover a variety of topics essential to understanding the nature of heritable information. Major themes include genetic variation, the Hardy-Weinberg principle, and the four major influences that drive evolution – drift, mutation, migration, and selection. This is a necessary primer for participants that have not previously taken a genetics course or are in need of a refresher course in molecular evolution.
Beginner ‘Omics and Bioinformatics
These lectures include how to use genetics and transcriptomics to answer biological questions, the preservation of genetic or transcriptomic material, sequencing platforms, library creation, sequence assembly, RADseq, RNAseq, and data processing pipelines. The lectures will be followed by hands-on, computer-based sessions that introduce the basic bioinformatics tools of UNIX command line and regular expressions. Participants will learn to process a genomic dataset beginning with examining raw sequences for quality and content. Participants will use a data processing pipeline to create a de novo assembly, map reads, and call variants (SNPs).
Intermediate ‘Omics and Bioinformatics
Monday starts with a one-hour morning lecture session focused on choosing the appropriate analyses to answer biological questions and a primer on the most common file formats used for analyses. The lecture session is followed by quality filtering of the variant call format (vcf) file generated at the end of week two. Tuesday-Friday sessions are entirely hands-on. Participants will finish quality filtering their dataset and learn how to analyze both genomics and transcriptomics data using a variety of programs and tools that will allow them to explore the population dynamics of a species.
This year’s ‘Omics Workshop dates:
Date is to be determined pending the status of COVID-19.
Registration:
The workshop is free. Space in the workshop is limited. Reservations for workshop participants are arranged by invitation only. Travel, lodging and meals are the responsibility of the participant. To register please fill out the registration form below.
If you are interested in the workshop and either you or your supervisor did not receive and invitation, do not fill out the registration. Please send an email to philippinespire@gmail.com first.
Advances in Philippines Marine Research APMaR Symposium:
The APMaR symposium is held at the Silliman University Audio Visual Theater. It is a one day event from 9:00 AM to 5:00 PM. The event is introduced by Dr. Angel Alcala, National Scientist of the Philippines. It begins with a capstone talk on marine extinction risk in the Philippines and the application of genomics to examine changes in genetic diversity and effective population sizes over the past century by Dr. Kent Carpenter from Old Dominion University. The capstone lecture will be followed by presentations from leading scientists and students performing marine research in the Philippines.
The purpose of this symposium is to provide a multinational network of scientists a
platform to highlight marine research in the Philippines and to foster collaboration
between researchers from Silliman University, Old Dominion University, the
National Fisheries Research and Development Institute, Mindanao State University,
De La Salle University, the University of the Philippines Marine Science Institute and
beyond.
As a participant in the workshop, we cordially invite you to an oral presentation of your current research during this symposium. A limited number of spaces are available for 12 minute oral presentations followed by a 3 minute period for questions or discussion. Priority will be given to talks that highlight research currently using ‘omics techniques or that address questions that would benefit from an ‘omics approach in the future, however, we encourage the submission of any current marine research conducted in the Philippines.
To sign up for a presentation slot, please include the proposed title of your talk as you would like it listed in the symposium schedule along with a 350 word abstract when you register for the workshop using the link below.
A list of speakers and topics will be made available on this page: APMar symposium.
This year’s APMaR is on:
Date is to be determined pending the status of COVID-19.
Register here
Required Computer software:
Now that you are registered, if you are bringing you own computer please install the software listed below prior to the workshop.
1. PuTTY. Windows users only (not needed for anyone using a Mac or Unix-based computer). This is used to access to the Old Dominion University cluster from Windows
2. Virtual Box with an Ubuntu environment. Windows and MAC.
https://www.ubuntu.com/download/desktop
3. WinSCP
https://winscp.net/eng/download.php
4. Microsoft Excel
5. R and RStudio with the following packages downloaded (with all dependencies):
adegenet
ggplot
DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)