18 – 21 June 2018
Kasetsart University, Bangkok
Computational biology is the new skill set for understanding agricultural systems. We empower you with a hands-on workshop that blends theory and bioinformatics practicals for 21st century skills.
Associate Professor Arinthip Thamchaipenet, Kasetsart University, Thailand
Associate Professor Aaron Darling, ARC Centre of Excellence for Mathematical and Statistical Frontiers, University Technology of Sydney, Australia
Assistant Professor Thomas Jeffries, Western Sydney University, Australia
Assistant Professor Alexie Papanicolaou, Hawkesbury Institute for the Environment, Australia
Non-Thai attendees please register here: https://onestop.westernsydney.edu.au/OneStopWeb/HIEEvents/booking
First day lectures only: 1,500 THB
- Registration costs do not include accommodation.
- Please note traffic in Bangkok is significant during peak hours so we recommend the following two hotels near the campus:
- KU Home (Deluxe Room) at 1400 baht a night (56 AUD) for up to 2 people, including breakfast.
- Recoftc Hotel (Deluxe or Suite) at 800-1000 baht a night (around 36 AUD) with a queen size bed, no breakfast available
Therefore if you are willing to share and stay for 5 nights (Sunday 17th to Friday 22nd), the total cost would be around AU$140 (double if you don’t want to share) or AU$180 respectively.
We have blocked-booked rooms in both places and will hold them until 25th of May. If you want to choose one the two options please contact us with the contact form below indicating which one. If you’re willing to share in the KU Home, please provide your gender and we will let you know if another participant is available to share with you.
Frequently Asked Questions
- The workshop includes wet- and dry-lab as well lectures. The topic is geared towards research scholars such as PhD students, Post-Docs, and Faculty who wish to up-skill.
- If you are PhD student from a non-biomedical laboratory that has limited funding, please use the contact form below and we can negotiate a discount after Early Bird Registration closes.
- Can’t come for the whole week? You can come for the first day only!
Looking forward seeing you:
Date: June 18-21, 2018
Place: Davi Yanasugondha Building, Faculty of Science, Kasetsart University, Thailand
|Monday, June 18, 2018 Davi Yanasugondha Building; Room 202|
|8:30-9:15||Opening ceremony (Dean, Faculty of Science, KU)|
|09:15-10:00||Lecture 1: Bioinformatics and agriculture (Dr. Sissades Tongsima, BIOTEC)|
|10:15-10:45||Lecture 2: Metagenomics in agricultural research (Assoc. Prof. Arinthip Thamchaipenet, KU)|
|10:45-11:45||Lecture 3: Basic description of sequencing, assembly, genome comparison, and phylogenetics (Asst. Prof. Alexie Papanicolaou, WSU)
We provide an overview of the state of the art in (meta)genome bioinformatics, how it can be used in agriculture, and how bioinformatic skills can be learned
|11:45-12:45||Lunch and networking|
|Lecture 4: Metagenomics: Recent advances and ongoing challenges (Assoc. Prof. Aaron Darling, UTS)
We describe the state of the art in metagenome analysis methods for taxonomic assignment, community profiling, and metagenome assembly.
Ongoing challenges in metagenome assembly will be discussed in detail, and emerging solutions such as time series analysis and metagenomic Hi-C will be described.
|Lecture 5: Next generation microbial ecology (Asst. Prof. Thomas Jeffries, WSU)
We explain how Microbial Ecology benefits from these new genomic / bioinformatic approaches.
How biodiversity can be assessed and microbial interactions described.
How we can understand – better – the function of ecosystems and microbiomes using metagenomics
|16:15-17:00||3 minute Lighting Talks|
|Tuesday, June 19, 2018 Davi Yanasugondha Building; Room 202 and lab at 905|
|09:00-10:00||Lecture 6: Technological capabilities for amplicon metagenomics (Dr. Kay Anantanawat, WSU)
We showcase the technological options for assessing microbial biodiversity using modern sequencing technologies
|10:00-10:30||Overview of Wet Laboratory exercise|
|10:45-12:00||Lecture 7: Recap of Wet lab; Quality assessment of amplicon libraries and sequencing data (Asst. Prof. Thomas Jeffries and Dr. Kay Anantanawat, WSU)
Scaffolding the lessons from the previous day and learning how to do Quality Assessment of the sequencing data.
|12:00-13:00||Lunch and networking|
|13:00-16:30||Wet Laboratory: 16S amplicon library construction (Dr. Kay Anantanawat, WSU)*
In this laboratory exercise, students learn how to make their own libraries for microbial biodiversity analyses
|Wednesday, June 19, 2018 Davi Yanasugondha Building; Room 202 and lab at 306|
|09:00-10:00||Demonstration of Amplicon Analysis of Microbial diversity (Asst. Prof. Thomas Jeffries, WSU)
In this lecture we run a demonstration of the bioinformatic toolkit that will be used in the afternoon computer laboratories.
|10:15-12:00||Computer Lab 1: Command Line Bioinformatic skills; High Throughput Computing using the Galaxy Graphical User Interface
(Assoc. Prof. Aaron Darling, Asst. Prof. Thomas Jeffries and Asst. Prof. Alexie Papanicolaou)
In this computer lab we provide an overview of the basic skills needed to undertake the exercises in the course.
NOTE: We provide access to our High Throughput Computers for the duration of the course. Students need to bring their own laptop
|12:00-13:00||Lunch and networking|
|13:00-17:00||Computer Lab 2a: Phylogenetic Analysis of Microbial Biodiversity (Asst. Prof. Thomas Jeffries, WSU)*
Using the QIIME2 package, we learn how to analyse microbial biodiversity data as acquired from 16S rRNA amplicon sequencing.
|Thursday, June 21, 2018 Davi Yanasugondha Building; Room 202 and lab at 306|
|09:00 – 09:45||Open Panel Q&A with Speakers|
|09:45 -12:00||Computer Lab 2b: Genomic Analysis of Microbial Biodiversity (Asst. Prof. Thomas Jeffries, WSU)
Here we continue QIIME 2 software plus learning about inferring gene function from this data; the benefits and problems and ecological statistics.
|12:00-13:00||Lunch and Networking|
|13:00 -13:30||Closing ceremony; Certificates; Awards for best Lighting Talk (Asst. Prof. Alexie Papanicolaou, WSU)|
|13:30-16:00||Free Consultation and networking with Asst. Prof. Thomas Jeffries, Asst. Prof. Alexie Papanicolaou, and Dr. Kay Anantanawat, WSU|
Contact us for queries: