Helminth Bioinformatics
21 - 26 May 2023, Khon Kaen University, Thailand
Practical hands-on training in helminth genome analysis.
Course overview
Helminths, commonly referred to as parasitic worms, are a broad group of organisms that have a signfiicant impact on humans, animals, and plants worldwide. Helminths infections contribute significantly to the burden of neglected tropical diseases (NTDs) in many low- and middle- income countries (LMICs). Despite important efforts to tackle these diseases through mass drug administration programs and other methods of control and containment, NTDs due to helminths such as schistosomiasis and soil-transmitted helminthiases continue to be among the most debilitating and morbidity-causing diseases in LMICs adding significantly to the economic burden in the strained economies. Moreover, decreased susceptibility to the most used chemotherapies is emerging in the field, raising concerns about the rise of drug-resistant helminths.
Advances in sequencing technologies have enabled the production of draft and high-quality genome assemblies for the most important disease-causing helminths. In addition, reduced costs of next-generation sequencing (NGS) techniques make sequencing accessible to the wider scientific community of researchers and organisations, providing unprecedented access to genomics. Data manipulation and computational analyses are still the main challenges that limit the realization of maximum benefit and appropriate interpretation of these data.
The course Helminth Bioinformatics aims to equip participants with the skills needed to access, analyse and display large-scale genomic data. The course will provide hands-on training in read mapping, transcriptomics and genetic variation analysis, all tailored to address the challenges presented by large helminth genomes. Participants will acquire basic and advanced techniques in bioinformatics while getting familiar with computer command-line languages and public data repositories.
Target audience
The course is targeted at researchers at various stages of their career who are interested in accessing and analysing genetic and genomic data of helminth parasites. We cover a range of topics are a relatively high-level, and therefore, little prior experience is necessary. The course will be taught in English.
Prerequisites and Introductory materials
There are no formal prerequisties for the course. However, the practical computational sessions will be taught exclusively through Unix/Linux, and therefore, participants with some familiarity with the Linux operating system will allow them to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:
- https://www.futurelearn.com/courses/linux-for-bioinformatics
- http://www.ee.surrey.ac.uk/Teaching/Unix
- http://swcarpentry.github.io/shell-novice/
Participants may find a short online course on Introduction to Genomics beneficial for a quick recap and preparation. The course was designed specifically for the participants of Helminth Bioinformatics course, but is open for all. The course is on KKUMedX online-learning platform. The instruction on how to register is available here.
We are fortunate to be supported by DataCamp, who are providing full classroom access for participants. DataCamp is an intuitive learning platform for data science and analytics. Participants can learn any time, anywhere and become an expert in R, Python, SQL, and more. DataCamp’s learn-by-doing methodology combines short expert videos and hands-on-the-keyboard exercises to help learners retain knowledge. DataCamp offers 350+ courses by expert instructors on topics such as importing data, data visualization, and machine learning. They’re constantly expanding their curriculum to keep up with the latest technology trends and to provide the best learning experience for all skill levels. This is a fantastic resource for participants to continue developing their skills beyond the course.
Instructors
- Arporn (Koi) Wangwiwatsin (co-lead), Khon Kaen University, Thailand
-
Steve Doyle (co-lead), Wellcome Sanger Institute, UK
- Matt Berriman, University of Glasgow, UK
- Dionysis Grigoriadis, EMBL-EBI, UK
- Siriyakorn Kulwong, Khon Kaen University, Thailand
- Heerman Kumar, Monash University, Malaysia
- Yi-Chien Lee, Academia Sinica, Taiwan
- Marina Papaiakovou, University of Cambridge, UK
- Sirinya Sittirak, Khon Kaen University, Thailand
- Isheng Jason Tsai, Academia Sinica, Taiwan
Timetable
- overview
| Sunday | Monday | Tuesday | Wednesday | Thursday | Friday | Saturday | |
|---|---|---|---|---|---|---|---|
| Morning | WormBase Parasite 1 | WormBase Parasite 2 | Genome Variation | Transcriptomics | Project | Public Engagement Event | |
| Afternoon | Welcome session & Public Engagement | Intro to Linux | R and RStudio | Genome Variation | Transcriptomics | Presentations | Public Engagement Event |
Course manual
- https://wcscourses.github.io/HelminthBioinformatics_2023/
Module 1 - WormBase Parasite 1
- Introductory presentation
- Presentation on Genome Assemblies
- Online manual
- Exercise answers
- Survey
Module 2 - Introduction to Linux
- Introductory presentation
- Online manual
- Survey
Module 3 - WormBase Parasite 2
- Introductory presentation
- Online manual
- Exercise answers
- Survey
Module 4 - Project Introduction and Planning
- Introductory presentation
- Online manual
- Survey
Module 5 - Introduction to R and RStudio
- Online manual
- Survey
Module 6 - Genome Variation
- Introductory presentation
- Online manual
- Survey
Module 7 - Transcriptomics
- Introductory presentation
- Online manual
- Survey
Module 8 - Project
- Online manual
- Survey
Appendix
- Genome Assembly Variation
- Creating a shared folder between your computer and VM
- Finding and download sequence data from public repository
- Downloading GO term annotation from WormBase ParaSite and formatting it for topGO
Any reuse of the course materials, data or code is encouraged with due acknowledgement.
License
This work is licensed under a Creative Commons Attribution 4.0 International License.