Train-the-Trainer: Course Design and Delivery for Bioinformatics Trainers

: Course; 03 October 2022; Hits: 2935

Train-the-Trainer: Course Design and Delivery for Bioinformatics Trainers

Course Overview/description:

H3ABioNet, Wellcome Connecting Science and the European Bioinformatics Institute are hosting a Train-the-Trainer workshop. The aim of the workshop is to empower trainers and educators focused on bioinformatics and data science to design, develop, and deliver effective training in their field of expertise. Trainers will learn how to plan, design, and deliver training in bioinformatics to impart skills to students, professionals, and future experts.

Objectives:

Provide instruction, coaching and feedback (theory and practice) to prepare participants to effectively design and deliver training to others in bioinformatics skills.
Promote participation and involvement using group work and presentation
Promote interpersonal skills, collaboration, and networking through community development, mentorship, and expert support.
Raise awareness of creation and use of open and accessible training
Enable trainers to evaluate their teaching/learning.

Keywords: Genomics, Bioinformatics, Education, Training

Skill level of training: Beginner

Language: English

Credential awarded: letter of completion

Type of training: online

Prerequisites: Trainers and educators who have an understanding of the topic they wish to teach (bioinformatics, genomics, data science).

Learning objectives/outcomes:

After this workshop participants should be able to:

Apply theoretical and pedagogical concepts to learning
Describe the pipeline for effective design and development of
Define factors that influence training design and promote
Design a short training course on a specific
Plan training evaluation using appropriate
Critically review the design of bioinformatics

Venue of workshop: Zoom

Dates for the workshop: 22 November – 8 December 2022, Tuesday and Thursday, 14h00 – 17h00 CAT.

Workshop organisers: Nicola Mulder, Alice Matimba, Dusanka Nikolic, Verena Ras, Benjamin Moore, Piv Gopalasingham, Isabela Malta, Sarah Morgan, Sindiswa Lukhele.

Registration opens: 30 September 2022

Registration closes: 21 October 2022

Notification date: 11 November 2022

Link to application form: Train the Trainer Participant Registration Form

Workshop Sponsors: H3ABioNet, Wellcome Connecting Science, and the European Bioinformatics Institute.

Intended Audience: Applicants must be individuals involved in genomics or bioinformatics and interested in developing their skills in effectively training others in specific topics.

Course schedule:

Week	Dates	Time	Topics	Session content
1	17 Nov 2022	14h00 – 17h00 CAT		Get to know each other and course overview
2	22 Nov 2022		Training theory and practical aspects	Theoretical aspects
2	24 Nov 2022		Training theory and practical aspects	Course design elements and factors
3	29 Nov 2022		Training design elements	Design your own training Part 1
3	02 Dec 2022		Training design elements	Design your own training Part 2
4	06 Dec 2022		Training evaluation	Feedback and evaluation
4	08 Dec 2022		Training design project	Project presentation and peer review
5	Online		Course evaluation, wrap-up	Post-course feedback and certificates

current , education

Introduction to Bioinformatics Training 2022

: Course; 08 August 2022; Hits: 2243

Look Out for IBT 2021 Classroom Call

: Course; 20 April 2021; Hits: 3429

H3ABioNet‘s IBT 2021 Classroom Call

H3ABioNet‘s Introduction to Bioinformatics course (IBT) provides an introduction to the field of bioinformatics with a focus on important bioinformatics tools and resources. The 2021 iteration will be running soon.

Kindly watch out for the call for classrooms by 26th April 2021.

current , bioinformatics introduction

Next Generation Sequencing Bioinformatics Course 2022

: Course; 02 December 2021; Hits: 12111

Course Overview/description:

Next generation sequencing (NGS) has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by next generation sequencers. This course will equip participants with the essential informatics skills required to begin analysing NGS data and apply some of the most commonly used tools and resources for sequence data analysis.

The programme will cover prominent sequencing technologies, algorithmic theory and principles of bioinformatics, with a strong focus on practical computational sessions using sequence analysis techniques and tools applicable to any species or genome size. A variety of applications will be covered from post-sequencing analysis - QC, alignment, assembly, variant calling and RNA-Seq.

This course will apply a blended learning format consisting of locally coordinated classrooms referred to as “remote classrooms”. Click here for more information. Please note: Due to the COVID-19 pandemic, the local classrooms will likely run virtually, using Zoom and downloadable virtual machines.

Would you like to enroll in the course in 2022?

Please apply to take the course by clicking here

Applications close 21 February 2022 at midnight (CAT)

Intended Audience:

Applicants should be postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals actively engaged in or soon to commence research involving next generation sequencing data analysis.

Priority will be given to applicants who 1) currently or will soon have NGS experimental data to analyse 2) will utilise the bioinformatics techniques taught in at least two of the modules/topic areas listed in the programme outline in their experiments 3) have a clear plan/opportunity to disseminate the knowledge amongst their peers. We encourage applicants to highlight these areas in their application.

Learning objectives/outcomes: After this workshop participants should be able to:

• Use the unix command-line as a tool for data analysis
• Describe the different NGS data file formats available
• Perform QC assessment of high throughput sequencing data
• Explain the algorithmic concepts behind read alignment, variant calling and structural variant detection
• Perform read alignment, variant calling and structural variation detection using standard tools
• Analyse RNA-Seq and CHiP-seq data
• Perform a genome assembly using NGS data

Prerequisites:

The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some previous experience using the Linux operating system. This will be essential for participants to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:

Syllabus and Tools:

The course will cover the following topics:

• Intro to Unix/Linux & running workflows
• Introduction to NGS Technologies
• NGS data pre-processing and QC
• Alignment to reference sequences
• Variant calling and annotation
• ChipSeq
• RNASeq
• Genome assembly

Dates for the workshop:

Tuesdays & Thursdays from 22/03/2022 until 20/06/2022 (staff training will happen ahead of this)

Classroom registration opens:

03/12/2021

Classroom registration closes:

10/01/2022

Notification date:

17/01/2022

Participant applications:

Applications are now open and will close on 21 February at midnight (CAT). Apply here.

Workshop organisers:

WGC WCS and H3ABioNet

Workshop Sponsors:

Wellcome Genome Campus/ Wellcome Connecting Science and H3ABioNet

Keywords:

NGS, Data analysis, Genomics, Sequence analysis

Skill level of training:

Advanced

Language:

English

Credential awarded:

Letter of completion

Type of training:

Likely to be run in a virtual format

Workshop limitations:

The course aims to provide a hands-on introduction to bioinformatics for next generation sequencing, and should not be considered a complete education in the theoretical and mathematical foundations of the topics.

Workshop Programme:

The workshop will run for ~10 weeks, on Tuesdays and Thursdays from the 22nd of March until the 20th of June.

Please apply to take the course by clicking here

current , ngs

Introduction to Bioinformatics Training 2021

: Course; 28 January 2021; Hits: 19627

Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for participants to gain practical experience in using various tools and resources.

Intended Audience: The course is aimed at individuals from a molecular biology background who have a basic understanding of biochemistry and/or genetics and would like to become bioinformatics users. For an explanation on who 'bioinformatics users' might be, see Figure 2 in http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.

Keywords: Genetics, Genomics, Nucleic acids analysis

Skill level of training: Beginner

Language: English

Credential awarded: Letter of completion

Type of training: Blended/hybrid learning

Logistics

Venue of workshop: Local classrooms ( usually ~40 physical/online sites across Africa). Please be aware that the course is likely to make use of a combination of both physical and online sites depending on ongoing Covid-19 restrictions.

Dates for the workshop: 06 July – 12 October 2021; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.

Workshop organisers: Paballo Chauke, Verena Ras, Shaun Aron, Sumir Panji and Nicola Mulder

Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical/online classroom, provided they have been selected via the selection process. Should a classroom decide to host a face-to-face classroom, the participant must be able to attend this classroom in person for the duration of the course.

Workshop Sponsors: H3ABioNet + Local Classrooms

Classroom applications:

Registration for classrooms opens: 26 April 2021

Registration for classrooms closes: 11 May 2021

Link to classroom application form: <Classroom registration is now closed>

Notification date for successful classrooms: 19 May 2021

Participant applications:

Registration for participants opens: 20 May 2021

Registration for participants closes: 14 June 2021 at 11:59 pm CAT

Application instructions: Participants must select a classroom within their region and that they are able to attend physically should that particular classroom choose to go ahead as a face-to-face classroom. Please be sure to adhere to this as selecting a classroom outside of your region/location may result in your application being rejected. Please also be aware that applying for the course does not guarantee entry - you will undergo a formal selection process.

Syllabus and Tools:

The course curriculum will cover the following main themes (subject to slight changes):

Bioinformatics resources and databases
- Introduction to bioinformatics, biological databases and resources (NCBI and EBI), data formats, ontologies
Linux
- Introduction to Linux, general overview of Linux environment, overview of command line interface, navigating Linux directory structure, manipulating files and directories, basic Linux commands
Sequence alignment theory and applications
- Introduction to searching and sequence alignment, BLAST, pairwise sequence alignment
Multiple sequence alignment (MSA)
- MSA theory, generating and interpreting MSAs using various tools, visualising and assessing MSA quality
Genomics
- Overview of sequencing and annotation, Ensembl genome browser, Genetic variation, HapMap, 1000 genomes
Molecular evolution and phylogenetics
- Molecular evolution, phylogenetic approaches and methods (Introduction and overview of methods)

**All modules make use of predominantly web-based tools such as NCBI, Ensembl, etc.

Prerequisites: A basic background/understanding of of biochemistry and/or genetics.

Objectives: After this workshop participants should be able to:

Explain the use of bioinformatics
Name the key bioinformatics techniques and tools
Locate important biological databases and retrieve data
Use selected tools effectively to run specific bioinformatics analyses
Understand the strengths and limitations of the various techniques

Workshop limitations: This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.

Training Material Availability:

Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:

Module 1: Databases and Resources