Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Mathematical Models for
Infectious Disease
Dynamics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live/Online
With subtitles
UK
Mathematical review (calculus, probability, etc.).
Population dynamics. Deterministic and stochastic
models. Modelling structured populations:
age-structured, spatial and network models. Applied
programming with R. Statistical estimation of models.
Computer-based simulations.
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Computational Molecular
Evolution
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Data retrieval and assembly. Alignment techniques.
Phylogeny reconstruction (including maximum likelihood
and Bayesian methods). Hypothesis testing. Population
genetics approaches. Protein and nucleotide sequence
analysis, including NGS data (Please note however that
the course focuses on NGS analyses for molecular
evolution, we do not cover traditional NGS analyses
e.g., QC, read mapping, variant calling, assembly etc.).
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Systems Biology: From Large
Datasets to Biological Insight
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Data reduction and data integration methods – including
comparison of major approaches through lectures and
practical exercises. Machine and deep learning –
practical exercises on supervised machine learning,
including classification and regression, and deep
learning. Functional inference from omics data –
approaches to extract signatures of cell state from
-omics data including transcription factor activation
and kinase activity states. Extraction of upstream
signalling pathways from transcriptomics datasets.
Network inference and signal propagation – network
inference approaches from -omics data.
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Working with Protozoan Parasite
Database
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Visualisation of sequence features and next generation
sequencing data using the Artemis genome browser and
annotation tool. Genome browsing and comparative
genomics (ACT and JBrowse/GBrowse). Formulating complex
biological queries in computationally accessible form.
Web-based resources including the GeneDB.org and
VEuPathDB.org family of databases. Integrating
functional genomics data (RNA-seq, ChIP-seq, ChIP-chip,
microarrays, proteomics, etc) with genome sequence data.
Theoretical aspects of genome re-sequencing. Querying
genetic diversity on a genome-wide scale. Metabolic
pathways and pathway and GO enrichment analysis. Working
with next-generation sequence data (mapping, variant
calling, RNA-Seq etc) using both command-line and
web-based (Galaxy) methods. Introduction to community
curation tools
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
RNA transcriptomics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Overview of single molecule long read sequencing
technologies. Full length total RNA sequencing. Full
length cDNA sequencing. Small RNA sequencing. Single
cell transcriptome data generation and analysis.
Identification of post-transcriptional modifications in
RNA (epi-transcriptomics). Functional assays for lncRNA
biology. Integration of microRNA and mRNA data;
functional analysis of microRNAs. Expression network and
pathway integration and analysis
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Fungal Pathogen Genomics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Perform RNA-seq and SNP analysis and visualization via
EuPathDB Galaxy workspace in FungiDB. Identify secondary
metabolite clusters in MycoCosm. Find virulence genes
and annotation in Ensembl. Access genetic interactions
in CGD/SGD. Comparative genomics and browsers: GBrowse,
JBrowse, ACT, Artemis, Ensembl. Use of Apollo annotation
tools for fungal genomes. Web-based resources for fungal
genomic data including: FungiDB, EnsemblFungi, PomBase,
SGD/CGD, MycoCosm/JGI, etc.. Identification of
orthologs, and orthology-based inference (using
OrthoMCL, Compara, etc.). Next generation sequence
analysis, including variant calling (EuPathDB Galaxy).
RNA-Seq analysis and visualization. Developing advanced
biologically relevant queries, using FungiDB ‘search
strategies’. Best practices using ontologies to generate
hypotheses and analyse data (ontology structure,
evidence, available tools, slimming and enrichment,
etc.).
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Genomics and Clinical Virology
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Background to viral WGS approaches. Sample handling and
preparation. Library preparation techniques. Target
enrichment methods e.g. probe-based sequence capture or
PCR-based. Viral metagenomics. Technique discrimination
– the appropriate technique to use in different
scenarios. Next generation and third generation
sequencing platforms. Bioinformatics analysis including
different viral genome assembly approaches. Data
interpretation. Validation and accreditation of viral
WGS diagnostic service, Case studies in outbreak
investigation and infection control.
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Genomics and Clinical Virology
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Data analysis, display and dissemination. Design,
implementation, and interpretation of real-time PCR
tests for pathogen detection. Molecular approaches to
detect multiple pathogens. Whole genome sequencing
(WGS). PCR and sequence-based isolate characterisation.
Outbreak investigation and applications to public
health. Bioinformatics and data interpretation. Data
analysis, display and dissemination
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Malaria Experimental Genetics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
CRISPR-Cas9 based approaches. Consideration of the
relative merits of different conditional expression
approaches. Mechanics of transfection in P. falciparum
and P. knowlesi. Verification of gene targeting using
multiple genotyping techniques. Drug-response assays of
genome edited parasites. Application of next generation
sequencing to transcriptional profiling and quantitating
parasite growth. Flow cytometry-based phenotyping
platforms.
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Antimicrobial Resistance in
Bacterial Pathogens
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Historical and epidemiological aspects of antimicrobial
resistance (AMR). Clinical importance of AMR. Causes and
biological mechanisms of resistance in Gram-positive and
Gram-negative bacteria. Antimicrobial susceptibility
testing (AST) methods, e.g. disc testing, automated
systems, minimum inhibitory concentration (MIC),
breakpoints and reporting. Molecular methods for
detection of AMR. Internal quality control (QC) and
external quality assurance (QA) for AST. AMR pathogens
in Africa. AMR in veterinary medicine. Antibiotic
policies and stewardship. AMR surveillance methods and
study design. Tackling AMR using a One Health Approac.
Introduction to genomic surveillance of AMR. Local AMR
epidemiology – investigating transmission of clones and
AMR. Analysis of resistance in genomes
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Next Generation Sequencing
Bioinformatics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Introduction to NGS technologies. Introduction to the
unix command line. NGS data formats and tools. Sequence
alignment and QC. SNP/indel theory and practical.
Structural variation theory and practical. RNA-seq
analysis. ChiP-seq analysis. Sequencing data
visualisation with the Integrated Genomics Viewer (IGV).
Accessing public sequencing repositories. Genome
assembly theory and practical. Participant projects and
presentations
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Viral Genomics and
Bioinformatics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Uganda
Introduction to Linux/Unix. NGS file formats. NGS data
quality check and cleaning. Reference assembly. Assembly
statistics and visualisation. Consensus and variant
calling. De novo assembly. De novo contig consolidation
and gap filling. Pathogen sequence detection using
sequence classifiers. BLAST. Sequence submission.
Multiple sequence alignment. Recombination detection.
Introduction to phylogenetics methods. BASH scripting
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Molecular Approaches to Clinical
Microbiology in Africa
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Fundamental molecular biology techniques including
preparing, handling, and storing DNA. PCR, including
real-time PCR, with an emphasis on, methods,
applications and data interpretation. Determining
sequence variation, its visualisation and
interpretation, concentrating on conventional
approaches. Bioinformatic analysis of molecular and
genomic data, particularly the exploitation of web-based
tools. An overview of future technologies, and their
potential for application in clinical microbiology.
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Genomics and Epidemiological
Surveillance of Bacterial
Pathogens
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
UK
Practical bioinformatics skills needed to manipulate raw
sequence data (some of which will be generated on the
course), including: mapping and de novo assemblies, SNP
calling, annotation and analysis of genomic information.
Sequence analysis and comparative genomics of next
generation sequencing data using Artemis and ACT.
Principles of phylogeny and construction of accurate
phylogenies. Group exercises designed to teach everyday
skills required to work in genomic surveillance.
Practical exercises for using GPS to map cases of
infectious disease and phenotypes (such as AMR) across
the world.
COVID-19 Virtual Lab
Training for Genomic Epidemiology
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
USA
RNA extraction in BSC Clinical specimen (mock NP swab
sample) Library Preparation in Sequencing Lab
Pre-amplification area and Post-amplification area
Reagent preparation at start of day Qubit Analyzer to
check libraries for concentration and quality Load
sequencer flow cells and reagent cartridge Sequencing
run- Miseq Review of results after sequencing run Upload
of data to Explify or Illumina software
Module 1.Introduction to Pathogen Sequencing
Module 2.Introduction to Genomic Epidemiology
Module 3.Sequencing with the MinION: Laboratory Methods
Module 4.Sequencing with the MinION: Loading and
Interpretation
Module 5.Introduction to Bioinformatics
Module 6.Running the Assembly Pipeline (including
Command Line
Introduction)
Module 7.Working with Sequence Data
Module 8.Sequence Alignments and Building Trees
Module 9.Interpreting Phylogenetic Trees
No
No
Other
Two 1-2 hour Zoom sessions per week for 4 weeks.
Participants are expected to watch up to 1 hour of
pre-recorded material between sessions, and to attempt
laboratory methods or bioinformatic analysis as
appropriate.
Pre-recorded materials
Yes - pre-recorded videos will have English and French
subtitle options. All materials and slides will be
available in English.
Graduates, postgraduates, staff bioinformaticians, laboratory technologists, medical
microbiologists and PIs working with or about to embark on analysis of genomic and
metagenomics
data for epidemiological investigations.
Epidemiology, Pathogen genomics for clinicians, Bioinformatics, Data analysis, data
visualization, data management or a related topic
Canadian Bioinformatics
Workshop: Infectious Disease
Epidemiology Analysis
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Canada
Understand next generation sequencing (NGS) platforms
as applied to pathogen genomics and metagenomics
sequencing - Analyze NGS data for pathogen surveillance
and outbreak investigations - Analyze antimicrobial
resistance genes - Detect emerging pathogens in
metagenomics data - Perform phylogeographic analysis -
Use different visualization tools for genomic
epidemiology analysis
No
No
Presented at regular intervals
3-day workshop with lectures and hands-on tutorials
usually in-person although digital during COVID.
Bioinformaticians based at health institutes, and experimental biologists at research
institutions
Epidemiology, Pathogen genomics for clinicians, Sample processing, DNA/RNA extraction,
Bioinformatics, Data analysis, data visualization, data management or a related topic
Applied
bioinformatics, molecular epidemiology, and the SARS-CoV-2 pandemic
State, local, and territorial public health laboratories in the United States.
Sequencing, Bioinformatics, Data analysis, data visualization, data management or a
related
topic
AMD
Academy Bioinformatics course
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
USA
Introduction to Bioinformatics Introduction to Bacterial
Genomics Intro to Linux Environment Bioinformatics
resources for public health Getting things done in Linux
Quality control of NGS Data Genome Assembly Sequence
alignment and searching Pathogen Characterization and
Annotation Genetic inference Data Visualization
Communication of NGS data
Yes
No; the course does offer CEU via APHL.
Other
Typically 5-day in person workshop. Other offerings were
in place during COVID-19.
Epidemiologists working in US state and local health departments.
Epidemiology, Data analysis, data visualization, data management or a related topic
Molecular
Epidemiology for Epidemiologists
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
USA
Microbial evolution Next-gen sequencing technology
Genome assembly Phylogenetic trees hqSNP and MLST
Epidemiologic inference from sequence data Phenotypic
inference (antimicrobial resistance) Outbreak
investigation Network analysis (contact tracing)
Diagnostics Challenges in IT and data integration
Not at present, planned for online
Not at present, planned for online
Present at regular intervals
Two-day workshop with lectures and hands-on exercises.
Postdoctoral scientists, senior PhD students, junior faculty members or
clinicians/healthcare professionals based in Africa who are actively engaged in or soon
to
commence research involving next generation sequencing data analysis.
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic, Biostatistics
Next
Generation Sequencing Bioinformatics Training Course
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Cape Town South Africa
The programme 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, ChIP-Seq • RNA-Seq and Genome assembly
Includes multiple tests and assignments
Course certificate will be offered
Present at regular intervals
The course will run for 8 weeks on Tuesdays and
Thursdays (4 hours per session) from the 13th of April
until the 10th of June 2021
Bioinformatics, Data analysis, data visualization, data management in the context of
public health, pathogen genomics and epidemiology
Glasglow
Bioinformatics Summerschool
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Glasglow, UK
Basics of Linux Introduction to R Introduction to
next-generation sequencing Data visualization SNP
analysis Transcriptomics: bulk RNA-Seq and single-cell
RNA-Seq Databases Data processing
No
No, just internal for PhD students
Presented at regular intervals
5 day workshop
Live, remote sessions, Face to Face
Now all material availble through zoom, where an
automatic transcript is available.
Bioinformatics, Data analysis, data visualization, data management or a related topic
as would be applicable in the context of public health, pathogen genomics and
epidemiology
VEuPathDB
workshop
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Philadelphia, USA
See this years course, material and recordings:
https://veupathdb.org/veupathdb/app/static-content/workshops.html#veupath2021
No
No
Other
5-day workshop with lectures and hands on exercises.
Students work both individually and in groups to achieve
exercise objectives.
Introduction to pathogen genomics Introduction to
Artemis Using the Linux operating system for
bioinformatics Comparative genomics using the Artemis
Comparison Tool (ACT) Mapping Illumina sequence data
against a reference genome Genome-wide phylogenetic
analysis using SNPs Genome assembly Genome annotation
Transcriptome analysis using RNA-seq data Two extended
practical sessions applying the above topics
No
No
Presented at regular intervals
5 day course
Live, Remote sessions, Face to Face, Pre-recorded
materials
No
Monash University
SARS-CoV-2 Sequencing and bioinformatics
Beginner
Research/academia
Researchers and public health officials interested in viral genomics and bioinformatics.
Library prep, Sequencing, Bioinformatics, Data analysis, data visualization, data
management or a related topic as applicable to public health, pathogen and genomics
exercises were used to consolidate participants learning
Yes
Other
5-day workshop
Live, remote sessions, Face to Face
A handbook was provided, but presentations were given
live
University of Ibadan
Introduction to Bioinformatics for Bacterial Genomics
Beginner
Public health
Postgraduate students
Bioinformatics, Data analysis, data visualization, data management or a related topic as
would be applicable in the context of public health, pathogen genomics and epidemiology
Introduction to Bioinformatics
for Bacterial Genomics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Ibadan, Nigeria
Introduction to Bioinformatics Theoretical Concepts and
Approaches in Bioinformatics Hands-on Bioinformatics
Analyses (GUI and Web-based Tools) Introduction to the
Unix Command Line
No
No
Presented at regular intervals
10 day workshop
Live, remote sessions, Pre-recorded materials
Course offered in English only
University of Ibadan
Sustainable development in bioinformatics to support public
health
Beginner
Public health
Hospital Laboratory Scientists and Field epidemiologists interested in integrating
bioinformatics within their health institute and field.
Pathogen genomics for clinicians, Bioinformatics, Data analysis, data visualization,
data
management or a related topic
Sustainable development in
bioinformatics to support public
health
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Nigeria
1. Next-Generation Sequencing technologies 2. The use of
online platforms and user-friendly workflows to conduct
bioinformatic analyses (genome assembly, speciation, SNP
phylogeny, AMR gene prediction), 3. How to visualize and
interpret the results from bioinformatic analyses
No
No
Other
A one or two-week course every month for three months
Pre-recorded materials
No
Makerere University
Applied Microbial Genomics
Intermediate
Research/academia
Bioinformaticians based at health institutes, experimental biologists at research
institutions
Epidemiology, Pathogen genomics for clinicians, Sequencing, Bioinformatics, Data
analysis,
data
visualization, data management or a related topic
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Bioinformatics, Data analysis, data visualization, data management or a related topic
(as would be applicable in the context of public health, pathogen genomics and
epidemiology
Bioinformatics for
Biologists: An Introduction to Linux, Bash
Scripting, and R
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Cambridge, UK
What is Linux? Why Linux for biologists? The Linux file
system and navigating around it via the command line
Manipulation and searching of data files using the
command line to access useful biological data The basics
of writing Bash scripts and its use for process
automation Guidelines and recommendations for best
practice preparation of data files under Linux for
exporting to other environments (use of R for further
analysis and visualisation) Exercising on biological
data using different case scenarios
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics
Introduction to bacterial genomics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Cambridge, UK
Significance and challenges of AMR and the need for
control of antibiotic use Mechanisms of antibiotic
action, resistance and evolution Antimicrobial
susceptibility testing Molecular detection and
characterisation of AMR resistance genes Recent
developments in genomic technology for tackling AMR
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics Data analysis, data visualization, data
management or a related topic as would be applicable in the context of public health,
pathogen genomics and epidemiology
Bacterial
Genomes I: From DNA to Protein Function Using
Bioinformatics
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Cambridge, UK
Bioinformatics tools, DNA and protein sequences
Retrieving DNA and protein sequences from repositories
Databases for protein annotation • Inferring function
from sequence
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics Data analysis, Data visualization, data
management or a related topic as would be applicable in the context of public health,
pathogen genomics and epidemiology
Bacterial Genomes II: Accessing and Analysing Microbial Genome
Data Using Artemis
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Cambridge, UK
Multi-FASTA files Reference and draft bacterial genomes
Introduction to Artemis, an open source genome browser
Genome annotation Genomic regions defined by GC
(guanine-cytosine) content Accessing and downloading
whole genome sequences Pathogenicity islands
Peer-reviewed project: Ecological niche adaptation
between two Mycobacterium species Pseudogenes in
Mycobacterium species
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Pathogen genomics for clinicians, Bioinformatics, Data analysis, Data visualization,
data management or a related topic as would be applicable in the context of public
health, pathogen genomics and epidemiology
Bacterial Genomes III: Comparative Genomics using Artemis
Comparison Tool (ACT)
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Cambridge, UK
Introduction to comparative genomics, Introduction to
ACT, Analyse available data, Generate your own
comparison files, Make your own comparisons in ACT,
Identify pseudogenes in Mycobacterium leprae using ACT,
Peer review project: Comparative genomics on two
clinically relevant plasmids from Shigella
Bioinformaticians based at health institutes and experimental biologists at research
institutions
Bioinformatics, Data analysis, data visualization, data management or a related topic as
would be applicable in the context of public health, pathogen genomics and
epidemiology
Train the Trainer: Design
Genomics and Bioinformatics
Training
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Cambridge, UK
Adult learning and teaching principles and approaches
for small or large groups. Social learning through
knowledge sharing; role of teacher/trainer in a learner
centred environment. Iterative process of learning
design and development applied to genomics training.
Common educational methods to teach and assess
bioinformatics and laboratory methods required for
genomics. Peer review project: design training in
genomics, evaluate, reflect and improve.
Biologist with no prior experience in bioinformatics
Data analysis, data visualization, data management or a related topic (as would be
applicable in the context of public health, pathogen genomics and epidemiology)
Bioinformatics for molecular
biologists
Location
Sub-topics
Formal assessment
Accredited
Available
Duration
Live or Online
With subtitles
Johannesburg, South Africa
Course is broken up in 3 modules namely Linux
Python/Pearl MySQL The aim is to provide introductory
training in order to get participants comfortable to
script and start using linux based software
No
yes, Training Certificate from Thermo Fisher
Course is scheduled as needed, with standing courses as
well through the year
5 day hands on instructor led training either face to
face or virtual