Training given to the ACE Centers in Mali and Uganda. The African Centers of Excellence in Bioinformatics and Data Intensive Sciences (ACE) are a consortium of research and training centers facilitated by the National Institute of Allergy and Infectious Diseases (NIAID) in collaboration with research institutions, African governments, private sector companies, and the Foundation for the NIH (FNIH). ACE delivers and maintains high performance computing infrastructure, distance learning facilities, and training to collaborating research and academic institutions through a public-private partnership based on in-kind contributions.
High Throughput Sequencing
GWAS training for ACE Mali - utilizing PLINK, a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses
programming
An introduction to the R programming language and the components of programming including syntax, data types, dataframes and basic data analysis.
General Bioinformatics
Advanced literature search in PubMed with an overview of PubMEd and exercise including general and clinical search, building queries and collections.
Cheminformatics
Cheminformatics training covering an intro to drug discovery, molecular file formats and databases, aligning molecules, QSAR, screening and de novo design.
General Bioinformatics
Sequence retrieval tools (SRA) for downling bulk geneomic or protein sequence data
phylogenetics
Survey of molecular and population mechanisms creating and maintaining genetic diversity.
metagenomics
Learn about shotgun metagenomics with a visual and interactive community exploration software MEGAN6-CE
General Bioinformatics
Introduction to protein databases, their contents and uses in bioinformatics research
metagenomics
Metagenomics overview (Shotgun metagenomics)
programming
Introduction to Statistical Analysis in R
programming
Introduction to Awk and Sed programming
programming
Introduction to R markdown
High Throughput Sequencing
Managing data and simple analyses in the Galaxy cyber-environment (Practical)
programming
Introductory Training on Bash scripting. It covers basic concepts on programming. Students will be able to follow along to create various loops and other simple operations. Materials include the code used.
programming
Manipulating files and data on Linux
Data Science
Generating graphics in R - using ggplo2 from beginning with graphics through saving plots, themes, and facets.
programming
Tutorial for learning to use the editor VIM for Unix. Demo to show file manipulation and basic command line operations using an editor.
metagenomics
Metagenomics overview (Metataxonomics)
Data Science
Generating data and manipulating objects will introduce data object, structure, some useful functions to describe data, and data manipulation. (Part II - includes dplyr)
High Throughput Sequencing
How to Check the Quality of Illumina Sequencing Reads with FastQC
General Bioinformatics
A tour of primary sequence databases including NCBI, Array Express, GEO, PDB, Intro Pro, UniProt and Ensembl.
High Throughput Sequencing
Processing of Aligned Reads for RNA-seq using R from QC and trimming, to mapping and differential analysis
High Throughput Sequencing
Intro to NGS and Sanger Sequencing including the technology, sequencers and their applicability to differen research questions.
programming
Introduction to UNIX editors: Vi
programming
Introduction to UNIX and Text Editing
General Bioinformatics
Public Projects - Human NGS Data training covering sequence file formats, WES vs WGS, common NGS methods, and HapMap
General Bioinformatics
Basic conceps and use of UCSC Genome Browser Tutorial to visualize genomes, genes and other sequence entities in context.
High Throughput Sequencing
Haplotype-based Association Test, Linkage Analysis for Binary Traits and Quantitative Traits
phylogenetics
Mechanisms of Evolution including mutations, chromosomal variations and genomic variations
programming
Python programming training covering the excellent DnaFeaturesViewer genome and protein visualization package.
Level