Course given at BioSB 2019 for biologists about SPARQL.
Scientific topics: Biology
Operations: Query and retrieval
Keywords: Sparql queries, Sparql syntax
Resource type: Tutorial
This course focuses on genomic sequencing.
Topics covered:
- The changing landscape of genomics: From Sanger sequencing to Next Generation Sequencing
- Overview of Next Generation Sequencing platforms and their methodology
- Targeted resequencing
- Alignment, variant calling and...
Scientific topics: Rare diseases
Keywords: Rare Diseases & Research
Resource type: e-learning
Workshop of 1.5h where the eNanoMapper ontology and a few uses are discussed. The exercises walk the audience trough the principles, uses, and demonstrates how they can actively work with the ontology.
Scientific topics: Ontology and terminology, Toxicology
Resource type: Tutorial
Book that describes the cheminformatics functionality of the Chemistry Development Kit taking advantage of the Groovy programming language.
Scientific topics: Chemistry, Cheminformatics
Resource type: Book
BridgeDb is a combination of an application programming interface (API), library, and set of data files for mapping identifiers for identical objects [1]. Identifier mapping databases are available for gene products and metabolites. This Bioconductor Vignette explains how to use BridgeDb in the R...
Keywords: ELIXIR RIR, BridgeDb
Resource type: Tutorial, Vignette
Clinical Bioinformatics I is a 10 credit module of the new MSc in Clinical Bioinformatics, delivered by Nowgen/NGRL and the University of Manchester in the UK. Clinical Bioinformatics is one of the streams of the NHS Scientific Training Programme (STP). The programme is a mixture of work...
Keywords: Clinical bioinformatics, Genomics, Introduction bioinformatics
This presentation examines the available in silico tools for protein structure and function prediction. It examines the major protein family databases (PROSITE, PRINTS, Pfam, etc.), and explores why tools like PSI-BLAST, while convenient and easy to use, may not always give optimal results. The...
Keywords: Expert systems, Genequiz, Protein family characterisation, Protein family databases, Protein sequence analysis, Psi blast
This presentation introduces the background to the InterPro database: what it is, where it came from, and what was the vision behind its creation. It examines in particular whether the database has evolved in line with its original vision, and asks whether the resource is still fit for purpose.
Keywords: Integrated diagnostic tools, Protein family characterisation, Protein sequence analysis
A presentation designed to introduce the concept of protein family analysis and characterisation using motif-based methods, with a particular focus on protein fingerprinting. Following a general introduction to sequence analysis, and the fingerprint approach, specific examples are given to...
Keywords: Functional diagnosis, Protein family characterisation, Protein sequence analysis