The exponential growth of scientific data across disciplines has created a pressing need for robust, flexible tools that enable harmonisation and standardisation of metadata to ensure data interoperability and reusability. A major barrier to effective data sharing lies in the heterogeneity of data formats, vocabularies, and annotation practices, which can hinder discovery, integration, and…
Date:
11 June 2025
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Lessons from 20 years of Open Source Development
Computational biology has undergone a significant transformation since the advent of high-throughput sequencing, a pivotal breakthrough that democratized large-scale genomic analyses for researchers. However, even prior to this technological advancement, several of the most widely utilized tools in the field prioritized reliable software development practices, with data reproducibility being a…
Date:
23 April 2025
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Pangenome-based structure deconvolution of the amylase locus
The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake, although evidence of recent selection is lacking. Here, using 94 long-read haplotype-resolved assemblies and short-read data from approximately…
Date:
13 September 2024
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Exploring the application of pangenome reference graphs to rare disease diagnosis
Although the CHM13 reference represents a complete human genome, it lacks the full diversity of human haplotypes present in Africa. Analysis pipelines which map sequencing reads to a single linear reference may suffer from “reference genome bias”, where unmapped reads bias downstream analysis. The impact of reference genome bias in the clinical evaluation of genome sequencing data from African…
Date:
10 September 2024
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Introduction to the Gen3 Data Commons system
This workshop will provide an overview of the Gen3 Data Commons Framework. We will describe the core microservices used to create a data service that can be used to harmonize data, facilitate access, and assist new research projects to identify relevant data and will provide a demonstration using two of our current data commons.
Date:
23 June 2022
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Introduction to Terra: A scalable platform for biomedical research
Terra is a cloud-native platform for biomedical researchers to access data, run analysis tools, and collaborate. This interactive workshop on Terra will teach you the skills you need to know to start working and collaborating securely in Terra. Specifically, you’ll learn about the architecture of Terra as it relates to cloud-based data sets, tools, and…
Date:
12 April 2022 - 13 April 2022
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