Matt Ralston
M.Sc. Bioinfo + 5 years industry exp. - - - Currently writing a DNA sequence alignment, quasi-mapper, and graph algorithm and manuscript (for bioRxiv). I play math rock on my guitar, I write open-source software on GitHub, I pay my bills in the DE-NJ-PA tri-state area near Delco, and I'm launching a DE-based LLC for Univ. of Delaware and local NGS sequencing projects.
- Newark DE
- University of Delaware
- Website
- Google Scholar
- PubMed
- Github
- Stackoverflow
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Thoughts on ML deployments, containerized workflows, and notebooks.
6 minute read
Published:
This article hopes to bring the reader up to date (ca. 2017-2022) on modern cloud-native and scalable solutions for data science and natural science research application stacks using the Docker container standard for container specification (vs Singularity, Podman, or containerd containers that are equally valid). First I will provide a brief description of the goal of Docker containers. Next I’ll touch on the kubernetes architecture for distributed data processing and application service management. Finally, I’ll describe code repository, container registries, and Markdown/Rmarkdown/LaTeX documentation as it purtains to a service’s lifespan w.r.t. notebooks and documentation of custom services and their orchestration.
Benchmarking Aligners
1 minute read
Published:
Short-read aligners make up the core of modern bioinformatics program technologies. The aligners are responsible for mapping (rather than aligning) short reads (typically produced by Illumina sequencers) to their most likely originating loci with gapped and ungapped, genomic and transcriptomic methods. For lists of both aligners and short-read mappers and their pros/cons, see the Wikipedia article.
Youth Falls In Night
less than 1 minute read
Published:
I came to life from two unknown trees, Roots tangled deep in mystery’s seas. Yet arms reached out, so strong, so kind, To plant me anew, a love redesigned.
Roots And Wings
less than 1 minute read
Published:
I came to life from two unknown trees, Roots tangled deep in mystery’s seas. Yet arms reached out, so strong, so kind, To plant me anew, a love redesigned.