Recent Posts
Build and deploy an NCBI GEO metadata fetch API
Build, containerize, and then deploy a simple serverless web API
that returns json-formated metadata for any GEO accession.
Building R Binary Packages for Linux
Background One of the challenges of producing a performant build environment for linux, such as what might be used to have developers test software in identical environments, is the need to compile R packages from source on linux. If, however, one had an identical set of installed libraries, kernel version, compiler, etc., we could use binary packages in linux as well. Docker provides just such a shareable and identical environment for linux.
Experimenting with Github Actions
GitHub actions allow flexible and potentially complicated
actions that comprise workflows that respond to events on Github. Continuous integration, messaging Slack, greeting new contributors, deploying applications, and many other templates are ready for customization and integration into any repo.
OmicIDX on BigQuery
Availability: This ipython notebook is available at https://github.com/seandavi/omicidx_examples.
OmicIDX is a project to democratize access to omics metadata. As the sizes of omics repositories have grown into the millions of available samples, thinking of the metadata themselves as Big Data seems reasonable. Additionally, by making the metadata more fit-for-use for text mining, natural language processing, ingestion into machine learning or search engines, OmicIDX aims to facilitate augmentation and analysis of these metadata.
Using directory-local variables to customize the emacs project experience
I use emacs for nearly all my editing and interactive analysis. As one typically does, more than one project is the norm, not the exception. Discovering projectile for project-specific buffers and controls, combined with helm for very fast, fuzzy completions, makes emacs a very convenient and efficient environment for most task.
One challenge I ran into was the need to have multiple interactive python buffers, typically one per project. However, the out-of-the-box behavior of python-mode is to have only one python interactive buffer named “Python”.
