Calling the AWS Java SDK from a static Rhino JavaScript context — When working with HL7 v2 and web services such as Amazon SQS, I’d typically reach for Serverless HAPI as a lightweight interfacing option. …

Health Level 7 (HL7) Version 2 was developed in the late 80s and for many years was the most popular data exchange standard in the world. The standard was more recently superseded by the HL7 Fast Healthcare Interoperability Resources (FHIR) but the adoption rate has been slower than expected so…

In bioinformatics, computational pipelines developed as a bunch of shell scripts are ubiquitous. Although modern applications like Apache Airflow and cloud services such as Prefect offer more elegant, feature-rich solutions, the reality is that re-implementing an entire shell-scripted pipeline on a completely new platform is often too big a step…

Streaming tar and zip file downloads on-the-fly — One of my first challenges for Weill Cornell Medicine was to develop a file distribution portal that allowed genomic sequencing labs to distribute big data files to collaborators over the web. …

In this post I outline my journey creating a dynamic NFT on the Ethereum blockchain with IPFS and discuss the possible use cases for scientific data. I do not cover algorithmic generation of static images (you should read Albert Sanchez Lafuente’s neat step-by-step for that) but instead demonstrate how I…

Scientific data that demands the flexibility of spreadsheets with the integrity of databases — Back in 2018 I was tasked with implementing a Laboratory Information Management System (LIMS) for a genomic sequencing core facility at Weill Cornell Medicine. A LIMS is essentially a database with a few key features: Dynamic Tables: sequencing is a bleeding edge field and it’s not unusual to modify columns…