psprings

bugsnag-release-action

client-go

code-concierge

This is a supplemental binary for a code-server environment which will automate fetching dependencies for a GitHub repo

devops-stack-sample

docker-grafeas

Repository to build Grafeas images from

docker-ipfs

Dockerized IPFS experimentation focused on private network and ipfs-cluster features.

grafeas

Artifact Metadata API

grafeas-cli

TODO: A CLI and API wrapper around the Grafeas API for use with local dev and CI/CD

kafcker

Collection of Docker resources for Kafka in a sandbox environment

switch

Short for "switchboard" -- used to proxy webhook requests through queues

psprings/docker-ipfs

Dockerized IPFS experimentation focused on private network and ipfs-cluster features.

psprings/bugsnag-release-action

psprings/docker-grafeas

Repository to build Grafeas images from

psprings/grafeas-cli

TODO: A CLI and API wrapper around the Grafeas API for use with local dev and CI/CD

psprings/client-go

psprings/ex-supply-chain

Reference DAML application demonstrating a supply chain use case.

psprings/kafcker

Collection of Docker resources for Kafka in a sandbox environment

psprings/s3-website-pr-action

🚀 Automatically deploy built PR bundles to an S3 static website 🚀

psprings/switch

Short for "switchboard" -- used to proxy webhook requests through queues

psprings/code-concierge

This is a supplemental binary for a code-server environment which will automate fetching dependencies for a GitHub repo

psprings/grafeas

Artifact Metadata API

psprings/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273

RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.

psprings/aws-es-kibana

AWS ElasticSearch Kibana Proxy

psprings/aws-labs

This tool is for use with AWS Training Labs. If you want to run through labs multiple times, or just hate all of the manual steps involved in initial setup, then try this out.

psprings/damlgen

Generate daml files from Go definitions

psprings/developer-website

Source code for the New Relic Developer Site.

psprings/drone-cicd

psprings/eks-workshop-sample-api-service-go

Sample Kubernetes service used in the EKS Workshop CI/CD CodePipeline module

psprings/first-order-model

This repository contains the source code for the paper First Order Motion Model for Image Animation

psprings/forfend

Cloud Compliance as Code with Open Policy Agent

psprings/go-daml

Library to interact with Go types/structs to generate DAML

psprings/iamlive

Generate a basic IAM policy from AWS client-side monitoring (CSM)

psprings/jenkins-pipeline-shared-library-example

Basic template example of a Jenkins Pipelines Shared Library that is tested using https://github.com/mkobit/jenkins-pipeline-shared-libraries-gradle-plugin

psprings/jenkins-scriptler-libs

This project is intended to overcome some of the limitations of the Jenkins API by implementing custom endpoints on a Jenkins server using the Scriptler plugin.

psprings/library

psprings/saml2aws

CLI tool which enables you to login and retrieve AWS temporary credentials using a SAML IDP

psprings/simple-go-server

A simple golang web server with basic logging, tracing, health check, graceful shutdown and zero dependencies

psprings/solc-js

Javascript bindings for the solidity compiler

psprings/sourcecred

a social algorithm for computing cred

psprings/website

Kubernetes website and documentation repo: