vladikoff

ArchiveRoom

🎮 GitHub ArchiveRoom - Explore your GitHub archive data in 3D!

chromeos-apk

☢️ Run Android Apps in Chrome OS OR Chrome in OS X, Linux and Windows.

grunt-devtools

🛠 Grunt Task Runner Extension for Chrome Developer Tools

InsideReCaptcha

Reverse-engineering the new “captchaless” ReCaptcha system...

netflix-1080p-firefox

🍿 Force 1080p Netflix playback in Firefox

playwright-ai

Command-line utility to generate LLM-based Playwright tests

PWAify

🖥 Brings Progressive Web App to your desktop.

send-to-google-glass

👓 Chrome Extension that let's you send text notes and images to Google Glass

node-geckodriver

Mozilla's Geckodriver for Node.js

vladikoff/chromeos-apk

☢️ Run Android Apps in Chrome OS OR Chrome in OS X, Linux and Windows.

vladikoff/netflix-1080p-firefox

🍿 Force 1080p Netflix playback in Firefox

vladikoff/PWAify

🖥 Brings Progressive Web App to your desktop.

vladikoff/playwright-ai

Command-line utility to generate LLM-based Playwright tests

vladikoff/fenix

Fenix is not your parent's Android browser.

vladikoff/Test

Test

vladikoff/experimenter

A web application for managing user experiments for Mozilla Firefox.

vladikoff/firefox-ios

Firefox for iOS

vladikoff/fxa-dev-launcher

fxa-dev-launcher

vladikoff/lock-rust-desktop-wise-box

vladikoff/stripe-node

Node.js library for the Stripe API.

vladikoff/android-components

A collection of Android libraries to build browsers or browser-like applications.

vladikoff/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.

vladikoff/bedrock

Making mozilla.org awesome, one pebble at a time

vladikoff/cannon-es

💣 A lightweight 3D physics engine written in JavaScript.

vladikoff/clap

A full featured, fast Command Line Argument Parser for Rust

vladikoff/content

The content behind MDN Web Docs

vladikoff/gpt-home

ChatGPT at home! Basically a better Google Nest Hub or Amazon Alexa home assistant. Built on the Raspberry Pi using the OpenAI API.

vladikoff/grcov

Rust tool to collect and aggregate code coverage data for multiple source files

vladikoff/home-assistant.io

:blue_book: Home Assistant User documentation

vladikoff/killedbygoogle

Part guillotine, part graveyard for Google's doomed apps, services, and hardware.

vladikoff/lit.dev

The Lit website

vladikoff/next.js

The React Framework

vladikoff/node-getobject

get.and.set.deep.objects.easily = true;

vladikoff/node-uap

Wrapper around ua-parser/uap-core and ua-parser/uap-ref-impl

vladikoff/project-rvs

vladikoff/puppeteer

Node.js API for Chrome

vladikoff/release-it

🚀 Automate versioning and package publishing

vladikoff/rustup

The Rust toolchain installer

vladikoff/update-notifier

Update notifier for crates on crates.io