djeikyb's Stars
getify/You-Dont-Know-JS
A book series on JavaScript. @YDKJS on twitter.
swc-project/swc
Rust-based platform for the Web
ibraheemdev/modern-unix
A collection of modern/faster/saner alternatives to common unix commands.
Textualize/textual
The lean application framework for Python. Build sophisticated user interfaces with a simple Python API. Run your apps in the terminal and a web browser.
sharkdp/hyperfine
A command-line benchmarking tool
typesense/typesense
Open Source alternative to Algolia + Pinecone and an Easier-to-Use alternative to ElasticSearch ⚡ 🔍 ✨ Fast, typo tolerant, in-memory fuzzy Search Engine for building delightful search experiences
basarat/typescript-book
:books: The definitive guide to TypeScript and possibly the best TypeScript book :book:. Free and Open Source 🌹
sindresorhus/pure
Pretty, minimal and fast ZSH prompt
Shawn-Shan/fawkes
Fawkes, privacy preserving tool against facial recognition systems. More info at https://sandlab.cs.uchicago.edu/fawkes
lotabout/skim
Fuzzy Finder in rust!
mergestat/mergestat-lite
Query git repositories with SQL. Generate reports, perform status checks, analyze codebases. 🔍 📊
NAalytics/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.
einaregilsson/Redirector
Browser extension (Firefox, Chrome, Opera, Edge) to redirect urls based on regex patterns, like a client side mod_rewrite.
robinsloan/perfect-edition
A lightweight, responsive web e-book template
lukasmartinelli/pgfutter
Import CSV and JSON into PostgreSQL the easy way
graceavery/tamagotchiTemp
everestpipkin/image-scrubber
A friendly browser-based tool for anonymizing photographs taken at protests
ozh/ascii-tables
⚡ Quickly format table in ASCII. Great for code comments, or Github Markdown!
KentBeck/TestDesiderata
Optimize the value of your tests by choosing how to tradeoff among various valuable properties.
bradleytaunt/ET-Jekyll
A minimal Jekyll theme inspired by Tufte CSS
nathanielw/party-ify
Website that turns any image into party-parrot style animated GIF
nenoNaninu/Tapper
A Tool Transpiling C# Type into TypeScript Type. (Support JSON & MessagePack Serialization)
ttscoff/niftymenu
abock/dotnet-ecoji
😻 Encode and decode data using emoji in .NET❣️ Like base64, except base1024, and uses an emoji alphabet. 🎉
mamift/LinqToXsdCore
LinqToXsd ported to .NET Core (targets .NET Standard 2 for generated code and .NET Core 3.1, .NET 5+ for the code generator CLI tool).
morphatic/v-stripe-elements
A Vue component that styles Stripe Elements to match the Vuetify UI library.
claui/wishfish
SSH wrapper for macOS that binds to a specific network interface, e. g. Wi-Fi
justinribeiro/lite-tiktok
A web component that lazy loads TikTok embeds. Currently experimental and a work in progress.
tchapeaux/alcazar-clone
An open-source clone of Alcazar (www.theincrediblecompany.com/try-alcazar)
littlefires/littlefires.github.io
a thousand little fires is a space to see and share what we create while reconciling with self-isolation.