Pinned Repositories
3D-linux
A 3d Linux desktop environment (and game engine)
Aiwnios
A HolyC Compiler/Runtime for 64bit ARM/X86
android-4.3
android 4.3 source code, ISO package http://pan.baidu.com/s/1kT7hgAr
android_fde_bruteforce
Scripts to bruteforce Android's Full Disk Encryption off the device
ARMaHYDAN
A tool for manipulating 'optional' bits in ARM processor instructions.
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.
BootGenie
Patches for Boot Sector Games for Cheating
notepad-plus-plus
Notepad++ official repository
syncthing
Open Source Continuous File Synchronization
templenes
NES Emulator for TempleOS
elijahflowers's Repositories
elijahflowers/syncthing
Open Source Continuous File Synchronization
elijahflowers/3D-linux
A 3d Linux desktop environment (and game engine)
elijahflowers/Aiwnios
A HolyC Compiler/Runtime for 64bit ARM/X86
elijahflowers/audio-Sample-Data-testing
Collection of demos testing out features of the threejs javascript librray, as well as project protoype examples, modules, and more
elijahflowers/blankos
Simple i386 hobby operating system
elijahflowers/CPU-X
CPU-X is a Free software that gathers information on CPU, motherboard and more
elijahflowers/cpython
The Python programming language
elijahflowers/dawproject
Open exchange format for DAWs
elijahflowers/developer-roadmap
Interactive roadmaps, guides and other educational content to help developers grow in their careers.
elijahflowers/FL-Studio-SDK-CMake-Template
A CMake template for developing FL Studio plugins, using the C++ API
elijahflowers/FL_Studio_Piano_Roll_Scripts
Wisteria Motif's FL Studio Piano Roll Scrips
elijahflowers/ghidra-ida-pro-alt
Ghidra is a software reverse engineering (SRE) framework
elijahflowers/HolyC-for-Linux
run HolyC on Linux secularly
elijahflowers/i2pdbrowser
i2pd browser bundle
elijahflowers/image-downloader
A browser extension for Google Chrome, Microsoft Edge, and Brave that lets you download images from the web more easily.
elijahflowers/kanji-data-media
Japanese language data on kanji, radicals, media files, fonts and related resources from Kanji alive
elijahflowers/macports-base
The MacPorts command-line client
elijahflowers/macports-ports
The MacPorts ports tree
elijahflowers/MIDIApps
MIDI apps for Mac OS X: MIDI Monitor and SysEx Librarian.
elijahflowers/Mubert-Text-to-Music
A simple notebook demonstrating prompt-based music generation via Mubert API
elijahflowers/onlinegriddaw
GridSound (0.42.0) wants to be an open source online digital audio workstation following the new WebAudio API 🎛🎹🎵✨ -- If you can, please sponsor us a little on our Patreon ❤️
elijahflowers/PlatformerMovement
SMB3 Inspired Controls & Movement Demo
elijahflowers/project-slippi
Project for building a replay/metadata infrastructure for Super Smash Bros Melee
elijahflowers/prvhash
PRVHASH - Pseudo-Random-Value Hash. Hash functions, PRNG with unlimited period, randomness extractor. (Codename Gradilac/Градилак)
elijahflowers/riffusion
Stable diffusion for real-time music generation
elijahflowers/riffusion-app
Stable diffusion for real-time music generation (web app)
elijahflowers/shutter-encoder
A professional video compression tool accessible to all, mostly based on FFmpeg.
elijahflowers/stable-diffusion-webui
Stable Diffusion web UI
elijahflowers/wiringbits.github.io
The wiringbits website and blog
elijahflowers/ZealOS
The Zeal Operating System is a modernized fork of the 64-bit Temple Operating System, TempleOS.