elijahflowers

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/FL-Studio-SDK-CMake-Template

A CMake template for developing FL Studio plugins, using the C++ API

elijahflowers/Mubert-Text-to-Music

A simple notebook demonstrating prompt-based music generation via Mubert API

elijahflowers/riffusion-app

Stable diffusion for real-time music generation (web app)

elijahflowers/HolyC-for-Linux

run HolyC on Linux secularly

elijahflowers/stable-diffusion-webui

Stable Diffusion web UI

elijahflowers/i2pdbrowser

i2pd browser bundle

elijahflowers/MIDIApps

MIDI apps for Mac OS X: MIDI Monitor and SysEx Librarian.

elijahflowers/FluidX3D

The fastest and most memory efficient lattice Boltzmann CFD software, running on any GPU via OpenCL.

elijahflowers/FL-Studio-API-Stubs

Basic definitions for functions in the FL Studio Python API

elijahflowers/kinto

Mac-style shortcut keys for Linux & Windows.

elijahflowers/templeos-color

Installation and synchronization scripts for use with QEMU, along with all of Terry's supplemental material and options for theme customization

elijahflowers/pure-data

Pure Data - a free real-time computer music system

elijahflowers/Camomile

An audio plugin with Pure Data embedded that allows to load and to control patches

elijahflowers/x86-bare-metal-examples

Dozens of minimal operating systems to learn x86 system programming. Tested on Ubuntu 17.10 host in QEMU 2.10 and real hardware. Userland cheat at: https://github.com/************/linux-kernel-module-cheat#userland-assembly ARM baremetal setup at: https://github.com/************/linux-kernel-module-cheat#baremetal-setup

elijahflowers/sound-usb-kernel-module

Latest driver development code for Focusrite Scarlett on Linux

elijahflowers/roadmap_v1.0

elijahflowers/pascalscript

pascalscript

elijahflowers/wine-mono

elijahflowers/holy-shoot

A shoot 'em up game for TempleOS written in HolyC

elijahflowers/onedrive

#1 Free OneDrive Client for Linux

elijahflowers/wav-editing-in-c

Process wave files

elijahflowers/Kitsune

Next-generation paysite scraper.

elijahflowers/Kemono2

HTML/Python frontend designed for paysite leaking.

elijahflowers/focusrite-scarlett-backports

Backports of Focusrite Scarlett gen2/gen3 driver to the older linux kernel

elijahflowers/fsearch

A fast file search utility for Unix-like systems based on GTK+3

elijahflowers/tracktion_engine

Tracktion Engine module

elijahflowers/JUCE

JUCE is an open-source cross-platform C++ application framework for desktop and mobile applications, including VST, VST3, AU, AUv3, RTAS and AAX audio plug-ins.

elijahflowers/jack2

jack2 codebase

elijahflowers/jackaudio.github.com

jackaudio's Website and Wiki hosted at github

elijahflowers/jack1

jack1 codebase