Keiichi Watanabe

nanochat. The best ChatGPT that $100 can buy.

kind2. Multi-engine SMT-based automatic model checker for safety properties of Lustre programs

cline. Autonomous coding agent as an SDK, IDE extension, or CLI assistant.

hyperlight. Hyperlight is a lightweight Virtual Machine Manager (VMM) designed to be embedded within applications. It enables safe execution of untrusted code within micro virtual machines with very low latency and minimal overhead.

openvmm. Home of OpenVMM and OpenHCL

Awesome-Rust-Checker. A curated list of awesome Rust checkers

android-cuttlefish. Cuttlefish host support debian package.

iip. iip: an integratable TCP/IP stack

zpoline. system call hook for Linux

binary-hacks-rebooted. 『Binary Hacks Rebooted』のサポートリポジトリ

alioth. Experimental Type-2 hypervisor, written from scratch in Rust, runs on Linux and macOS.

depth-of-field. Depth of field simulator

gimli. A library for reading and writing the DWARF debugging format

gem5. The official repository for the gem5 computer-system architecture simulator.

GNews. A Happy and lightweight Python Package that Provides an API to search for articles on Google News and returns a JSON response.

llm.c. LLM training in simple, raw C/CUDA

user-tools. Community contributed tools

prusti-dev. A static verifier for Rust, based on the Viper verification infrastructure.

akari. VMM-based macOS Native Container Runtime

monoio. Rust async runtime based on io-uring.

bpftop. bpftop provides a dynamic real-time view of running eBPF programs. It displays the average runtime, events per second, and estimated total CPU % for each program.

bpftrace. High-level tracing language for Linux

erg. A statically typed language compatible with Python

gprof2dot. Converts profiling output to a dot graph.

ext2-parser. Navigating the ext2-fs data-structures

glibc. Unofficial mirror of sourceware glibc repository.

e2fsprogs. Ext2/3/4 file system utilities

hacktricks. Welcome to the page where you will find each trick/technique/whatever I have learnt in CTFs, real life apps, and reading researches and news.

pprof. pprof is a tool for visualization and analysis of profiling data

mise. dev tools, env vars, task runner

fuse-overlayfs. FUSE implementation for overlayfs

wasker. WebAssembly AoT compiler for your favorite Operating System

mewz. A unikernel designed specifically for running Wasm applications and compatible with WASI

flamescope. FlameScope is a visualization tool for exploring different time ranges as Flame Graphs.

hotspot. The Linux perf GUI for performance analysis.

ros3fs. ros3fs is a Linux FUSE adapter for AWS S3 and S3 compatible object storages.

spec. The Rust specification

zerocopy. Zerocopy makes zero-cost memory manipulation effortless. We write `unsafe` so you don’t have to.

libffi. A portable foreign-function interface library.

flamegraph. Easy flamegraphs for Rust projects and everything else, without Perl or pipes <3

FlameGraph. Stack trace visualizer

DuVisor. Rust

rust-p9. Rust

samply. Command-line sampling profiler for macOS, Linux, and Windows

hyperkernel. C

uberspark. Modular Provable Security on Commodity System and Application Software Stacks

trace-cruncher. Trace-Cruncher provides an interface between the existing instrumentation for collection and visualization of Linux kernel tracing data and the ecosystem of instruments for data analysis available in Python.

sedmario. NES Super Mario Bros level 1 written in pure sed!

MilvusVisor. A thin-hypervisor that runs on aarch64 CPUs.

sysbench. Scriptable database and system performance benchmark

operating-system-in-1000-lines. Writing an OS in 1,000 lines.

NOVA. NOVA Microhypervisor

octox. Unix-like OS in Rust inspired by xv6-riscv

mincs. MINCS - Mini Container Shellscript

sold. The sold linker

criu. Checkpoint/Restore tool

libtracecmd-rs. Rust wrapper of libtracecmd

comprehensive-rust. This is the Rust course used by the Android team at Google. It provides you the material to quickly teach Rust.

kvmsample. minivm based on kvm

sudo-rs. A memory safe implementation of sudo and su.

fq. jq for binary formats - tool, language and decoders for working with binary and text formats

ott. The Ott tool for writing definitions of programming languages and calculi

jendeley. jendeley is a JSON-based document organizing software.

virtio-video-spec. Staging area for the virtio-video specification

guider. The All-in-One System Profiling and Fault Detection Tool for Linux & Android

perf-tools. Performance analysis tools based on Linux perf_events (aka perf) and ftrace

userfaultfd-rs. Rust bindings for the Linux userfaultfd functionality

alphatensor. Python

cppfront. A personal experimental C++ Syntax 2 -> Syntax 1 compiler

dbgee. The zero-configuration debuggee for debuggers. Handy utility that allows you to launch CLI debuggers and VSCode debuggers from the debuggee side.

english-words. :memo: A text file containing 479k English words for all your dictionary/word-based projects e.g: auto-completion / autosuggestion

carbon-lang. Carbon Language's main repository: documents, design, implementation, and related tools. (NOTE: Carbon Language is experimental; see README)

piping-server. Infinitely transfer between every device over pure HTTP with pipes or browsers

salus. Risc-V hypervisor for TEE development

Vale. Compiler for the Vale programming language - http://vale.dev/

fluster. Testing framework for decoders conformance

deep-learning-from-scratch-2. 『ゼロから作る Deep Learning ❷』(O'Reilly Japan, 2018)

a-puzzle-a-day-solver. A-Puzzle-A-Day solver

itzmono-vite. A project template for Vite + TypeScript + React + Tailwind CSS + Blueprint apps :rocket:

pcimem. Simple program to read & write to a pci device from userspace

wazero. wazero: the zero dependency WebAssembly runtime for Go developers

system-design-primer. Learn how to design large-scale systems. Prep for the system design interview. Includes Anki flashcards.

kani. Kani Rust Verifier

cargo-ebuild. [MIRROR] cargo extension that can generate ebuilds using the in-tree eclasses

upx. UPX - the Ultimate Packer for eXecutables

case-studies. Analysis of various tricky Rust code

mdbook-linkcheck. A backend for `mdbook` which will check your links for you.

puroro. Rust Protocol buffer implementation

fuzzuf. Fuzzing Unification Framework

nc-vsock. netcat-like utility for AF_VSOCK

lisp-in-life. A Lisp interpreter implemented in Conway's Game of Life

argh. Rust derive-based argument parsing optimized for code size

getopts. The getopts repo maintained by the rust-lang project

io-uring. The `io_uring` library for Rust

Logout4Shell. Use Log4Shell vulnerability to vaccinate a victim server against Log4Shell

crosvm. The Chrome OS Virtual Machine Monitor - Mirror of https://chromium.googlesource.com/crosvm/crosvm/

libvfio-user. framework for emulating devices in userspace

cross. “Zero setup” cross compilation and “cross testing” of Rust crates

refined-github. :octocat: Browser extension that simplifies the GitHub interface and adds useful features

wsl-distrod. Distrod is a meta-distro for WSL 2 which installs Ubuntu, Arch, Debian, Gentoo, etc. with systemd in a minute for you. Distrod also has built-in auto-start feature on Windows startup and port forwarding ability.

kerla. A new operating system kernel with Linux binary compatibility written in Rust.

nsh. A command-line shell like fish, but POSIX compatible.

v86. x86 PC emulator and x86-to-wasm JIT, running in the browser

act. Run your GitHub Actions locally 🚀

actionlint. :octocat: Static checker for GitHub Actions workflow files

magit-delta. Use delta (https://github.com/dandavison/delta) when viewing diffs in Magit

delta. A syntax-highlighting pager for git, diff, grep, rg --json, and blame output

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.

loom. Concurrency permutation testing tool for Rust.

counterexamples. Counterexamples in Type Systems

digital_video_introduction. A hands-on introduction to video technology: image, video, codec (av1, vp9, h265) and more (ffmpeg encoding). Translations: 🇺🇸 🇨🇳 🇯🇵 🇮🇹 🇰🇷 🇷🇺 🇧🇷 🇪🇸

mouse-dictionary. 📘Super fast browser dictionary

linux. Adding support for the Rust language to the Linux kernel.

watchexec. Executes commands in response to file modifications

oreboot. oreboot is a fork of coreboot, with C removed, written in Rust.

deskreen. Deskreen turns any device with a web browser into a secondary screen for your computer. ⭐️ Star to support our work!

dpdk. Data Plane Development Kit

vhost. Rust

cosmopolitan. build-once run-anywhere c library

rust-search-extension. 🦀 The ultimate search extension for Rust

cloud-hypervisor. A Virtual Machine Monitor for modern Cloud workloads. Features include CPU, memory and device hotplug, support for running Windows and Linux guests, device offload with vhost-user and a minimal compact footprint. Written in Rust with a strong focus on security.

gron. Make JSON greppable!

mold. mold: A Modern Linker 🦠

just. 🤖 Just a command runner

engineer-vocabulary-list. Engineer Vocabulary List in Japanese/English

gdbstub. An ergonomic, featureful, and easy-to-integrate implementation of the GDB Remote Serial Protocol in Rust (with no-compromises #![no_std] support)

quickjs. Public repository of the QuickJS Javascript Engine.

rust-verification-tools. RVT is a collection of tools/libraries to support both static and dynamic verification of Rust programs.

oak. Meaningful control of data in distributed systems.

liburing. Library providing helpers for the Linux kernel io_uring support

fio. Flexible I/O Tester

wasmserve. An HTTP server for testing Wasm

gotenksfs. A file system on top of your file system

quine. Quines

smallfile. distributed metadata-intensive workload generator for POSIX-like filesystems

icfpc2020. Rust

shell-words. Rust

deno. A modern runtime for JavaScript and TypeScript.

rvemu. RISC-V emulator for CLI and Web written in Rust with WebAssembly. It supports xv6 and Linux (ongoing).

awer. Another World Engine in Rust

WSL2-Linux-Kernel. The source for the Linux kernel used in Windows Subsystem for Linux 2 (WSL2)

v4l2r. Rust bindings for V4L2

padding-detector. Detect implicit paddings in C structs and unions

syn. Parser for Rust source code

YUView. The Free and Open Source Cross Platform YUV Viewer with an advanced analytics toolset

Operating-Systems-Three-Easy-Pieces-in-japanese.

wally. The Flash(ing tool)

bottlerocket. An operating system designed for hosting containers

covid19. 東京都 新型コロナウイルス感染症対策サイト / Tokyo COVID-19 Task Force website

easy-scraper. Easy scraping library

rust-analyzer. A Rust compiler front-end for IDEs

verona. Research programming language for concurrent ownership

kvm-kernel-example. Examples for: Learning KVM - implement your own kernel

bcc. BCC - Tools for BPF-based Linux IO analysis, networking, monitoring, and more

resea. A microkernel-based hackable operating system.

guake. Drop-down terminal for GNOME

lucet. Lucet, the Sandboxing WebAssembly Compiler.

rustynes. 👾 An NES emulator by Rust and WebAssembly

vmmfuzzer. A hypervisor or virtual machine monitor (VMM) fuzzer

virtio-spec. OASIS Virtual I/O Device TC: Source code for the VIRTIO (Virtual I/O) Specification maintained by the OASIS Virtual I/O Device (VIRTIO) Technical Committee

patterns. A catalogue of Rust design patterns, anti-patterns and idioms

spacemacs. A community-driven Emacs distribution - The best editor is neither Emacs nor Vim, it's Emacs *and* Vim!

minigo. Minimum Go compiler

chibicc. A small C compiler

linux-kernel-module-rust. Framework for writing Linux kernel modules in safe Rust

rustwasm-prime. Rust

codesearch. Fast, indexed regexp search over large file trees

semantic. Parsing, analyzing, and comparing source code across many languages

structopt. Parse command line arguments by defining a struct.

klib. A standalone and lightweight C library

PySnooper. Never use print for debugging again

rustic. Rust development environment for Emacs

mlir. "Multi-Level Intermediate Representation" Compiler Infrastructure

MIRAI. Rust mid-level IR Abstract Interpreter

prog-edu-assistant. An easy system to create autograding tests in Jupyter Python notebook and deploy to cloud.

seL4. The seL4 microkernel

cc-rs. Rust library for build scripts to compile C/C++ code into a Rust library

assert_matches. Provides macro `assert_matches` for testing pattern matching

chainer-compiler. Experimental toolchain to compile and run Chainer models

MSEdge. Microsoft Edge

linux-insides-ja. Japanese version of linux-insides book

firecracker. Secure and fast microVMs for serverless computing.

rlundo. undo in any program that uses readline

fialyzer. [WIP] Faster Implementation of Dialyzer

pml. A ML-like programming language with type-based probabilistic behavior specification, developed as part of PFN summer internship 2018.

gdb-dashboard. Modular visual interface for GDB in Python

typed-egison. Haskell

BOLT. Binary Optimization and Layout Tool - A linux command-line utility used for optimizing performance of binaries

rust-raspberrypi-OS-tutorials. :books: Learn to write an embedded OS in Rust :crab:

inkwell. It's a New Kind of Wrapper for Exposing LLVM (Safely)

minigo. minigo🐥is a small Go compiler made from scratch. It can compile itself.

sevendayshpc. 一週間でなれる！スパコンプログラマ

bat. A cat(1) clone with wings.

hoice. An ICE-based predicate synthesizer for Horn clauses.

done. A fish-shell package to automatically receive notifications when long processes finish.

evcxr. Rust

elkdat. ELKDAT: easy linux kernel development and test tool

marinara. Pomodoro® time management assistant for Chrome

os-tutorial. How to create an OS from scratch

egison. The Egison Programming Language