Lukas Velikov

sweetgreen-rs. Rust

healthchecks. Open-source cron job and background task monitoring service, written in Python & Django

utils. Utility crates used in RustCrypto

audit-userspace. Linux audit userspace repository

memfd-rs. A pure-Rust library to work with Linux memfd

cargo-modules. Visualize/analyze a Rust crate's internal structure

saphyr. A set of crates dedicated to parsing YAML.

serde-saphyr. A strongly typed, comment-supporting YAML deserializer that deserializes YAML directly into your Rust types without constructing an intermediate tree of “abstract values.”

pkl. A configuration as code language with rich validation and tooling.

resolv-conf. The /etc/resolv.conf file parser in rust

advisory-db. Security advisory database for Rust crates published through crates.io

nixos-configuration. Much better than a .dotfiles repo

bpftrace. High-level tracing language for Linux

rust-landlock. A Rust library for the Linux Landlock sandboxing feature

cedar-spec. Definitional implementation of Cedar language and utilities for DRT

lean4. Lean 4 programming language and theorem prover

typst. A markup-based typesetting system that is powerful and easy to learn.

testcontainers-rs. A library for integration-testing against docker containers from within Rust.

resolv-rs. DNS resolution via glibc for rust

rayon. Rayon: A data parallelism library for Rust

bubblewrap. Low-level unprivileged sandboxing tool used by Flatpak and similar projects

Verify-jsmn. C

kani. Kani Rust Verifier

oxidd. Concurrent decision diagram framework written in Rust

ARMOR. C

rpm-rs. A pure rust library for working with RPM files.

cargo-generate-rpm. Cargo helper command to generate a binary RPM package

vault. A tool for secrets management, encryption as a service, and privileged access management

spiffe. The SPIFFE Project

cedar. Implementation of the Cedar Policy Language

srv-rs. Rust client for communicating with services located by DNS SRV records.

ProfileCreator. macOS app to create standard or customized configuration profiles.

rust-syslog. Send syslog messages from Rust

linux-pam. Linux PAM (Pluggable Authentication Modules for Linux) project

pam-rs. Simplified PAM module creation in Rust

cargo-deb. Make Debian packages directly from Rust/Cargo projects

adcs-rs. Active Directory Certificate Services (AD CS) protocol crates for Rust

tpm. Tmux Plugin Manager

tmux-resurrect. Persists tmux environment across system restarts.

buildah. A tool that facilitates building OCI images.

pcb. PCB tooling by Diode Computers, Inc.

rust-dnsclient. A simple and secure DNS client crate for Rust.

socket2. Advanced configuration options for sockets.

cargo-llvm-cov. Cargo subcommand to easily use LLVM source-based code coverage (-C instrument-coverage).

procfd. Linux lsof replacement to list open file descriptors for processes

iris. A neurosymbolic framework for vulnerability detection in code

obsidian-sort-and-permute-lines. Sort and Permute lines in whole file or selection.

gxhash. Unsafely fast hashing algorithm 📈

drawio. draw.io is a JavaScript, client-side editor for general diagramming.

SaneSideButtons. A macOS menu bar app that enables system-wide navigation functionality for side buttons on third-party mice.

flox. The Deterministic Foundation for your SDLC

slirp4netns. User-mode networking for unprivileged network namespaces

rootlesskit. Linux-native "fake root" for implementing rootless containers

pytest. The pytest framework makes it easy to write small tests, yet scales to support complex functional testing

serde-ignored. Find out about keys that are ignored when deserializing data

unsure. Unsure Calculator

viu. Terminal image viewer with native support for iTerm and Kitty

garnet. Garnet is a remote cache-store from Microsoft Research that offers strong performance (throughput and latency), scalability, storage, recovery, cluster sharding, key migration, and replication features. Garnet can work with existing Redis clients.

prost. PROST! a Protocol Buffers implementation for the Rust Language

regex. An implementation of regular expressions for Rust. This implementation uses finite automata and guarantees linear time matching on all inputs.

rust-prometheus. Prometheus instrumentation library for Rust applications

awesome-rive. An awesome list that curates Rive runtime examples, articles and tutorials, videos, resources and more!

lima. Linux virtual machines, with a focus on running containers

rust-refreshable. A simple wrapper around a value that changes over time

zotero. Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share your research sources.

elf-info. Inspect and dissect an ELF file with pretty formatting.

ocicrypt. Encryption libraries for Encrypted OCI Container images

rust-clippy. A bunch of lints to catch common mistakes and improve your Rust code. Book: https://doc.rust-lang.org/clippy/

sysstat. Performance monitoring tools for Linux

hyperfine. A command-line benchmarking tool

nix. Rust friendly bindings to *nix APIs

libc. Raw bindings to platform APIs for Rust

mold. mold: A Modern Linker 🦠

reanimator-strace. An strace fork compatible with DataSeries

strace. strace is a diagnostic, debugging and instructional userspace utility for Linux

toy-queue. A minimal blocking queue backed by a circular buffer

serde. Serialization framework for Rust

rust-base64. base64, in rust

uuid. Generate and parse UUIDs.

clap. A full featured, fast Command Line Argument Parser for Rust

rpmautospec. Automatically generate release values and changelog entries from git history in RPM spec files

rust-pretty-assertions. Overwrite `assert_eq!` with a drop-in replacement, adding a colorful diff.

quick-xml. Rust high performance xml reader and writer

opentitan. OpenTitan: Open source silicon root of trust

unit. Next Generation Visual Programming System

ouroboros. Easy self-referential struct generation for Rust.

prometheus. The Prometheus monitoring system and time series database.

patroni. A template for PostgreSQL High Availability with Etcd, Consul, ZooKeeper, or Kubernetes

pyo3. Rust bindings for the Python interpreter

indoc. Indented document literals for Rust

cryptography-rs. A collection of Rust crates in the cryptography space

rustc_codegen_cranelift. Cranelift based backend for rustc

wasmtime. A lightweight WebAssembly runtime that is fast, secure, and standards-compliant

aws-lc. AWS-LC is a general-purpose cryptographic library maintained by the AWS Cryptography team for AWS and their customers. It іs based on code from the Google BoringSSL project and the OpenSSL project.

formats. Cryptography-related format encoders/decoders: DER, PEM, PKCS, PKIX

thiserror. derive(Error) for struct and enum error types

evcxr. Rust

roslyn. The Roslyn .NET compiler provides C# and Visual Basic languages with rich code analysis APIs.

runtime. .NET is a cross-platform runtime for cloud, mobile, desktop, and IoT apps.

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

Catch2. A modern, C++-native, test framework for unit-tests, TDD and BDD - using C++14, C++17 and later (C++11 support is in v2.x branch, and C++03 on the Catch1.x branch)

json. JSON for Modern C++

asn1js. JavaScript generic ASN.1 parser

progenitor. An OpenAPI client generator

heimdal. Heimdal

cbindgen. A project for generating C bindings from Rust code

rcgen. Generate X.509 certificates, CSRs

krb5. mirror of MIT krb5 repository

docs.rs. crates.io documentation generator

fuser. Filesystem in Userspace (FUSE) for Rust

OsuBoost. An educational player piano bot for osu!mania

yasna.rs. ASN.1 library for Rust

rand. A Rust library for random number generation.

arc-swap. Support atomic operations on Arc itself

tracing. Application level tracing for Rust.

tower. async fn(Request) -> Result<Response, Error>

reqwest. An easy and powerful Rust HTTP Client

hyper. An HTTP library for Rust

tokio-rustls. Async TLS for the Tokio runtime

pemfile. Basic parser for PEM formatted keys and certificates

rust-atomics-and-locks. Code examples, data structures, and links from my book, Rust Atomics and Locks.

luminal. Inference at the speed of light.

hickory-dns. A Rust based DNS client, server, and resolver

x509-parser. X.509 parser written in pure Rust. Fast, zero-copy, safe.

rustls. A modern TLS library in Rust

webpki. WebPKI X.509 Certificate Validation in Rust

pki-types. Rust

terrors. ergonomic and precise error handling built atop type-level set arithmetic

aws-lc-rs. aws-lc-rs is a cryptographic library using AWS-LC for its cryptographic operations. The library strives to be API-compatible with the popular Rust library named ring.

orbstack. Fast, light, simple Docker containers & Linux machines

pip-chill. A more relaxed `pip freeze`

JniHelpers. Tools for writing great JNI code

abq. ABQ is a universal test runner that runs test suites in parallel. It’s the best tool for splitting test suites into parallel jobs locally or on CI

gradle2nix. Generate Nix expressions which build Gradle-based projects.

bcder. Handling of BER, CER, and DER encoded data in Rust.

reanimator-lttng. The orchestrator for Re-Animator LTTng, an LTTng fork designed for process re-animation

jwt-cpp. A header only library for creating and validating json web tokens in c++

leap.nvim. Neovim's answer to the mouse 🦘

music-keys. Send keystrokes to your computer with microphone pitch

reanimator-replayer. A tracing tool intended for extracting and replaying program I/O behavior

cotowali. A statically typed scripting language that transpile into POSIX sh

py-spy. Sampling profiler for Python programs

kernel-ml. Machine Learning Framework for Operating Systems - Brings ML to Linux kernel

eudyptula-boot. Boot a Linux kernel in a VM without a dedicated root filesystem.

movfuscator. The single instruction C compiler

elfcat. ELF visualizer. Generates HTML files from ELF binaries.

nushell. A new type of shell

distribution. Short, simple, direct scripts for creating ASCII graphical histograms in the terminal.

PySnooper. Never use print for debugging again

CrossHair. An analysis tool for Python that blurs the line between testing and type systems.

orbit. Experimental spaced repetition platform for exploring ideas in memory augmentation and programmable attention

heatwave-tpch. SQL scripts for HeatWave benchmarking

deep-daze. Simple command line tool for text to image generation using OpenAI's CLIP and Siren (Implicit neural representation network). Technique was originally created by https://twitter.com/advadnoun

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.

icecream. 🍦 Never use print() to debug again.

iotta-reanimator. Re-Animator is a Linux tool that can efficiently trace and replay system calls. It supports capturing all I/O-related and most other calls, including all arguments and data passed. Replay is designed to reproduce the original as faithfully as possible.

css-only-chat. A truly monstrous async web chat using no JS whatsoever on the frontend

nocode. The best way to write secure and reliable applications. Write nothing; deploy nowhere.

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SBUTextbook.github.io. HTML

pyaudio. http://people.csail.mit.edu/hubert/pyaudio/

data. Data and code behind the articles and graphics at FiveThirtyEight

data. An index of all open-source data

cadee. CADEE: Computer-Aided Directed Evolution of Enzymes

text-avatar. ionic - angular 2, 3 and 4.x text avatar custom directive

Validity91. Reverse engineering the Validity 138a:0091 fingerprint sensor (Dell XPS 15/13 2016-2017 9X50 and 9X60)

pytrends. Pseudo API for Google Trends

TinyTravelTracker. Private Android GPS tracker

paper_otp. One time pad message which can be decoded using only paper and a light source

pharos-linux. Allows remote printing from linux client to pharos uniprint printing system

Validity90. Reverse engineering of Validity/Synaptics 138a:0090, 138a:0094, 138a:0097, 06cb:0081, 06cb:009a fingerprint readers protocol

no-title-bar. Integrates maximized windows with the top panel

pt-voicebox. predictive text interface