Stephan Grein

NeuGen. NeuGen is made for generation of dendritic and axonal morphology of realistic neurons and networks in 3D

sam3. The repository provides code for running inference and finetuning with the Meta Segment Anything Model 3 (SAM 3), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

ShinyCell. Shiny Interactive Web Apps for Single-Cell Data

kubernetes. Production-Grade Container Scheduling and Management

containerd. An open and reliable container runtime

PEtab.jl. Create and fit parameter-estimation problems for ODE and SciML models in Julia, leveraging the Julia SciML ecosystem.

pyodide. Pyodide is a Python distribution for the browser and Node.js based on WebAssembly

theMLbook. The Python code to reproduce the illustrations from The Hundred-Page Machine Learning Book.

bump-my-version. A small command line tool to simplify releasing software by updating all version strings in your source code by the correct increment and optionally commit and tag the changes.

cursor.

julia_notebooks. Julia Jupyter/Colab Notebooks

cellranger. 10x Genomics Single Cell Analysis

asciichart. Nice-looking lightweight console ASCII line charts ╭┈╯ for NodeJS, browsers and terminal, no dependencies

termplotlib. :chart_with_upwards_trend: Plotting on the command line

JuMP.jl. Modeling language for Mathematical Optimization (linear, mixed-integer, conic, semidefinite, nonlinear)

vue-plotly. 📈 vue wrapper for plotly.js

protege. Protege Desktop

SDE-Identifiability. Supplementary material for the preprint "Identifiability analysis for stochastic differential equation models in systems biology" available on bioRxiv.

desktop. Mattermost Desktop application for Windows, Mac and Linux

free-programming-books. :books: Freely available programming books

ansible-lint. ansible-lint checks playbooks for practices and behavior that could potentially be improved and can fix some of the most common ones for you

vim-fugitive. fugitive.vim: A Git wrapper so awesome, it should be illegal

VueWordCloud. Generates a cloud out of the words.

nativefier. Make any web page a desktop application

MetaDataFormat. HTML

fiddy. Finite difference methods.

py-spy. Sampling profiler for Python programs

ts2gas. A function that transpiles TypeScript to Google Apps Script.

clasp. 🔗 Command Line Apps Script Projects

endoflife.date. Informative site with EoL dates of everything

Signal-Android. A private messenger for Android.

drawio-desktop. Official electron build of draw.io

design-resources-for-developers. Curated list of design and UI resources from stock photos, web templates, CSS frameworks, UI libraries, tools and much more

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

tech-interview-handbook. Curated coding interview preparation materials for busy software engineers

public-apis. A collective list of free APIs

build-your-own-x. Master programming by recreating your favorite technologies from scratch.

developer-roadmap. Interactive roadmaps, guides and other educational content to help developers grow in their careers.

python2jupyter. Convert from Python script to Jupyter notebook and vice versa

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.

book. The Rust Programming Language

download-artifact. TypeScript

tornadofx. Lightweight JavaFX Framework for Kotlin

javafx-gradle-plugin. Gradle plugin that makes it easy to work with JavaFX 11+

fonticon. 💙 Create beautiful favicons with ease.

neuromorpho. Making use of the REST API (NeuroMorpho.org v7) to query the database

homebrew-ug4. Ruby

docker4ug4.

from-java-to-kotlin. From Java to Kotlin Cheat Sheet

ConnectionViewer. A simple program to display matrix and vector data in scientific computing.

awesome-kotlin. A curated list of awesome Kotlin related stuff Inspired by awesome-java.

gradle-bintray-plugin. Groovy

valetudo. Valetudo RE - experimental vacuum software, cloud free

dockerfiles. Dockerfile

Neuro-VISOR. A research tool based in virtual reality. Produced by the Center for Computational Mathematics and Modeling at Temple University

BenchmarkDotNet. Powerful .NET library for benchmarking

tigervnc. High performance, multi-platform VNC client and server

meshlab. The open source mesh processing system

travis-ci. Free continuous integration platform for GitHub projects.

javalin. A simple and modern Java and Kotlin web framework

spark. A simple expressive web framework for java. Spark has a kotlin DSL https://github.com/perwendel/spark-kotlin

semver. Semantic Versioning Specification

KdTree. A fast, generic, multi-dimensional Binary Search Tree written in C#

eclipse-ui-theme. Dark UI Theme for Eclipse 4+

eclipse-color-theme. Color themes for Eclipse

awesome-vim-colorschemes. Collection of awesome color schemes for Neo/vim, merged for quick use.

gitpod. The developer platform for on-demand cloud development environments to create software faster and more securely.

vimium. The hacker's browser.

CppCoreGuidelines. The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++

gitinfo2. CTAN - gitinfo2.sty: Use git repository metadata in LaTeX documents

VUGShell. API for accessing precompiled UGShell distribution (https://github.com/UG4/ugcore) for VRL plugins and Java projects

todonotes. The package lets the user mark things to do later, in a simple and and visually appealing way.

neuro_collection. UG4 plugin for unified neuro-related functionality

ruby. The Ruby Programming Language

UnityNonNull. [NonNull] attribute to fields and classes in Unity

activizdotnet. Activiz.NET-7.1.1 a .NET wrapper for VTK 7.1.1

pcl. Point Cloud Library (PCL)

vscode. Visual Studio Code

activizdotnet. Periodically updated mirror of git://public.kitware.com/activizdotnet.git

Font-Awesome. The iconic SVG, font, and CSS toolkit

docs. Source repo for Docker's Documentation

gcc-cmake. Docker container build on top off the official gcc image including cmake

sol2. Sol3 (sol2 v3.0) - a C++ <-> Lua API wrapper with advanced features and top notch performance - is here, and it's great! Documentation:

RxJava. RxJava – Reactive Extensions for the JVM – a library for composing asynchronous and event-based programs using observable sequences for the Java VM.

bacon.js. Functional reactive programming library for TypeScript and JavaScript

en.javascript.info. Modern JavaScript Tutorial

progit2. Pro Git 2nd Edition

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

BurstImageProcessing. fast parallel image processing on the CPU, using Unity C# jobs and Burst compilation

EntityComponentSystemSamples. C#

magicka.vim. The Magicka colorscheme for Vim

tinyobjloader. Tiny but powerful single file wavefront obj loader

SpaceShooterECS. The ECS project originally developed with Intel for GDC 2018

job-system-cookbook. this is a guide to the Unity job system circa 2019

tool_tetgen. Tetgen generates delaunay tetrahedrizations. This mirror exists to simplify installation. Please have a look at www.tetgen.org

plugin_ProMesh. Interface and extensions to the meshing routines provided by ugcore/lib_grid.

MS-DOS. The original sources of MS-DOS 1.25, 2.0, and 4.0 for reference purposes

cookie-banner. JavaScript based cookie-info banner for complying with EU cookie law

Proton. Compatibility tool for Steam Play based on Wine and additional components

Cirq. Python framework for creating, editing, and running Noisy Intermediate-Scale Quantum (NISQ) circuits.

VTK. Mirror of Visualization Toolkit repository

quickhull. Header-only single-class implementation of Quickhull algorithm for convex hulls finding in arbitrary dimension (>1) space.

qhull. Qhull development for www.qhull.org -- Qhull 2020.2 (8.1-alpha1) at https://github.com/qhull/qhull/wiki

UnityCsReference. Unity C# reference source code.

thrust. [ARCHIVED] The C++ parallel algorithms library. See https://github.com/NVIDIA/cccl

tudev.github.io. A previous website of TUDev, Temple University's hacker organization.

ansible. Ansible is a radically simple IT automation platform that makes your applications and systems easier to deploy and maintain. Automate everything from code deployment to network configuration to cloud management, in a language that approaches plain English, using SSH, with no agents to install on remote systems. https://docs.ansible.com.

Vintage. Vintage mode adds a vi style command mode to Sublime Text 2

android-samples. Samples demonstrating how to use Maps SDK for Android

regexp.old. Henry Spencer's old regular expression library, also known as the book regex library, circa 1986.

gitignore. A collection of useful .gitignore templates

macbookpro-2015-config. My personal Gentoo config for MacBook Pro Retina 2015 13"

VRL-NeuroBox-Plugin. VRL-NeuroBox-Plugin is the plugin for detailed simulations in Neuroscience.

VRL-NeuGen-Plugin. The NeuGen VRL-Studio Plugin

topo-ff. Parametrize a LAMMPS data file with a CHARMM force field

ReScience. The ReScience journal. Reproducible Science is Good. Replicated Science is better.

rescience.github.io. ReScience website sources

r-source. Read-only mirror of R source code from https://svn.r-project.org/R/, updated hourly. See the build instructions on the wiki page.

che. Kubernetes based Cloud Development Environments for Enterprise Teams

Trainable_Segmentation. Fiji library to perform image segmentation based on the Weka learning schemes

holy-build-box. System for building cross-distribution Linux binaries

VRL-Neurolucida-Project. VRL-Neurolucida-Project for VRL-Studio (Frontend)

app_Neurolucida. Application for the Neurolucida ug4 Plugin (Backend)

neurobox-packages. Neurobox packages for UG4

plugin_Neurolucida. Neurolucida ug4 plugin (Backend)

lua-table-spec-proposal. Specification Proposal for Lua-Tables

OpenRA. Open Source real-time strategy game engine for early Westwood games such as Command & Conquer: Red Alert written in C# using SDL and OpenGL. Runs on Windows, Linux, *BSD and Mac OS X.

cpp-netlib. The C++ Network Library Project -- cross-platform, standards compliant networking library.

imageio-ext. Additional plugins and extension for the standard Java ImageIO library

reveal.js. The HTML Presentation Framework

mopidy. Mopidy is an extensible music server written in Python

jburkardt-cpp. Git Mirror of John Burkardt's great collection of C++ Software

jburkardt-m. Git Mirror of John Burkardt's great collection of MATLAB Software

jburkardt-c. Git Mirror of John Burkardt's great collection of C Software

package_control_channel. Default channel file for Package Control. Follow the directions at:

ProMesh. Grid generation for scientific computations

LaTeX-draftwatermark. The "draftwatermark" package extends LaTeX providing a means to add a textual, light gray watermark on every page or on the first page of a document. Typical usage may consist in writing words such as "DRAFT" or "CONFIDENTIAL" across document pages. The package may remind in some sense "draftcopy" by Dr. Juergen Vollmer, but its implementation is much lighter (as the reduced code footprint shows) and does not rely on postscript specials, making the package fully compatible with pdfLaTeX. The package depends on package "everypage" by the same author.

matlab-prettifier. A LaTeX2e package for typesetting Matlab code as it appears in the Matlab editor.

travis-api. The Travis CI API

certbot. Certbot is EFF's tool to obtain certs from Let's Encrypt and (optionally) auto-enable HTTPS on your server. It can also act as a client for any other CA that uses the ACME protocol.

frege. Frege is a Haskell for the JVM. It brings purely functional programing to the Java platform.

sphinx. The Sphinx documentation generator

external_BoostForUG4. C++

ug4-packages. Package list for ughub.

plugin_SmallStrainMechanics. Plugin implementing discretizations for small strain elasticity problems.

plugin_ConvectionDiffusion. Plugin implementing fe-/fv-discretizations for convection-diffusion problems.

ughub. UG4's package manager. Please use ughub to install all the other packages available in the UG4 group.

ug. UG Finite Element Software

pbctools. The VMD PBC tools are Tcl scripts to be used with the VMD software, that allow to handle periodic boundary conditions.

tclmpi. TclMPI - MPI Bindings for Tcl

topotools. VMD plugin for manipulating topology information

lammps. Public development project of the LAMMPS MD software package

mpitutorial. MPI programming lessons in C and executable code examples

mdanalysis. MDAnalysis is a Python library to analyze molecular dynamics simulations.

vim-instant-markdown. Instant Markdown previews from Vim

JCSG. Java implementation of BSP based CSG (Constructive Solid Geometry)

lanterna. Java library for creating text-based GUIs

VRL-Zoom. VRL zoom plugin

leathers. :rocket: Warning suppression library (C++)

hunter. CMake

cppbestpractices. Collaborative Collection of C++ Best Practices. This online resource is part of Jason Turner's collection of C++ Best Practices resources. See README.md for more information.

kdtree2. A kd-tree implementation in C++ (and Fortran) by Matthew B. Kennel

VRL-Hodgkin-Huxley-Plugin. Java

VRL_PE_NEURON. Java

gradle-versioneye-plugin. Plugin for Gradle to update your project's dependencies status on www.versioneye.com

cppcheck. static analysis of C/C++ code

jenkins. Jenkins automation server

pmd. An extensible multilanguage static code analyzer.

org.neuroml.model. NeuroML v2 Java API

mopidy-musicbox-webclient. Web Client for Mopidy Music Server and the Pi MusicBox

pimusicbox. An image (SD-card) to turn the Raspberry Pi into an easy to use MusicBox with Spotify playback and AirTunes streaming

ninja. a small build system with a focus on speed

java3d-core. Fork of the javax.media.j3d package

VMM. Multimarkdown Editor for VRL-Studio

uBlock. uBlock: a fast, lightweight, and lean blocker for Chrome, Firefox, and Safari.

mojo. :sparkles: Mojolicious - Perl real-time web framework

Dancer2. Perl Dancer Next Generation (rewrite of Perl Dancer)

JFXScad. JavaFX 3D CSG IDE

pyspotify. Python bindings for libspotify (no longer working as of May 2022)

piano-stairs. Arduino

piglow. Python library & examples for the Pimoroni PiGlow

documentation. The official documentation for Raspberry Pi computers and microcontrollers

sonic-pi. Code. Music. Live.

coveralls-gradle-plugin. 👨‍🔧 gradle plugin for coveralls

circos. Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

cdto. Finder Toolbar app to open the current directory in the Terminal

macvim. Vim - the text editor - for Mac OS X

svg3d. Add third dimension to SVG pictures, declare and manipulate 3d declared SVG.

ola. The Open Lighting Architecture - The Travel Adaptor for the Lighting Industry

rapidSTORM. rapidSTORM open-source localization microscopy software

vrapper. Vim-like editing in Eclipse

openmm. OpenMM is a toolkit for molecular simulation using high performance GPU code.

android-ffmpeg. a system for building custom ffmpeg binaries for Android

VWorkflows. Flow Visualization Library for JavaFX and VRL-Studio

VRL-Update-Creator. Simplifies VRL-Studio update deployment (experimental)

VRL-Studio. Innovative IDE based on VRL (Visual Reflection Library)

git-punchcard-plot. a tool to visualize the time distribution of commits

cpanminus. cpanminus - get, unpack, build and install modules from CPAN

Gitalist. A modern git web viewer

Gource. software version control visualization