Pinned Repositories
capsized-ludum-dare-54
CapSized: A Ludum Dare 54 Godot project
DeepDuBind
Convolutional neural network written in Tensorflow for genomic data
DeepNuc
Convolutional Neural Networks (CNN) for nucleotide sequences implemented in Tensorflow
DeepTaylorLayers
Deep Taylor Decomposition implemented in Tensorflow
DiffuMon
Basic Denoising Diffusion Probabilistic Model image generator implemented in PyTorch
LarryDuMarkdownResume
A resume made in markdown and easily converted to pdf, docx, and text (because I'm tired of using LaTeX)
OminousBeepingApp
Ominous Beeping App from Rick and Morty Season 4 created in Flutter.
PongRust
Pong written using Bevy ECS and Rust
simple_flutter_audio_recorder
A simple cross platform audio recording app for iOS and android made using Flutter
StarRust
Sidescrolling space shooter made from Rust and Bevy
LarsDu's Repositories
LarsDu/StarRust
Sidescrolling space shooter made from Rust and Bevy
LarsDu/capsized-ludum-dare-54
CapSized: A Ludum Dare 54 Godot project
LarsDu/PongRust
Pong written using Bevy ECS and Rust
LarsDu/LarryDuMarkdownResume
A resume made in markdown and easily converted to pdf, docx, and text (because I'm tired of using LaTeX)
LarsDu/dublog-examples
Code examples associated with posts on dublog.net
LarsDu/HugoFullStackTemplate
A template for a Hugo Static Site with deployment infrastructure on Google Cloud and Cloudflare written in Terraform.
LarsDu/EntropyGame
Game Created in 48 hours for Ludum Dare 50 (2022) using UnityEngine/C#
LarsDu/ray
Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a toolkit of libraries (Ray AIR) for accelerating ML workloads.
LarsDu/AllPythonPackageManagers
A listing of all python package managers
LarsDu/AMaze
A silly pygame based maze generation and pathfinding script.
LarsDu/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.
LarsDu/bevy
A refreshingly simple data-driven game engine built in Rust
LarsDu/bevy_animation_bug
Minimal working example for possible bug when using bevy gltf2.0 animation with keyboard input
LarsDu/bevy_asset_loader
Bevy plugin helping with asset loading and organization
LarsDu/bevy_hanabi
Hanabi — a GPU particle system plugin for the Bevy game engine.
LarsDu/bevy_particle_systems
A Particle System implementation for Bevy
LarsDu/bevy_prototype_particles
a prototype crate for creating modular and performant 3D CPU particle systems, inspired by Unity's Shuriken Particle System.
LarsDu/blender-addon-fbx-bundle
Unofficial Blender Addon: FBX Bundle ported to blender 2.8
LarsDu/BulletMaster
A side scrolling platformer engine written in Java. Can use Tiled as a level editor.
LarsDu/DigitalExtinctionGame
A 3D RTS game implemented in Rust.
LarsDu/geeky-hugo-code
Geeky is a Personal Hugo blog theme focused on high speed. Geeky is fully responsive, Superfast, and powered by Bootstrap v5.
LarsDu/hugo-apsho-space
A fork of the apsho theme with alterations to make it more appropriate for a space game themed product
LarsDu/ImageTemplateMatch
A simple example of using image templating to locate materials in two microscope views.
LarsDu/LarsDu
Config files for my GitHub profile.
LarsDu/LD51---DojoPanic
Partially complete Ludum Dare 51 3d platformer game
LarsDu/metaflow
Build and manage real-life data science projects with ease.
LarsDu/mlflow
Open source platform for the machine learning lifecycle
LarsDu/newsroom-gamedev
A simple, minimalistic Hugo theme. View Demo here
LarsDu/poetry
Python dependency management and packaging made easy.
LarsDu/RustyRayTracing
Ray Tracer in One Weekend implemented in Rust