Shafi Ahmed's repositories
3DTilesRendererJS
Renderer for 3D Tiles in Javascript using three.js
alphafold
Open source code for AlphaFold.
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.
box2d-wasm
Box2D physics engine compiled to WebAssembly. Supports TypeScript and ES modules.
butterchurn
Butterchurn is a WebGL implementation of the Milkdrop Visualizer
Calliar
A dataset for online arabic calligraphy
darktable
darktable is an open source photography workflow application and raw developer
deep-daze
Simple command line tool for text to image generation using OpenAI's CLIP and Siren (Implicit neural representation network)
Face_info
face recognition, detection of facial attributes (age, gender, emotion and race) for python.
foundations-of-information
A book to support the INFO 200 Intellectual Foundations of Information course.
Interactive_Tools
Interactive Tools for Machine Learning, Deep Learning and Math
lila
♞ lichess.org: the forever free, adless and open source chess server ♞
machine-learning-cheat-sheet
Classical equations and diagrams in machine learning
Machine-Learning-Tutorials
machine learning and deep learning tutorials, articles and other resources
mesh-transformer-jax
Model parallel transformers in JAX and Haiku
open-source-search-engine
Nov 20 2017 -- A distributed open source search engine and spider/crawler written in C/C++ for Linux on Intel/AMD. From gigablast dot com, which has binaries for download. See the README.md file at the very bottom of this page for instructions.
pear
WebRTC Library for IoT/Embedded Device using C
plot
A concise API for exploratory data visualization
quickwit
Quickwit is a big data search engine.
Robyn
Robyn is an experimental, automated and open-sourced Marketing Mix Modeling (MMM) code from Facebook Marketing Science. It uses various machine learning techniques (Ridge regression with cross validation, multi-objective evolutionary algorithm for hyperparameter optimisation, gradient-based optimisation for budget allocation etc.) to define media channel efficiency and effectivity, explore adstock rates and saturation curves. It's built for granular datasets with many independent variables and therefore especially suitable for digital and direct response advertisers with rich dataset.
Self-Supervised-Learning-for-Sketch
[CVPR 21] Vectorization and Rasterization: Self-Supervised Learning for Sketch and Handwriting, IEEE Conf. on Computer Vision and Pattern Recognition (CVPR), 2021.
semisupervised-FGSBIR
[CVPR 2021] "More Photos are All You Need: Semi-Supervised Learning for Fine-Grained Sketch Based Image Retrieval”, IEEE Conf. on Computer Vision and Pattern Recognition (CVPR), 2021.
three-mesh-bvh
A BVH implementation to speed up raycasting against three.js meshes.
traccar-sms-gateway
Traccar SMS Gateway for Android
triton
Development repository for the Triton language and compiler
winix
A UNIX-style Operating System for the Waikato RISC Architecture Microprocessor (WRAMP)