Pinned Repositories
100daysofweb-with-python-course
Demo code and resources for our 100 Days of Web in Python Course
booxtream-epub-drm-remover
Removes all "Social DRM" from booXtream ePub files
electrumx-no-bcash
Alternative implementation of spesmilo/electrum-server
fotowall
Pictures collage & creativity tool
two-scoops-of-django-1.11
The issue tracker, changelog, and code repository for Two Scoops of Django 1.11
vince06fr's Repositories
vince06fr/amicalespcontes
Reservation site for the association of Contes firefighters
vince06fr/Apprentissage
Science des Données Saison 3: Apprentissage Automatique / Statistique pour l'Intelligence Artificielle
vince06fr/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.
vince06fr/awesome-cli-apps
🖥 📊 🕹 🛠 A curated list of command line apps
vince06fr/battle
Projet "RPG Battle Script" du cours "Python 3: Beginner to Advanced" (udemy)
vince06fr/btcpy
A Python3 SegWit-compliant library which provides tools to handle Bitcoin data structures in a simple fashion.
vince06fr/charcha
Intermediate level hands on django tutorial. Build a discussion forum for employees using Django and deploy on Heroku.
vince06fr/course
Contenu pédagogique du MOOC Python3 sur fun-mooc.fr
vince06fr/datascience
Curated list of Python resources for data science.
vince06fr/Django-3-by-Example
Django 3 by Example, published by Packt
vince06fr/django-anymail
Django email backends and webhooks for Amazon SES, Mailgun, Mailjet, Postmark, Postal, SendGrid, Sendinblue, SparkPost and more
vince06fr/eCommerce
We're going to take you step-by-step to build a modern, fully open-source, eCommerce web application using Python, Django, Bootstrap, Javascript, and more.
vince06fr/FUN-MOOC-Python3
Learning Python3 with FUN-MOOC
vince06fr/Hover
A collection of CSS3 powered hover effects to be applied to links, buttons, logos, SVG, featured images and so on. Easily apply to your own elements, modify or just use for inspiration. Available in CSS, Sass, and LESS.
vince06fr/incus_container_gui_setup
Setup of running GUI applications in a incus container
vince06fr/JavaScript-for-Everyone
A step by step guide to learn JavaScript and programming
vince06fr/Kinetic-Text-Tags
Text Tags that add various effects to Ren'py text!
vince06fr/lnbook
Mastering the Lightning Network (LN)
vince06fr/lurch
XEP-0384: OMEMO Encryption for libpurple.
vince06fr/materials
Bonus materials, exercises, and example projects for our Python tutorials
vince06fr/MiUnlockTool
MiUnlockTool developed to retrieve encryptData(token) for Xiaomi devices for unlocking bootloader, It is compatible with all platforms.
vince06fr/nonoCAPTCHA
An asynchronized Python library to automate solving ReCAPTCHA v2 using audio
vince06fr/OSCP
Materials for OSCP exam
vince06fr/scribble-diffusion
Turn your rough sketch into a refined image using AI
vince06fr/Selfhosted-Google-Photos-Alternative
A complete guide on exiting Google, Amazon or any proprietary service Photos storage with all the features you would want.
vince06fr/SmartPoop
This is the repository of the book "SmartPoop".
vince06fr/SnuSlideshowGenerator
A Blender addon that assists in creation of high quality slideshows.
vince06fr/Spirit
Spirit is a modern Python based forum built on top of Django framework
vince06fr/startbootstrap-sb-admin
A free, open source, Bootstrap admin theme created by Start Bootstrap
vince06fr/Xiaomi_Kernel_OpenSource
Xiaomi Mobile Phone Kernel OpenSource