rwohleb

AjaxIM

instant messaging framework

aJson

aJson is an Arduino library to enable JSON processing with Arduino. It easily enables you to decode, create, manipulate and encode JSON directly from and to data structures.

akihabara

A game engine for making classic arcade style games using Javascript and HTML5

automongobackup

Nightly, rotated backups of MongoDB (port of AutoMySQLBackup for use with Mongo)

Autosmush

Losslessly compresses images in your Amazon S3 buckets on-the-fly.

imageresampler

Exported from code.google.com/p/imageresampler

pypep

A python version of propep

rwohleb/imageresampler

Exported from code.google.com/p/imageresampler

rwohleb/EggDuino

Arduino Firmware for Spherebot / Eggbot integration in Inkscape

rwohleb/kytelabs-board-index

Kytelabs Package Lists for the Arduino v1.6.4+ Board Manager https://rwohleb.github.io/kytelabs-board-index/package_kytelabs_index.json

rwohleb/Arduino

ESP8266 core for Arduino

rwohleb/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.

rwohleb/blt

Acquia's toolset for automating Drupal 8 development, testing, and deployment.

rwohleb/composer-patches

Simple patches plugin for Composer

rwohleb/Crunchyroll.bundle

Crunchyroll.bundle is a Plex Media Server plugin that provides access to the content available at Crunchyroll.com.

rwohleb/csr-spi-ftdi

USB SPI programmer/debugger for CSR BlueCore bluetooth chips, based on FTDI USB to UART converter, for Linux and Windows

rwohleb/docker-pantheon-ci

rwohleb/docker-plexconnect

Docker for plexconnect - https://hub.docker.com/r/rwohleb/plexconnect/

rwohleb/docker-templates

A repository of unRAID Server OS 6 Docker templates

rwohleb/EggBot

Software for the Original EggBot Kit

rwohleb/esp8266-robot

Build a WiFi Controlled Robot with the ESP8266

rwohleb/flexible_list

A flexible list field type for Drupal 8

rwohleb/graphql-search-api

GraphQL & Drupal Search API integration.

rwohleb/hakchi2

Tool that allows you to add more games to your NES/SNES Classic Mini

rwohleb/HttpClient

Arduino HTTP library

rwohleb/isotope_views

Views display plugin with isotope integration (drupal 8)

rwohleb/Mirai-Source-Code

Leaked Mirai Source Code for Research/IoC Development Purposes

rwohleb/neurosci-catalyst-web

Neuroscience Catalyst Website

rwohleb/open-demographics

Open Demographics Initiative: An open standard for collecting identity/demographic data in open source communities.

rwohleb/PlexConnect

Plex @ aTV - think different...

rwohleb/Prusa-Firmware

Firmware for Original Prusa i3 3D printer by PrusaResearch

rwohleb/qmk_firmware

Open-source keyboard firmware for Atmel AVR and Arm USB families

rwohleb/R2iPantheonCircleCI

rwohleb/sample-distribution

small minimal quantile and CDF estimator for multiple large data streams

rwohleb/SpaceEngineers

rwohleb/vwcdavr

AVR alternative to vwcdpic HW+SW

rwohleb/vwcdpic

This is my personal fork of k9spud vwcdpic project