Pinned Repositories
eBBS
Eagle BBS is F/OSS text mode BBS software from the 1990's. It's a classic and so lightweight that chances are it still has some uses in the twenty-first century.
exocortex
This is a rewrite and cleanup of the information gathering, indexing, and analysis system that I use to monitor information sources all over the Internet.
exocortex-agents
A collection of sample Huginn agents I use to demonstrate how they're put together, and a little of what they can do.
exocortex-faas
OpenFaaS functions I've written to work with Huginn.
exocortex-halo
Various and sundry additional pieces of software I've written to incorporate into my exocortex.
Experiments
Random scripts and other stuff I mess around with.
pwnagotchi-bt-power
A very simple, silly utility which monitors the Bluetooth interface of a Pwnagotchi and cleanly shuts it down on receiving a command.
ubuntu-hardening
A repository of configuration files for multiple versions of Ubuntu Server that increase the default security posture.
virtadpt's Repositories
virtadpt/exocortex-halo
Various and sundry additional pieces of software I've written to incorporate into my exocortex.
virtadpt/pwnagotchi-bt-power
A very simple, silly utility which monitors the Bluetooth interface of a Pwnagotchi and cleanly shuts it down on receiving a command.
virtadpt/Experiments
Random scripts and other stuff I mess around with.
virtadpt/paperless-ngx-files
Config files and scripts I wrote to make paperless-ngx a little easier to set up.
virtadpt/programming_templates
These are my templates for writing different kinds of scripts. Edit appropriately. I hope they help.
virtadpt/3d-printing-high-security-key
Get Your 3D Printed High Security Key
virtadpt/brutalist
My personal fork of the Brutalist Pelican theme by @mcman_s.
virtadpt/huginn
Build agents that monitor and act on your behalf. Your agents are standing by!
virtadpt/rickrollrc
Rick Astley invades your terminal.
virtadpt/adsb-wiki
Solutions to common problems using dump1090 variants and ADS-B feeders
virtadpt/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.
virtadpt/bpytop
Linux/OSX/FreeBSD resource monitor
virtadpt/Cohost.py
A python library for Cohost.org!
virtadpt/froopyland-dr
"What happens to their homelab?" A crowd-sourced guide to help techs help their non-tech spouses/partners/parents/kids when we ☠️
virtadpt/KelloggBot
Kellogg bad | Union good | Support strike funds
virtadpt/kickstart.nvim
A launch point for your personal nvim configuration.
virtadpt/krakensdr_pr
Passive Radar Code for the KrakenSDR
virtadpt/local_wordle
wordle but with saving and loading and in a single file
virtadpt/minipro
Notes on using TL866II Plus with minipro software on openSUSE
virtadpt/not-br
Site source for Not BR (https://not-br.neocities.org/)
virtadpt/pelican-html5up-striped
HTML5UP Striped Pelican Theme
virtadpt/personalsit.es
📇 A little directory of people's personal sites
virtadpt/pewpew
:star: :star: :star: Build your own IP Attack Maps with SOUND!
virtadpt/Plane-Tracking-ADSB
Tracking planes that pas over my house with the flightaware pro stick on raspberry pi...
virtadpt/readsb
ADS-B decoder swiss knife
virtadpt/rickroll
A website with the auto-playing song “Never Gonna Give You Up” that can be used to rickroll your friends. Please note that this does not fully support Android.
virtadpt/searxng
SearXNG is a free internet metasearch engine which aggregates results from various search services and databases. Users are neither tracked nor profiled.
virtadpt/twitter-verified-list
virtadpt/webring
Organizational repo for the OBEY THE SYSTEM chooms webring.
virtadpt/xp
💻 Windows XP All Editions Universal Product Keys Collection