pr3d4t0r

basdtracks2018

Bay Area Skydiving Tracking 2018

calendar

Baikal / SabreDAV robust calendar and address book server with scheduling and email notifications

lucyfer

Lucyfer - Jupyter transformed into a star (see 2010: Odyssey Two)

n1ql-vim-syntax

N1QL syntax file(s) for Vim 7.4 and later

paster

Vim paster tool - originally posted to vim.org and managed locally.

sabre.io

Dockerized package for deploying PHP 7, Composer, and Sculpin without having to install/update any of these.

sopel_ai

PerplexiPy / Perplexity AI / Ollama/llama.cpp plug-in for the Sopel bot

SSScoring

Speed Skydiving Scoring - Jupyter Lab notebooks and sample data

wee_slack_tokens

weechat-btc-ticker

WeeChat plugin for Bitcoin, Litecoin, other cyrptocurrency ticker reporting

pr3d4t0r/calendar

Baikal / SabreDAV robust calendar and address book server with scheduling and email notifications

pr3d4t0r/weechat-btc-ticker

WeeChat plugin for Bitcoin, Litecoin, other cyrptocurrency ticker reporting

pr3d4t0r/SSScoring

Speed Skydiving Scoring - Jupyter Lab notebooks and sample data

pr3d4t0r/lucyfer

Lucyfer - Jupyter transformed into a star (see 2010: Odyssey Two)

pr3d4t0r/n1ql-vim-syntax

N1QL syntax file(s) for Vim 7.4 and later

pr3d4t0r/sopel_ai

PerplexiPy / Perplexity AI / Ollama/llama.cpp plug-in for the Sopel bot

pr3d4t0r/basdtracks2018

Bay Area Skydiving Tracking 2018

pr3d4t0r/paster

Vim paster tool - originally posted to vim.org and managed locally.

pr3d4t0r/sabre.io

Dockerized package for deploying PHP 7, Composer, and Sculpin without having to install/update any of these.

pr3d4t0r/wee_slack_tokens

pr3d4t0r/announce_url_title

Announce URL title -- Python 3 version, with permission and blessing to carry it forward from the original author.

pr3d4t0r/aoc2020

Advent of Code 2020 exercises

pr3d4t0r/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.

pr3d4t0r/dart-vim-syntax

Dart syntax files for Vim 8.1 and later

pr3d4t0r/docker-stacks

Ready-to-run Docker images containing Jupyter applications

pr3d4t0r/dotfiles

pr3d4t0r/execnet

distributed Python deployment and communication - UNMAINTAINED

pr3d4t0r/flutter_book_examples

pr3d4t0r/gedim

gVim/MacVim Graphics Editor DIMensions

pr3d4t0r/ipwhere

IP geo location command line tool (relies on 3rd-party to provide actual location).

pr3d4t0r/pikache

pikache - ready to run PyPI cache, devpi Docker image

pr3d4t0r/skyderby

The most advanced flight analysis and competition scoring

pr3d4t0r/sopel

:robot::speech_balloon: An easy-to-use and highly extensible IRC Bot framework. Formerly Willie.

pr3d4t0r/trackodometer

Bay Area Skydiving - tracking odometer software, uses FlySight CSV data as input.

pr3d4t0r/usdmxn

pr3d4t0r/VeraCrypt

Disk encryption with strong security based on TrueCrypt

pr3d4t0r/viper-mf