adubovikov

adubovikov

angular-ui-tree

A tree component for AngularJS, without jQuery as dependency.

color-schemes

Color schemes I've used for an extended period of time and like

heplify

HEP Capture Client

heplify-server

HEP Capture Server

sipp-scenarios

SIPp scenarios I use for testing SIP stuff

stenographer

Stenographer is a packet capture solution which aims to quickly spool all packets to disk, then provide simple, fast access to subsets of those packets. Discussion/announcements at stenographer@googlegroups.com

storage-server

the storage server for recording and cdr

adubovikov/storage-server

the storage server for recording and cdr

adubovikov/asio

Asio C++ Library

adubovikov/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.

adubovikov/casaLoki

adubovikov/cLoki

Clickhouse Loki: Grafana Loki API + ClickHouse Backend in NodeJS

adubovikov/config-cpp

C++ Configuration management library inspired by the Viper package for golang.

adubovikov/eslgo

A GoLang FreeSWITCH ESL Library

adubovikov/FFmpeg

Mirror of git://source.ffmpeg.org/ffmpeg.git

adubovikov/ffmpeg-libav-tutorial

FFmpeg libav tutorial - learn how media works from basic to transmuxing, transcoding and more

adubovikov/galene

The Galène videoconferencing server

adubovikov/goav

Golang bindings for FFmpeg libraries

adubovikov/libntoh

User-friendly C Library to perform TCP streams reassembly and IPv4/6 defragmentation

adubovikov/memory

STL compatible C++ memory allocator library using a new RawAllocator concept that is similar to an Allocator but easier to use and write.

adubovikov/ngx-daterangepicker-material

Pure Angular 2+ date range picker with material design theme, a demo here:

adubovikov/opencv

Open Source Computer Vision Library

adubovikov/PcapPlusPlus

PcapPlusPlus is a multiplatform C++ library for capturing, parsing and crafting of network packets. It is designed to be efficient, powerful and easy to use. It provides C++ wrappers for the most popular packet processing engines such as libpcap, WinPcap, DPDK and PF_RING.

adubovikov/pistache

A high-performance REST Toolkit written in C++

adubovikov/quicktemplate

Fast, powerful, yet easy to use template engine for Go. Optimized for speed, zero memory allocations in hot paths. Up to 20x faster than html/template

adubovikov/robin-map

C++ implementation of a fast hash map and hash set using robin hood hashing

adubovikov/rtpdump

Extract audio file from RTP streams in pcap format

adubovikov/snuffy

Snuffy is a simple command line tool to dump the data sent and received by programs that use OpenSSL.

adubovikov/static-binaries

Various *nix tools built as statically-linked binaries

adubovikov/stealthpool

Off heap golang memory pool

adubovikov/stenoscope

SSTable Scanner & Parser for Stenographer Packet Indices

adubovikov/tcpscaler

libevent-based client and server, designed to explore the limit of a TCP-based server with a *huge* number of clients

adubovikov/testimony

Testimony is a single-machine, multi-process architecture for sharing AF_PACKET data across processes, allowsing packets to be copied from NICs into memory a single time, then shared across multiple processes.

adubovikov/VictoriaLogs

Loki On VictoriaMetrics

adubovikov/voip_patrol

VoIP signaling and media test automation

adubovikov/xenium

A C++ library providing various concurrent data structures and reclamation schemes.

adubovikov/zetcd

Serve the Apache Zookeeper API but back it with an etcd cluster