Pinned Repositories
80x40
80 by 40 canvas that anyone can draw on.
Agatha
Agatha Request-Response Service Layer for .NET
airflow-maintenance-dags
A series of DAGs/Workflows to help maintain the operation of Airflow
config-rc-files
Configuration Files for the terminal line of OSX
javaPERT
Dynamic Programming in JAVA for PERT (Program Evaluation and Review Technique)
mc-sim
Monte Carlo Simulation
MCNF
Multicommodity Network flow in JAva
ML_exersises
The solutions to the exercises to the Machine Learning course by Stanford
Queue-Simulation
A simulated queue for servicing customers
XpressIVE
Mosel mathematical modelling code samples
cmdel's Repositories
cmdel/Queue-Simulation
A simulated queue for servicing customers
cmdel/config-rc-files
Configuration Files for the terminal line of OSX
cmdel/XpressIVE
Mosel mathematical modelling code samples
cmdel/mc-sim
Monte Carlo Simulation
cmdel/80x40
80 by 40 canvas that anyone can draw on.
cmdel/Agatha
Agatha Request-Response Service Layer for .NET
cmdel/airflow-maintenance-dags
A series of DAGs/Workflows to help maintain the operation of Airflow
cmdel/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.
cmdel/boundary-layer
Builds Airflow DAGs from configuration files. Powers all DAGs on the Etsy Data Platform
cmdel/compose-postgres
Postgresql & pgadmin4 powered by compose
cmdel/Craig-s-Utility-Library
Main repo for Craig's Utility Library
cmdel/cryptostore
A storage engine for cryptocurrency data
cmdel/docker-airflow
Docker Apache Airflow
cmdel/dockerfiles-windows
Various Dockerfiles for Windows Containers
cmdel/finsharplib
Automatically exported from code.google.com/p/finsharplib
cmdel/git-sync
A sidecar app which clones a git repo and keeps it in sync with the upstream.
cmdel/handbook
The Jitsi Handbook
cmdel/Hygieia
CapitalOne DevOps Dashboard
cmdel/mortgage
Python mortgage amortization calculations
cmdel/mortgage-1
Mortgage is a simple calculator intended to aid comprehension of the true cost of a home mortgage.
cmdel/netmq
A 100% native C# implementation of ZeroMQ for .NET
cmdel/ofxstatement-revolut
ofxstatement plugin for parsing Revolut CSV bank statements
cmdel/piecash
Pythonic interface to GnuCash SQL documents
cmdel/pybuilder
Software build automation tool for Python.
cmdel/pyql
Cython QuantLib wrappers
cmdel/pyvenn
Python module for plotting Venn diagrams of 2..6 sets
cmdel/RapidTransit
An integration library for creating large applications built around MassTransit.
cmdel/rebalance
Simple portfolio rebalancing in Python
cmdel/TestAfterBuild
Visual Studio 2012 Package to automatically runs all any unit test runner or command after each build (Resharper, TestDriven, NUnit). Also works in combination with .NET Demon to provide continuous testing which each keystroke.
cmdel/wordpress-azure
wordpress for azure marketplace