Pinned Repositories
HackTheDeep
The 4th Annual American Museum of Natural History Hackathon produced by the BridgeUP: STEM program
HacktheDinos
The 2nd Annual American Museum of Natural History Hackathon produced by the BridgeUP: STEM program
HackTheSolarSystem
The 5th Annual American Museum of Natural History Hackathon produced by the BridgeUP: STEM program
HackTheStacks
The 3rd Annual American Museum of Natural History Hackathon produced by the BridgeUP: STEM program
emoji.sexy
a url shortener powered by emoji and leveldb
food-fiddle
F.I.D.D.L.E. -- The Food-borne Illness Data Dumps, Liberators, and Extractors
serkli
Create Circles Of Support To Prevent Breast Cancer
shoutboost
Submit, discover, curate, and promote breaking news videos across social platforms
Thinking-Like-A-Programmer-workshop-code-examples
The code examples used in the workshops, licensed in the public domain worldwide for all uses.
OpenSpace
This is the official GitHub repository for OpenSpace: an open source astrovisualization project. For instructions on how to build and run OpenSpace, see the Getting Started Guides on the wiki page at http://docs.openspaceproject.com.
mik3caprio's Repositories
mik3caprio/Thinking-Like-A-Programmer-workshop-code-examples
The code examples used in the workshops, licensed in the public domain worldwide for all uses.
mik3caprio/food-fiddle
F.I.D.D.L.E. -- The Food-borne Illness Data Dumps, Liberators, and Extractors
mik3caprio/tf2_gans
Implementations of GANs in Tensorflow 2.x
mik3caprio/abuse
Abuse SDL port originally from Crack-Dot-Com and released into the public domain
mik3caprio/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.
mik3caprio/brainewave_web
Website for Brainewave Consulting
mik3caprio/chip-os-pro
mik3caprio/CHIP-postchroot
mik3caprio/chip-power
mik3caprio/chip-theme
mik3caprio/CHIP-tools-backup
The repository CHIP-tools has been retired and cannot be reused. So this is a backup.
mik3caprio/CHIP-u-boot
mik3caprio/dalle-mini
DALL·E Mini - Generate images from a text prompt
mik3caprio/f1rmware
f1rmware for the rad1o
mik3caprio/github-slideshow
A robot powered training repository :robot:
mik3caprio/heissepreise
mik3caprio/hows_my_driving
Python script to respond to tweets about traffic violations using data about parking and camera violations from https://opendata.cityofnewyork.us/
mik3caprio/lagrange
A Robust Geometry Processing Library
mik3caprio/lovecraft
Analysis of original Lovecraft novels vs. Lovecraft-inspired boardgame text.
mik3caprio/marvel-cinematic-uni
mik3caprio/Misconceptions
Daily Myths — Visualize the “All-too-Common Astronomy/Solar System Misconceptions”
mik3caprio/moon_geology_atlas_of_space
Code, data, and instructions for mapping the geology of the moon
mik3caprio/Mycodo
An environmental monitoring and regulation system
mik3caprio/opensource.nextthing.co
mik3caprio/picamera
A pure Python interface to the Raspberry Pi camera module
mik3caprio/pose-search
x6ud.github.io/pose-search
mik3caprio/SOSgame
mik3caprio/sovereign
A set of Ansible playbooks to build and maintain your own private cloud: email, calendar, contacts, file sync, IRC bouncer, VPN, and more.
mik3caprio/weather-station
Data logging code for the Raspberry Pi Weather Station HAT
mik3caprio/weather-station-www
Demo display website for the Raspberry Pi Weather Station HAT