Pinned Repositories
CraneFoot
CraneFoot mirror from http://www.finndiane.fi/software/cranefoot/
ojdbc6-11.2.0.2.0.src
pycdc
C++ python bytecode disassembler and decompiler
pycdcj
Python bytecode disassembler and decompiler in Java
sas7bdat
mirror from https://bitbucket.org/jaredhobbs/sas7bdat.git
uncompyle2_ignore_the_first_8_bytes
decompile pyc that ignores the first 8 bytes
vue-jqueryui-require
require.js, jquery, jquery.ui, vue
caot's Repositories
caot/cpp
caot/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.
caot/Beej-s-Guide-to-Network-Programming
Beej's Guide to Network Programming source
caot/soaplib
This is a simple, easily extendible soap library that provides several useful tools for creating and publishing soap web services in python.
caot/navi.cat-tools
caot/luna
a USB multitool + nMigen framework for monitoring, hacking, and developing USB devices
caot/AmericaOpposeAmerica
《美国反对美国》是王沪宁先生在上世纪80年代末赴美观察写作的。我们知道在那个年代**对西方特别是美国的追捧有多高,所以突然看到一个学者在80年代就有如此清楚的认识,十分钦佩。由于网上只有效果很差的PDF扫描版,所以我想利用OCR技术和肉眼(人体OCR)来转成现代化的文本格式。目前已经全部完成。
caot/react-TDD-part-3-axios
caot/keycloak
Open Source Identity and Access Management For Modern Applications and Services
caot/samba
https://gitlab.com/samba-team/samba is the Official GitLab mirror of https://git.samba.org/samba.git -- Merge requests should be made on GitLab (not on GitHub)
caot/ansible-django-stack
Ansible Playbook for setting up a Django app with Nginx, Gunicorn, PostgreSQL, Celery, RabbitMQ, Supervisor, Virtualenv, and Memcached. A Vagrantfile for provisioning a VirtualBox virtual machine is included as well.
caot/openh264
Open Source H.264 Codec
caot/jSignature
jQuery plugin for adding web signature functionality
caot/kafka-streams-examples
Demo applications and code examples for Apache Kafka's Streams API.
caot/kafka-streams-machine-learning-examples
This project contains examples which demonstrate how to deploy analytic models to mission-critical, scalable production environments leveraging Apache Kafka and its Streams API. Models are built with Python, H2O, TensorFlow, Keras, DeepLearning4 and other technologies.
caot/vcpkg
C++ Library Manager for Windows, Linux, and MacOS
caot/closure-library
Google's common JavaScript library
caot/pdf.js.demo
caot/pdf.js
PDF Reader in JavaScript
caot/vue3-for-beginners
caot/python-spark-tutorial
caot/vuex_demo
Vuex crah course app
caot/vue-demo
caot/pdfjs-dist
Generic build of PDF.js library.
caot/hadoop_quick_guide_java
caot/SpringBootUploadingfiles
caot/shinyproxy
ShinyProxy - Open Source Enterprise Deployment for Shiny
caot/spring-kafka
Provides Familiar Spring Abstractions for Apache Kafka
caot/percona-xtrabackup
Open source hot backup tool for InnoDB and XtraDB databases
caot/TDengine
An open-source big data platform designed and optimized for the Internet of Things (IoT).