daunfamily's repositories
TSP-BnB-CP
Branch-and-Bound and Cutting plane algorithme for the TSP
ADMM_Python
Solomon benchmark instances
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.
Code
运小筹公众号是致力于分享运筹优化(LP、MIP、NLP、随机规划、鲁棒优化)、凸优化、强化学习等研究领域的内容以及涉及到的算法的代码实现。
Coluna.jl
Branch-and-Price-and-Cut in Julia
COVID-19-Governments-Responses
Governments' Responses to COVID-19
covid19_inference
Bayesian python toolbox for inference and forecast of the spread of the Coronavirus
create-react-app
Set up a modern web app by running one command.
diagnosis_covid19
OpenCovidDetector is an opensource COVID-19 diagnosis system implementing on pytorch, which is also as presented in our paper: Development and evaluation of an artificial intelligence system for COVID-19 diagnosis. Nat Commun 11, 5088 (2020).(https://doi.org/10.1038/s41467-020-18685-1)
EssayKiller_V2
基于开源GPT2.0的初代创作型人工智能 | 可扩展、可进化
Hands-On-Reinforcement-Learning-with-Python
Hands-On Reinforcement Learning with Python, published by Packt
julia
The Julia Programming Language
JuMPTutorials.jl
Tutorials on using JuMP for mathematical optimization in Julia
mapping_marine_debris
Scripts used to preprocess the 2015 DAR Aerial Imagery for use in deep learning.
MyFish
专注优化算法开发，包括以下方面： （1）启发式算法，元启发式算法，群智能优化算法（GA，PSO，GWO等） （2）凸优化（ADMM，Benders分解，内点法等） （3）多目标优化（NSGA-II，MOPSO，MOGWO等） （4）机器学习（神经网络，SVM，决策树，随机森林等） 电力系统优化建模，多学科优化建模，包括： （1）电力系统运行优化（日前优化调度，微电网运行优化，电动汽车调度优化，负荷调度，环境经济调度，风电储能优化，非侵入式负荷分解，神经网络分类预测）电力系统优化规划（可靠性评估，启发式算法优化，多阶段优化，鲁棒优化） （2）TSP,VRP经典算法问题（含时间窗VRPTW） （3）参数优化（PID智能优化调参，参数拟合，参数识别） （4）分类问题，回归问题求解（轴承故障诊断，曲线拟合） 有开发需求的请联系1006597080（有偿！有偿！有偿！） 闲鱼账号：aaaaa耀耀（沟通后可下单）
ocean-garbage-tracker
Messages in Bottles is an online platform containing interactive visualizations and information on coastal plastic waste using remote sensing data from Sentinel-2.
optaplanner-quickstarts
OptaPlanner quick starts for AI optimization: many use cases shown in many different technologies.
PathPlanning
Common used path planning algorithms with animations.
PV-forecasting-tensorflow
PV (power generation) forecasting with tensorflow
pymarl
Python Multi-Agent Reinforcement Learning framework
R3Det_Tensorflow
R3Det: Refined Single-Stage Detector with Feature Refinement for Rotating Object
Remote-sensing
Remote sensing: objects recognition on the satellite images using Keras.
Routing.jl
Vehicle Routing Problem with Time Windows (VRPTW) / Elementary Shortest Path Problem with Resource Constraints (ESPPRC)
SeaPearl.jl
Julian hybrid constraint programming solver enhanced by a reinforcement learning driven search.
SolarSailSpaceDebrisDe-Orbiter
Project for JSSF, uses Orekit package in eclipse environment. It simulates a solar sail in orbit that rotates itself according to its position relative to the sun's light to adjust its trajectory in order to de-orbit space debris.
SYMPHONY
SYMPHONY is an open-source solver, callable library, and development framework for mixed-integer linear programs (MILPs) written in C with a number of unique features