984 skills found · Page 1 of 33
appbaseio / DejavuA Web UI for Elasticsearch and OpenSearch: Import, browse and edit data with rich filters and query views, create reference search UIs.
ept / Ddia ReferencesLiterature references for “Designing Data-Intensive Applications”
Quartz / Bad Data GuideAn exhaustive reference to problems seen in real-world data along with suggestions on how to resolve them.
NAalytics / Assemblies Of Putative SARS CoV2 Spike Encoding MRNA Sequences For Vaccines BNT 162b2 And MRNA 1273RNA 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.
js-data / Js DataGive your data the treatment it deserves with a framework-agnostic, datastore-agnostic JavaScript ORM built for ease of use and peace of mind. Works in Node.js and in the Browser. Main Site: http://js-data.io, API Reference Docs: http://api.js-data.io/js-data
Time-Appliances-Project / Time CardDevelop an end-to-end hypothetical reference model, network architectures, precision time tools, performance objectives and the methods to distribute, operate, monitor time synchronization within data center and much more...
griffithlab / Rnaseq TutorialInformatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
manami-project / Anime Offline DatabaseA JSON based anime dataset containing the most important meta data as well as cross references to various anime sites such as MAL, ANIDB, ANILIST, KITSU and more...
killrweather / KillrweatherKillrWeather is a reference application (work in progress) showing how to easily integrate streaming and batch data processing with Apache Spark Streaming, Apache Cassandra, Apache Kafka and Akka for fast, streaming computations on time series data in asynchronous event-driven environments.
bterwijn / Memory GraphTeaching tool and debugging aid in context of references, mutable data types, and shallow and deep copy.
tajpouria / Algorithms And Data Structures Cheat SheetProviding a summary of important algorithms and data structures along with their key characteristics and use cases. It can be used as a quick reference for solving programming problems or refreshing knowledge of foundational computer science concepts.
intel / AI Reference ModelsIntel® AI Reference Models: contains Intel optimizations for running deep learning workloads on Intel® Xeon® Scalable processors and Intel® Data Center GPUs
rspatial / TerraR package for spatial data handling https://rspatial.github.io/terra/reference/terra-package.html
ethereum-oasis-op / BaselineThe Baseline Protocol is an open source initiative that combines advances in cryptography, messaging, and distributed ledger technology to enable confidential and complex coordination between enterprises while keeping data in systems of record. This repo serves as the main repo for the Baseline Protocol, containing core packages, examples, and reference implementations.
HillZhang1999 / MuCGECMuCGEC中文纠错数据集及文本纠错SOTA模型开源；Code & Data for our NAACL 2022 Paper "MuCGEC: a Multi-Reference Multi-Source Evaluation Dataset for Chinese Grammatical Error Correction"
geonetwork / Core GeonetworkGeoNetwork is a catalog application to manage spatially referenced resources. It provides powerful metadata editing and search functions as well as an interactive web map viewer. It is currently used in numerous Spatial Data Infrastructure initiatives across the world.
khusnetdinov / Ruby.fundamental:books: Fundamental programming with ruby examples and references. It covers threads, SOLID principles, design patterns, data structures, algorithms. Books for reading. Repo for website https://github.com/khusnetdinov/betterdocs
Timeverse / My TW CoverageEquity research coverage of 1,735 Taiwan-listed companies (TWSE + OTC). Business overviews, supply chain mapping, and financial data with wikilink cross-referencing.
NVIDIA-AI-Blueprints / AiqThe AI-Q NVIDIA Blueprint is an open reference example for building intelligent AI agents that connect to your enterprise data, reason using state-of-the-art models, and deliver trusted business insights.
peggy1502 / Amazing ResourcesList of references and online resources related to data science, machine learning and deep learning.
