4,018 skills found · Page 1 of 134
Aider-AI / Aideraider is AI pair programming in your terminal
karpathy / MinbpeMinimal, clean code for the Byte Pair Encoding (BPE) algorithm commonly used in LLM tokenization.
je-suis-tm / Quant TradingPython quantitative trading strategies including VIX Calculator, Pattern Recognition, Commodity Trading Advisor, Monte Carlo, Options Straddle, Shooting Star, London Breakout, Heikin-Ashi, Pair Trading, RSI, Bollinger Bands, Parabolic SAR, Dual Thrust, Awesome, MACD
theskumar / Python DotenvReads key-value pairs from a .env file and can set them as environment variables. It helps in developing applications following the 12-factor principles.
chaijs / ChaiBDD / TDD assertion framework for node.js and the browser that can be paired with any testing framework.
Jeffallan / Claude Skills66 Specialized Skills for Full-Stack Developers. Transform Claude Code into your expert pair programmer.
antinomyhq / ForgecodeAI enabled pair programmer for Claude, GPT, O Series, Grok, Deepseek, Gemini and 300+ models
jiangmiao / Auto PairsVim plugin, insert or delete brackets, parens, quotes in pair
kylechui / Nvim SurroundAdd/change/delete surrounding delimiter pairs with ease. Written with :heart: in Lua.
entropy-research / DevonDevon: An open-source pair programmer
tpope / Vim Unimpairedunimpaired.vim: Pairs of handy bracket mappings
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.
adambielski / Siamese TripletSiamese and triplet networks with online pair/triplet mining in PyTorch
jamesmawm / High Frequency Trading Model With IBA high-frequency trading model using Interactive Brokers API with pairs and mean-reversion in Python
square / MortarA simple library that makes it easy to pair thin views with dedicated controllers, isolated from most of the vagaries of the Activity life cycle.
MatthewKuKanich / FindMyFlipperThe FindMy Flipper app turns your FlipperZero into an AirTag or other tracking device, compatible with Apple AirTags and Samsung SmartTag and Tile Trackers. It uses the BLE beacon to broadcast, allowing users to clone existing tags, generate OpenHaystack key pairs for Apple's FindMy network, and customize beacon intervals and transmit power.
bonnyfone / VectalignTool for create complex morphing animations using VectorDrawables (allows morphing between any pair of SVG images)
google-deepmind / Mathematics DatasetThis dataset code generates mathematical question and answer pairs, from a range of question types at roughly school-level difficulty.
Fuco1 / SmartparensMinor mode for Emacs that deals with parens pairs and tries to be smart about it.
ECTO-1A / AppleJuiceApple BLE proximity pairing message spoofing
