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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.
openbabel / OpenbabelOpen Babel is a chemical toolbox designed to speak the many languages of chemical data.
seyonechithrananda / Bert Loves Chemistrybert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.
MLCIL / Scikit FingerprintsScikit-learn compatible library for molecular fingerprints and chemoinformatics
Kohulan / DECIMER Image TransformerDECIMER Image Transformer is a deep-learning-based tool designed for automated recognition of chemical structure images. Leveraging transformer architectures, the model converts chemical images into SMILES strings, enabling the digitization of chemical data from scanned documents, literature, and patents.
jrwnter / CdddImplementation of the Paper "Learning Continuous and Data-Driven Molecular Descriptors by Translating Equivalent Chemical Representations" by Robin Winter, Floriane Montanari, Frank Noe and Djork-Arne Clevert.
abusufyanvu / 6S191 MIT DeepLearningMIT Introduction to Deep Learning (6.S191) Instructors: Alexander Amini and Ava Soleimany Course Information Summary Prerequisites Schedule Lectures Labs, Final Projects, Grading, and Prizes Software labs Gather.Town lab + Office Hour sessions Final project Paper Review Project Proposal Presentation Project Proposal Grading Rubric Past Project Proposal Ideas Awards + Categories Important Links and Emails Course Information Summary MIT's introductory course on deep learning methods with applications to computer vision, natural language processing, biology, and more! Students will gain foundational knowledge of deep learning algorithms and get practical experience in building neural networks in TensorFlow. Course concludes with a project proposal competition with feedback from staff and a panel of industry sponsors. Prerequisites We expect basic knowledge of calculus (e.g., taking derivatives), linear algebra (e.g., matrix multiplication), and probability (e.g., Bayes theorem) -- we'll try to explain everything else along the way! Experience in Python is helpful but not necessary. This class is taught during MIT's IAP term by current MIT PhD researchers. Listeners are welcome! Schedule Monday Jan 18, 2021 Lecture: Introduction to Deep Learning and NNs Lab: Lab 1A Tensorflow and building NNs from scratch Tuesday Jan 19, 2021 Lecture: Deep Sequence Modelling Lab: Lab 1B Music Generation using RNNs Wednesday Jan 20, 2021 Lecture: Deep Computer Vision Lab: Lab 2A Image classification and detection Thursday Jan 21, 2021 Lecture: Deep Generative Modelling Lab: Lab 2B Debiasing facial recognition systems Friday Jan 22, 2021 Lecture: Deep Reinforcement Learning Lab: Lab 3 pixel-to-control planning Monday Jan 25, 2021 Lecture: Limitations and New Frontiers Lab: Lab 3 continued Tuesday Jan 26, 2021 Lecture (part 1): Evidential Deep Learning Lecture (part 2): Bias and Fairness Lab: Work on final assignments Lab competition entries due at 11:59pm ET on Canvas! Lab 1, Lab 2, and Lab 3 Wednesday Jan 27, 2021 Lecture (part 1): Nigel Duffy, Ernst & Young Lecture (part 2): Kate Saenko, Boston University and MIT-IBM Watson AI Lab Lab: Work on final assignments Assignments due: Sign up for Final Project Competition Thursday Jan 28, 2021 Lecture (part 1): Sanja Fidler, U. Toronto, Vector Institute, and NVIDIA Lecture (part 2): Katherine Chou, Google Lab: Work on final assignments Assignments due: 1 page paper review (if applicable) Friday Jan 29, 2021 Lecture: Student project pitch competition Lab: Awards ceremony and prize giveaway Assignments due: Project proposals (if applicable) Lectures Lectures will be held starting at 1:00pm ET from Jan 18 - Jan 29 2021, Monday through Friday, virtually through Zoom. Current MIT students, faculty, postdocs, researchers, staff, etc. will be able to access the lectures during this two week period, synchronously or asynchronously, via the MIT Canvas course webpage (MIT internal only). Lecture recordings will be uploaded to the Canvas as soon as possible; students are not required to attend any lectures synchronously. Please see the Canvas for details on Zoom links. The public edition of the course will only be made available after completion of the MIT course. Labs, Final Projects, Grading, and Prizes Course will be graded during MIT IAP for 6 units under P/D/F grading. Receiving a passing grade requires completion of each software lab project (through honor code, with submission required to enter lab competitions), a final project proposal/presentation or written review of a deep learning paper (submission required), and attendance/lecture viewing (through honor code). Submission of a written report or presentation of a project proposal will ensure a passing grade. MIT students will be eligible for prizes and awards as part of the class competitions. There will be two parts to the competitions: (1) software labs and (2) final projects. More information is provided below. Winners will be announced on the last day of class, with thousands of dollars of prizes being given away! Software labs There are three TensorFlow software lab exercises for the course, designed as iPython notebooks hosted in Google Colab. Software labs can be found on GitHub: https://github.com/aamini/introtodeeplearning. These are self-paced exercises and are designed to help you gain practical experience implementing neural networks in TensorFlow. For registered MIT students, submission of lab materials is not necessary to get credit for the course or to pass the course. At the end of each software lab there will be task-associated materials to submit (along with instructions) for entry into the competitions, open to MIT students and affiliates during the IAP offering. This includes MIT students/affiliates who are taking the class as listeners -- you are eligible! These instructions are provided at the end of each of the labs. Completing these tasks and submitting your materials to Canvas will enter you into a per-lab competition. MIT students and affiliates will be eligible for prizes during the IAP offering; at the end of the course, prize-winners will be awarded with their prizes. All competition submissions are due on January 26 at 11:59pm ET to Canvas. For the software lab competitions, submissions will be judged on the basis of the following criteria: Strength and quality of final results (lab dependent) Soundness of implementation and approach Thoroughness and quality of provided descriptions and figures Gather.Town lab + Office Hour sessions After each day’s lecture, there will be open Office Hours in the class GatherTown, up until 3pm ET. An MIT email is required to log in and join the GatherTown. During these sessions, there will not be a walk through or dictation of the labs; the labs are designed to be self-paced and to be worked on on your own time. The GatherTown sessions will be hosted by course staff and are held so you can: Ask questions on course lectures, labs, logistics, project, or anything else; Work on the labs in the presence of classmates/TAs/instructors; Meet classmates to find groups for the final project; Group work time for the final project; Bring the class community together. Final project To satisfy the final project requirement for this course, students will have two options: (1) write a 1 page paper review (single-spaced) on a recent deep learning paper of your choice or (2) participate and present in the project proposal pitch competition. The 1 page paper review option is straightforward, we propose some papers within this document to help you get started, and you can satisfy a passing grade with this option -- you will not be eligible for the grand prizes. On the other hand, participation in the project proposal pitch competition will equivalently satisfy your course requirements but additionally make you eligible for the grand prizes. See the section below for more details and requirements for each of these options. Paper Review Students may satisfy the final project requirement by reading and reviewing a recent deep learning paper of their choosing. In the written review, students should provide both: 1) a description of the problem, technical approach, and results of the paper; 2) critical analysis and exposition of the limitations of the work and opportunities for future work. Reviews should be submitted on Canvas by Thursday Jan 28, 2021, 11:59:59pm Eastern Time (ET). Just a few paper options to consider... https://papers.nips.cc/paper/2017/file/3f5ee243547dee91fbd053c1c4a845aa-Paper.pdf https://papers.nips.cc/paper/2018/file/69386f6bb1dfed68692a24c8686939b9-Paper.pdf https://papers.nips.cc/paper/2020/file/1457c0d6bfcb4967418bfb8ac142f64a-Paper.pdf https://science.sciencemag.org/content/362/6419/1140 https://papers.nips.cc/paper/2018/file/0e64a7b00c83e3d22ce6b3acf2c582b6-Paper.pdf https://arxiv.org/pdf/1906.11829.pdf https://www.nature.com/articles/s42256-020-00237-3 https://pubmed.ncbi.nlm.nih.gov/32084340/ Project Proposal Presentation Keyword: proposal This is a 2 week course so we do not require results or working implementations! However, to win the top prizes, nice, clear results and implementations will demonstrate feasibility of your proposal which is something we look for! Logistics -- please read! You must sign up to present before 11:59:59pm Eastern Time (ET) on Wednesday Jan 27, 2021 Slides must be in a Google Slide before 11:59:59pm Eastern Time (ET) on Thursday Jan 28, 2021 Project groups can be between 1 and 5 people Listeners welcome To be eligible for a prize you must have at least 1 registered MIT student in your group Each participant will only be allowed to be in one group and present one project pitch Synchronous attendance on 1/29/21 is required to make the project pitch! 3 min presentation on your idea (we will be very strict with the time limits) Prizes! (see below) Sign up to Present here: by 11:59pm ET on Wednesday Jan 27 Once you sign up, make your slide in the following Google Slides; submit by midnight on Thursday Jan 28. Please specify the project group # on your slides!!! Things to Consider This doesn’t have to be a new deep learning method. It can just be an interesting application that you apply some existing deep learning method to. What problem are you solving? Are there use cases/applications? Why do you think deep learning methods might be suited to this task? How have people done it before? Is it a new task? If so, what are similar tasks that people have worked on? In what aspects have they succeeded or failed? What is your method of solving this problem? What type of model + architecture would you use? Why? What is the data for this task? Do you need to make a dataset or is there one publicly available? What are the characteristics of the data? Is it sparse, messy, imbalanced? How would you deal with that? Project Proposal Grading Rubric Project proposals will be evaluated by a panel of judges on the basis of the following three criteria: 1) novelty and impact; 2) technical soundness, feasibility, and organization, including quality of any presented results; 3) clarity and presentation. Each judge will award a score from 1 (lowest) to 5 (highest) for each of the criteria; the average score from each judge across these criteria will then be averaged with that of the other judges to provide the final score. The proposals with the highest final scores will be selected for prizes. Here are the guidelines for the criteria: Novelty and impact: encompasses the potential impact of the project idea, its novelty with respect to existing approaches. Why does the proposed work matter? What problem(s) does it solve? Why are these problems important? Technical soundness, feasibility, and organization: encompasses all technical aspects of the proposal. Do the proposed methodology and architecture make sense? Is the architecture the best suited for the proposed problem? Is deep learning the best approach for the problem? How realistic is it to implement the idea? Was there any implementation of the method? If results and data are presented, we will evaluate the strength of the results/data. Clarity and presentation: encompasses the delivery and quality of the presentation itself. Is the talk well organized? Are the slides aesthetically compelling? Is there a clear, well-delivered narrative? Are the problem and proposed method clearly presented? Past Project Proposal Ideas Recipe Generation with RNNs Can we compress videos with CNN + RNN? Music Generation with RNNs Style Transfer Applied to X GAN’s on a new modality Summarizing text/news articles Combining news articles about similar events Code or spec generation Multimodal speech → handwriting Generate handwriting based on keywords (i.e. cursive, slanted, neat) Predicting stock market trends Show language learners articles or videos at their level Transfer of writing style Chemical Synthesis with Recurrent Neural networks Transfer learning to learn something in a domain for which it’s hard or risky to gather data or do training RNNs to model some type of time series data Computer vision to coach sports players Computer vision system for safety brakes or warnings Use IBM Watson API to get the sentiment of your Facebook newsfeed Deep learning webcam to give wifi-access to friends or improve video chat in some way Domain-specific chatbot to help you perform a specific task Detect whether a signature is fraudulent Awards + Categories Final Project Awards: 1x NVIDIA RTX 3080 4x Google Home Max 3x Display Monitors Software Lab Awards: Bose headphones (Lab 1) Display monitor (Lab 2) Bebop drone (Lab 3) Important Links and Emails Course website: http://introtodeeplearning.com Course staff: introtodeeplearning-staff@mit.edu Piazza forum (MIT only): https://piazza.com/mit/spring2021/6s191 Canvas (MIT only): https://canvas.mit.edu/courses/8291 Software lab repository: https://github.com/aamini/introtodeeplearning Lab/office hour sessions (MIT only): https://gather.town/app/56toTnlBrsKCyFgj/MITDeepLearning
XinhaoLi74 / SmilesPESMILES Pair Encoding: A data-driven substructure representation of chemicals
thsa / DatawarriorInteractive data analysis and visualisation with chemical intelligence
rxn4chemistry / Rxn YieldsCode complementing our manuscript on the prediction of chemical reaction yields (https://iopscience.iop.org/article/10.1088/2632-2153/abc81d) and data augmentation strategies (https://doi.org/10.26434/chemrxiv.13286741).
sustainable-processes / ORDerlyChemical reaction data & benchmarks. Extraction and cleaning of data from Open Reaction Database (ORD)
molinfo-vienna / CDPKitThe Chemical Data Processing Toolkit
orbkit / OrbkitA Toolbox for Post-Processing Quantum Chemical Wavefunction Data
Fangyinfff / KCLCode and Data for the paper: Molecular Contrastive Learning with Chemical Element Knowledge Graph [AAAI 2022]
rinikerlab / Lightweight Registrationlwreg is a lightweight registration system for chemical registration and data storage.
FiammettaC / Chemical Reaction Engineering In PythonThis repository contains a practical course designed for chemical engineers that want to learn how to solve exercises and program in Python. The course will cover various topics, such as basic Python syntax, data structures, solving ODEs, stoichiometry, data visualization and basic data analysis.
LopezGroup-ICIQ / CareAutomated creation and manipulation of Chemical Reaction Networks (CRNs) in heterogeneous catalysis, allowing the evaluation of species and reaction properties with data-driven ML models and the network simulation with microkinetic modelling.
FiammettaC / AI For Chemical EngineersThis is a practical course designed for chemical engineers that want to learn the basics of AI. The course is very practical and will cover various topics, such as basic Python syntax, data visualization, machine learning and deep learning models, natural language processing, image processing and explainability.
hkaneko1985 / DcekitDCEKit (Data Chemical Engineering toolKit)
aksub99 / Molecular VaePytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"
