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21 results for “papyrus”
Dataset - Papyrus 05.4 - A large scale curated dataset aimed at bioactivity predictions
<div> <p>This repository contains the version 05.5 of the Papyrus dataset, an aggregated dataset of small molecule bioactivities, as described in the article "Papyrus - A large scale curated dataset aimed at bioactivity predictions" <a href="https://doi.org/10.26434/chemrxiv-2021-1rxhk">https://doi.org/10.26434/chemrxiv-2021-1rxhk</a>.</p> <p> </p> <p>With the ongoing rapid growth of publicly available ligand-protein bioactivity data, there is a trove of valuable data that can be used to train a plethora of machine learning algorithms. However, not all data is equal in terms of size and quality and a significant portion of researchers’ time is needed to adapt the data to their needs. On top of that, finding the right data for a research question can often be a challenge on its own. To meet these challenges we have constructed the Papyrus dataset. Papyrus is comprised of around 60 million datapoints. This dataset contains multiple large publicly available datasets such as ChEMBL and ExCAPE-DB combined with several smaller datasets containing high-quality data. The aggregated data has been standardised and normalised in a manner that is suitable for machine learning. We show how data can be filtered in a variety of ways and also perform some example quantitative structure-activity relationship analyses and proteochemometric modelling. Our ambition is that this pruned data collection constitutes a benchmark set that can be used for constructing predictive models, while also providing a solid baseline for related research.</p> </div>
Accompanying data - Papyrus - A large scale curated dataset aimed at bioactivity predictions
<p><strong>Addition of supporting files:<br>- </strong>LICENSE.txt<strong><br>- </strong>data_types.json<strong><br>- </strong>data_size.json</p> <p> </p> <p><strong>Fixed version of Papyrus++ 05.5:<br>- In the previous 05.5 version </strong>data was incorrectly duplicated based on assay type. This resulted in unintended data augmentation.<br><strong>- In this fixed 05.5 version</strong> the duplicates have been eliminated, now reporting the correct amount of data per assay type.</p> <p> </p> <p>This repository contains the version 05.5 of the Papyrus dataset, an aggregated dataset of small molecule bioactivities, as described in the article "Papyrus - A large scale curated dataset aimed at bioactivity predictions" <a href="http://doi.org/10.1186/s13321-022-00672-x">http://doi.org/10.1186/s13321-022-00672-x</a>.</p> <p> </p> <p>With the ongoing rapid growth of publicly available ligand-protein bioactivity data, there is a trove of valuable data that can be used to train a plethora of machine learning algorithms. However, not all data is equal in terms of size and quality and a significant portion of researchers’ time is needed to adapt the data to their needs. On top of that, finding the right data for a research question can often be a challenge on its own. To meet these challenges we have constructed the Papyrus dataset. Papyrus is comprised of around 60 million datapoints. This dataset contains multiple large publicly available datasets such as ChEMBL and ExCAPE-DB combined with several smaller datasets containing high-quality data. The aggregated data has been standardised and normalised in a manner that is suitable for machine learning. We show how data can be filtered in a variety of ways and also perform some example quantitative structure-activity relationship analyses and proteochemometric modelling. Our ambition is that this pruned data collection constitutes a benchmark set that can be used for constructing predictive models, while also providing a solid baseline for related research.</p>
Dataset - Papyrus 2024 - A large scale curated dataset aimed at bioactivity predictions
<p><strong>This update of release 2024.1 fixes the following:</strong></p> <ul> <li>Metadata in the columns <em>type_IC50</em>, <em>type_EC50</em>, <em>type_KD</em>, <em>type_Ki</em>, and <em>type_other</em> did not contain multiple values when multiple pChEMBL values where available but reported only a single value. This fix ensures all values are reported.</li> <li>Molecules were incorrectly standardized and mixtures were included in the dataset. Standardization (using the <a href="https://github.com/OlivierBeq/papyrus_structure_pipeline" target="_blank" rel="noopener">papyrus_structure_pipeline</a>) is now correctly enforced and mixtures have been removed.</li> </ul> <p><strong>Changes since version 05.6</strong></p> <ul> <li>ChEMBL data was updated to ChEMBL version 34</li> <li>data from the IUPHAR/BPS Guide to PHARMACOLOGY has been included</li> <li>data from Pickett et al.'s publication on MMP-12 has been included (<a href="https://doi.org/10.1021/ml100191f">ACS Med Chem Lett. 2011 Jan 13; 2(1): 28–33. DOI: 10.1021/ml100191f</a>)</li> </ul> <p><strong>Papyrus++:</strong></p> <p>Previous versions mistakenly considered a deviation of 2 log units around compound-target pairs to determine the reproducibility of assays (see published article for more details). This has been fixed to 0.5 log units to ensure data points fall within a maximum range of 1 log unit. As a result, the number of entries in the Papyrus++ set from this release has drastically reduced compared to previous releases.</p>
Papyrus dataset postgres dump
<p>The dataset that the database dump was created from is described here: <a href="https://doi.org/10.33774/chemrxiv-2021-1rxhk">10.33774/chemrxiv-2021-1rxhk</a><br> <br> A dump of the postgres database created from the code in the 'postgres' directory (<a href="https://github.com/reskyner/Papyrus-scripts">Papyrus-scripts</a>/<a href="https://github.com/reskyner/Papyrus-scripts/tree/master/src">src</a>/<a href="https://github.com/reskyner/Papyrus-scripts/tree/master/src/papyrus_scripts">papyrus_scripts</a>/<strong>postgres</strong>/) of Rachael Skyner's fork (https://github.com/reskyner/Papyrus-scripts) of Oliver Bequignon's Papyrus-scripts github (https://github.com/OlivierBeq/Papyrus-scripts). The database was created by:</p> <p>1. Download the papyrus csv files from Oliver's code using the download functionality</p> <p>2. Spin up a 'papyrus' container using the docker-compose.yml file in Rachael's fork (running on a machine with access to the postgres instance you want to add the database to)</p> <p>3. Start a shell in the papyrus container with docker exec -it papyrus /bin/bash</p> <p>4. Start a jupyter notebook server with jupyter notebook --ip 0.0.0.0 --allow-root --no-browser</p> <p>5. Run the two notebooks (<a href="https://github.com/reskyner/Papyrus-scripts/blob/master/src/papyrus_scripts/postgres/notebooks/1-insert_molecule_data.ipynb">1-insert_molecule_data.ipynb</a> and <a href="https://github.com/reskyner/Papyrus-scripts/blob/master/src/papyrus_scripts/postgres/notebooks/2-insert_activities.ipynb">2-insert_activities.ipynb</a>) in order</p> <p>6. Create a dump of the database</p>
Dataset - Papyrus - A large scale curated dataset aimed at bioactivity predictions
<p><strong>Fixed version of additional_files:</strong></p> <p><strong>- In the previous version of 05.6_additional_files</strong> the data type of some descriptors was assigned incorrectly</p> <p><strong>- In this fixed version </strong>data types are correct </p> <p>This repository contains version 05.6 of the Papyrus dataset, an aggregated dataset of small molecule bioactivities, as described in the article "Papyrus - A large scale curated dataset aimed at bioactivity predictions" doi.org/10.1186/s13321-022-00672-x.</p> <p>Changes compared to version 05.5</p> <p>- applied small molecule filter that filters out compounds with a MW < 200 or > 800, heavy metal containing compounds and mixtures</p> <p>- include TID column which contains information on the original protein identifier</p>
FIG. 2 in The Brooklyn snake papyrus: why the enigmatic k could be a chameleon
FIG. 2. — Common chameleon (Chamaeleo chamaeleon (Linnaeus, 1758)) tongue protrusion. Photo credit: Mehmetkrckrc (CC BY-SA 4.0). https://commons. wikimedia.org/wiki/File:Hunter_chameleon.jpg, last consultation on 22 November 2022.
FIG. 1 in The Brooklyn snake papyrus: why the enigmatic k could be a chameleon
FIG. 1. — Common chameleon (Chamaeleo chamaeleon (Linnaeus, 1758)). Photo credit: mirecca (https://www.istockphoto.com).
Papyrus
Egyptian papyrus roll for your 3d level, scene whatever.. old model and 512 map.. but still pretty cool tho. color spec and normal map. Source: Objaverse 1.0 / Sketchfab
Egyptian papyrus column
Pretty low poly and low res Egyptian Papyrus Column for WebGL rendering. Source: Objaverse 1.0 / Sketchfab
A binding model of Greek Papyrus 28
Peri palmon mantike (Divination by twitches) Egypt, 4th century AD Greek Papyrus 28 This manuscript is composed of four papyrus sheets, each with four pages of text (two on each side). The four sheets were put one on top of the other, folded and then stitched together. There are remains of sewing thread on some sheets. The subject of the book is prognostications to be derived from involuntary movement (quivering or twitching) of various parts of the body. That such movements portended certain events was a popular belief which finds expression in both Greek and Latin classical literature. The various members of the body are taken one after the other, starting from the head downwards, and the omens associated with their movement are concisely enumerated. After the prognostications, directions are given to pray to or propitiate appropriate divinities. Source: Objaverse 1.0 / Sketchfab
Papyrus
Ancient papyrus. Maybe this papyrus was created by the Aztecs or the tribe Autodesk Maya; Used: Autodesk Maya, Zbrush, Substance Painter; Instagram: Evgenius.blat; Telegram: EvGusAr; Source: Objaverse 1.0 / Sketchfab
Byzantine-Medieval Papyrus
Demo of converting existing 2D > 3D to show the ability to re-unite a 2 sided object previously displayed as two separate images. https://findit.library.yale.edu/catalog/digcoll:2759453 Source: Objaverse 1.0 / Sketchfab
Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands
<p>Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of <em>Cyperus papyrus</em> in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream of the Zambezi river basin. Our results also point to the very low genetic diversity of <em>C</em>. <em>papyrus</em> populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.</p>
The PAPYRUS Study: Permanent vs. Absorbable Sutures in PrimarY Repair of Umbilical HerniaS: A Multicentre, Single-blind, Non-inferiority, Randomized Controlled Trial
ClinicalTrials.gov study NCT07156188. IPD Sharing: NO. Countries: 1. Publications: 32.
Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands
Open the record for dataset details and reuse information.
Social Network. El infinito en un junco. Papyrus: The Invention of Books in the Ancient World
Open the record for dataset details and reuse information.
Papyrus Scroll (New Kingdom)
This is a papyrus scroll from the Egyptian New Kingdom. It is from a sarcophagus and is written in demotic script. This artifact was obtained by Edwin Osgood Grover and is currently housed in the Rollins College Archives. This model was made by Ellie Minette. Created in RealityCapture by Capturing Reality from 249 photos. Source: Objaverse 1.0 / Sketchfab
egyptian papyrus
Created in RealityCapture by Capturing Reality from 23 images in 00h:04m:16s. austinbeaulier.com ufosnap.com Source: Objaverse 1.0 / Sketchfab
Papyrus
* Nome do aluno: Víctor Costa Pôças * Disciplina: Modelagem de objetos * Curso: Curso superior de tecnologia em Jogos Digitais da Puc Minas * Nome do modelo: Papiro * Descrição: Modelo feito para composição de cenário, possui 40 vertices, 32 faces e 64 tris. * Contato: victu.draw@gmail.com * This model was made in: June 2018 Source: Objaverse 1.0 / Sketchfab
PK Papyrus Covered Coronary Stent System
ClinicalTrials.gov study NCT06223633. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.