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4,090 results for “Protocol”
scGPT: End-to-End Protocol for Fine-tuned Retina Cell Type Annotation
<h1>Abstract</h1> <p>Single-cell research faces challenges in accurately annotating cell types at high resolution, especially when dealing with large-scale datasets and rare cell populations. To address this, foundation models like scGPT offer flexible, scalable solutions by leveraging transformer-based architectures. This protocol provides a comprehensive guide to fine-tuning scGPT for cell-type classification in single-cell RNA sequencing (scRNA-seq) data. We demonstrate how to fine-tune scGPT on a custom retina dataset, highlighting the model’s efficiency in handling complex data and improving annotation accuracy achieving 99.5% F1-score. This protocol automates key steps, including data preprocessing, model fine-tuning, and evaluation. This protocol enables researchers to efficiently deploy scGPT for their own datasets. The provided tools, including a command-line script and Jupyter Notebook, simplify the customization and exploration of the model, proposing an accessible workflow for users with minimal Python and Linux knowledge. The protocol offers an off-the-shell solution of high-precision cell-type annotation using scGPT for researchers with intermediate bioinformatics.</p>
GIS Protocol for Multy-Scale Emerging Hot Spot Analysis
<p>This GIS protocol is primarily intended as supplementary material to the article (Štular et al., 2022). The article contains important contextual information about its intended use. In short, this GIS protocol was developed for the purposes of archaeological regional analysis of spatial data. The data are provided elsewhere in spreadsheet format (Štular et al., 2021). Data in GIS format are included in this repository. The GIS protocol can be used with any relevant data for any purpose as long as the data format matches the format of the included data.</p> <p>Includes GIS protocol (textual description) and GIS data in *.shp format.</p>
Compliance of the Parties to the Kyoto Protocol: 2008-19
<p>Addition of Latest data available on Second Commitment Period (2012-20), extracted from final data for national GHG emissions from OECD Statistics </p>
Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination
<p>Submissions for the Tractostorm 2 Project [1] from our collaborators (raters) are available for new analysis.<br> Contains regions of interest (ROIs) as well as resulting bundles. Segmentations were performed with MI-Brain [2] (<a href="https://github.com/imeka/mi-brain">MI-Brain</a>)</p> <p>Initial data is the same as in the initial <a href="https://zenodo.org/record/2547025#.YRV2S3VKiUk">Tractostorm Project</a> [3]<br> Contains the data as sent to collaborators and the written document containing the dissection protocol in detail.</p> <p>[1] Rheault, Francois, et al. "Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination." <em>Human Brain Mapping</em> (2022).<br> [2] Rheault, Francois, et al. "MI-Brain, a software to handle tractograms and perform interactive virtual dissection." <em>Proceedings of the ISMRM Diffusion study group workshop, Lisbon</em>. 2016.<br> [3] Rheault, Francois, et al. "Tractostorm: The what, why, and how of tractography dissection reproducibility." <em>Human brain mapping</em> 41.7 (2020): 1859-1874.</p> <p>Data Organization:<br> The 5 HCP subjects were duplicated 4 times each.<br> 193441 -> A111, B218, C317, D418<br> 219231 -> A127, B228, C320, D426<br> 286650 -> A136, B237, C338, D436<br> 486759 -> A149, B246, C344, D443<br> 615441 -> A156, B252, C359, D450<br> <br> Bundles can be segmented automatically using the <a href="https://github.com/scilus/scilpy">scilpy</a> toolbox.<br> scil_filter_tractogram.py ${INPUT} ${OUTPUT} ${OPTIONS}</p> <ul> <li>${INPUT} would be the whole brain tractogram of an HCP subject in data_to_segment.zip</li> <li>${OUTPUT} would be the bundle filename (preferably .trk format)</li> <li>${OPTIONS} would be the sequence of ROIs to apply, one for each bundle. <ul> <li><strong>CC</strong>: '--drawn_roi CENTRAL_CC.nii.gz any include --drawn_roi LOWER_AXIAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude --drawn_roi POST_C_R.nii.gz any exclude --drawn_roi PRE_C_R.nii.gz any exclude'</li> <li><strong>AF_L</strong>: '--drawn_roi CENTRAL_CS_L.nii.gz any include --drawn_roi MEDIAL_SAGITTAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any include --drawn_roi PRE_C_L.nii.gz any include --drawn_roi TEMPORAL_ENTRY.nii.gz any include --drawn_roi TEMPORAL_STEM.nii.gz any exclude'</li> <li><strong>PYT_L</strong>: '--drawn_roi IC_L.nii.gz any include --drawn_roi MO_L.nii.gz any include --drawn_roi MB_L.nii.gz any include --drawn_roi MO_L_NOT.nii.gz any exclude --drawn_roi MID_SAGITTAL_PLANE.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude'</li> </ul> </li> </ul>
MIDAS2 protocol example output files
<p>Example output for MIDAS2 protocols including all the basic and supporting protocols.</p>
MIDAS2 protocol example custom genome collection dataset v1
<p>Example input database of custom genome collection for MIDAS2 protocols.</p> <p>Two genomes from two species (<em>Staphylococcus epidermidis </em>and <em>Streptococcus mutans </em>)</p>
MIDAS2 protocol example input dataset v1
<p>Example input dataset for MIDAS2 protocols. </p> <p>Include single-end sequencing reads for two HMP mock community samples: SRR172902 and SRR172903.</p>
Raw Data for the Protocol: Antibody-Assisted Selective Isolation of Purkinje Cell Nuclei
<p>Sun1/sfGFP+, Pcp2-Cre+ and Sun1/sfGFP+, Pcp2-Cre- cryosectioned cerebella immunostained for the Myc tag (files 3037, 3046), which is fused to the GFP protein, Calbindin (files 3038, 3047) and Hoechst (files 3036, 3045). </p> <p> </p> <p>Original uncropped images from western blot analysis of TOM20, Histone H3, and GAPDH.</p>
BRAIN Journal-About the Design of QUIC Firefox Transport Protocol-Figure 2. QUIC vs TLS handshake protocol
<p>Figure 2 describes a sequence diagram using QUIC VS TLS handshake protocol. The right<br> side of Figure 2 shows the seven steps of calls and returns until a HTTP Get() method is<br> successfully implemented using a TLS handshake. In contrast, on the left side of Figure 2, we see<br> the implementation of HTTP Get() method using a single call of QUIC handshake.<br> Firefox is a completely open source browser with a tremendous community support. The<br> latest version of Firefox supports TLS 1.3 protocol in an experimental stage. The primary purpose<br> of this study was integrating the QUIC protocol in the Firefox web browser. The source code of this<br> software product is as large as 650MB. </p> <p> </p>
BRAIN Journal-About the Design of QUIC Firefox Transport Protocol-Figure 1. TLS vs QUIC protocol stack
<p>QUIC addresses many network problems such as the Head Of Line (HOL) blocking as well as the TCP reconnection over a subnet/network change. In addition, QUIC has many features such as connection IDs, which can overcome the challenge of changing networks. In this way, if someone switches from a WIFI network to a cellular network, the connection to the server will not be broken or lost. Paper (Langley and Chang, 2016) described the QUIC crypto protocol, representing the part of QUIC that provides transport security to a connection. The QUIC crypto protocol is now replaced by TLS 1.3. Currently, QUIC provides security of TLS 1.3 (in an experimental stage), considered the highest security standards for the communication protocols (Valsorda; 2016). </p> <p>Figure 1 describes the TLS vs. QUIC protocol user level stack in the context of application layer and transport layer.</p>
Supporting Jupyter Python notebook for "A new class of efficient randomized benchmarking protocols"
<p>Python notebook containing the code used to generate the data for figure 2 in the appendix of "A new class of efficient randomized benchmarking protocols" (arXiv:1806.02048).</p>
Genome alignments for the project "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol" - Protocol optimization
<p>Genome alignments for data generated in the project "<em>Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol – Optimization of the protocol.</em>" Files names indicate unique identifiers of MOIRAI workflow runs, with the following structure: library name, dot, workflow ID (OP-WORKFLOW-CAGEscan-short-reads-v2.0.), dot, timestamp. The raw (FASTQ) data of each library is also deposited in Zenodo (<a href="https://doi.org/10.5281/zenodo.250156">10.5281/zenodo.250156</a>). Library names correspond to the following runs:</p> <ul> <li> NC33: 151007_M00528_0161_000000000-AEBDC</li> <li> NC37: 151204_M00528_0173_000000000-AEBEF</li> <li> NC38: 151211_M00528_0175_000000000-AE9PJ</li> <li> NC39: 160122_M00528_0185_000000000-AEB18</li> <li> NC42: 160302_M00528_0192_000000000-AELYK</li> </ul> <p>This data can be analysed using the "CAGEr" software package available from Bioconductor. The "multiplex_files.zip" file contains tables indicating which samples are biological replicates of each other or negative controls.</p>
Benchmark protocol for exoplanet forward model and retrieval
<p>Benchmark protocol for giant exoplanet atmosphere tools, presented in Baudino et al. 2017 <a href="https://doi.org/10.3847/1538-4357/aa95be">https://doi.org/10.3847/1538-4357/aa95be</a></p> <p>The original data to reproduice the protocol are used in a jupyter notebook "Tutorial.ipynb" including all the plot routines to help to compare with you own models</p>
Additional data for publication: Simple protocol for combined extraction of exocrine secretions and RNA in small arthropods.
<p>Additional data and results are given in this repository. It contains the trimmed reads (fastp; raw reads also on SRA accession numbers SRR29851544-SRR29851549, Bioproject PRJNA1136254), full busco reports for individual transcriptomes, assembly of all six RNAseqs together (transcriptome as base for differential expression analysis) and results of salmon.</p>
Dataset for Advanced Persistent Threat (APT) Attacks on Power Substation Networks via GOOSE Protocol Exploitation
<p>This dataset captures network traffic from a simulated Advanced Persistent Threat (APT) campaign targeting a power substation's communication network. The attacker maintains a prolonged presence within the network, conducting low-profile scans using Nmap to stealthily discover the network configuration. The focus is on the communication between the Remote Terminal Unit (RTU), the Programmable Logic Controller (PLC), and the Bay Protection Unit, all of which utilize the Generic Object Oriented Substation Event (GOOSE) protocol for critical operations.</p>
Dataset for DoS and DDoS Attacks on Digital Meter SICAM via GOOSE Protocol Flooding
<p>This dataset presents network traffic data from simulated Denial of Service (DoS) and Distributed Denial of Service (DDoS) attacks on a Digital Meter SICAM device using the GOOSE protocol. An unauthorized attacker floods the SICAM meter's communication by initially sending 100 GOOSE packets at 1 ms intervals, followed by an intensified attack of 500 GOOSE packets. These actions render the meter unreachable by the legitimate Control Station, disrupting normal operations and data retrieval processes.</p>
Climate Policy Modelling Protocol
<p>This protocol includes current energy and climate policies for major economies, and details the instruments, targets and sectors for each policy. It provides a detailed list of climate policies as well as their quantification (following the Integrated Assessment Modelling Community (IAMC) conventions where possible). The final goal is to translate climate policies into energy and climate model input, and facilitate policy impact projections on greenhouse gas emissions.</p> <p>Climate policy on the national level, is defined as the result of climate policy formulation and climate policy implementation that encompasses aspirational goals not secured by legislation, national targets that are secured by legislation, and policy instruments designed to implement these targets. Only implemented policies are included in this protocol, and are defined as policies adopted by the government through legislation or executive orders, and non-binding targets backed by effective policy instruments.</p> <p>To compose the protocol, first a selection of climate policies with potentially high impact in terms of emission reductions is performed by the policy teams of PBL and NewClimate (<a href="https://www.climatepolicydatabase.org/">Climate Policy Database</a>), and translated into model input indicators. Then, with the help of (inter)national experts and partners, an evaluation round of the selected policies is performed, before finalizing the complete policy list. Policy instruments are represented in the integrated assessment models as explicit as possible, but simplification is sometimes necessary; replicating the impact on greenhouse gas emissions and the energy system transformation is considered as the most important factor. </p> <p>It should be noted that the policy environment is constantly changing, thus policy changes with a possibly high impact may occur between protocol updates that are not included in certain versions. Under ELEVATE, the protocol received major updates in terms of standardization of policy and target variable names and units - according to IAMC conventions, to facilitate use from all Integrated Assessment Models in the community.</p>
Dataset used for: Effectiveness of Acute Malnutrition Treatment at Health Center and Community Level with a Simplified, Combined Protocol in Mali: An Observational Cohort Study
<p>This dataset contains the variables used in the analysis of the body composition and outcomes of the Acute Malnutrition Treatment at Health Center and Community Level with a Simplified, Combined Protocol in Mali pilot study, from December 2018 to December 2021</p>
Dataset supporting publication: "A novel ROM methodology to support the estimation of the energy savings under the Measurement and Verification protocol."
<p>DATASET suporting: "A novel ROM methodology to support the estimation of the energy savings under the Measurement and Verification protocol."</p> <p>Piccinini, Alessandro; Hajdukiewicz, Magdalena; D'Angelo, Letizia; Blanes, Luis Miguel; Keane, Marcus M.</p> <p>This paper presents a novel Reduced Order grey box Model (ROM) methodology, based on a ResistorCapacitor (RC) network, which supports the creation of the baseline energy consumption and the estimation of energy savings due to Energy Conservation Measures (ECMs) under the Measurement and Verification protocol. Within this scope, a description of the RC network, including a calculation of the parameters’ needed to execute the ROM, are presented. This ROM methodology is demonstrated on an educational building located in Sant Cugat, Spain as part of the H2020 GEOFIT project. The results presented in this paper demonstrate that the ROM is sufficiently accurate for the creation of the baseline energy consumption and for estimating the energy savings of different ECMs.</p>
Multidimensional pain profiling in people living with obesity and attending weight management services: a protocol for a longitudinal cohort study
<p><strong>Please note: The final dataset will not be available until data collection has been completed in the Autumn of 2024.<br> This dataset currently contains the following:</strong></p> <p>1. Details of the study, including authorship, ethical approval, funding, registration details, an abstract for the protocol of the study and details of data being collected (both in Microsoft Word and open access .txt formats)</p> <p>2. Outline of the data in the process of collection (Microsoft Excel)</p> <p>3. Ethical approval letters from relevant Research Ethics Committees (PDF)<br> <br> </p> <p> </p> <p><strong>Project Title: </strong>Multidimensional pain profiling in people living with obesity and attending weight management services: a longitudinal cohort study</p> <p> </p> <p><strong>Authors:</strong> Keith M. Smart<sup>1,2</sup>, Natasha Hinwood<sup>1</sup>, Colin G. Dunlevy<sup>3</sup>, Catherine Doody<sup>1</sup>, Catherine Blake<sup>1</sup>, Brona Fullen<sup>1</sup>, Jean O’Connell<sup>3</sup>, Carel W. Le Roux<sup>4</sup>, Clare Gilsenan<sup>5</sup>, Francis M. Finucane<sup>6,7</sup>, Gráinne O’Donoghue<sup>1</sup>.</p> <p> </p> <p><strong>Corresponding author</strong>: Natasha Hinwood</p> <p><strong>Address:</strong> UCD School of Public Health, Physiotherapy and Sport Science, University College Dublin, Dublin, Ireland</p> <p><strong>Email:</strong> <a href="mailto:natasha.hinwood@ucdconnect.ie">natasha.hinwood@ucdconnect.ie</a></p> <p><strong>Phone:</strong> +353 1 716 6511</p> <p> </p> <p>Full name, department, institution, city, and country of all co-authors.</p> <p><sup>1</sup>UCD School of Public Health, Physiotherapy and Sport Science, University College Dublin, Dublin, Ireland</p> <p><sup>2</sup>Physiotherapy Department, St. Vincent’s University Hospital, Dublin, Ireland</p> <p><sup>3</sup>Weight Management Service, St Columcille’s Hospital, Dublin, Ireland</p> <p><sup>4</sup>Diabetes Complications Research Centre, University College Dublin, Dublin, Ireland</p> <p><sup>5</sup>Physiotherapy Department, Beaumont Hospital, Dublin, Ireland</p> <p><sup>6</sup> School of Medicine, College of Nursing and Health Sciences, University of Galway</p> <p><sup>7</sup>Bariatric Medicine Service, Centre for Diabetes, Endocrinology and Metabolism, Galway University Hospitals</p> <p> </p> <p><strong>ORCID</strong></p> <p>1. Keith M. Smart: 0000-0002-1598-5215</p> <p>2. Natasha Hinwood: 0000-0001-9382-716X</p> <p>3. Colin G. Dunlevy:</p> <p>4. Catherine Doody:</p> <p>5. Catherine Blake: 0000-0002-0600-629X</p> <p>6. Brona Fullen: 0000-0003-4408--2063</p> <p>7. Carel W. Le Roux: 0000-0001-5521-5445</p> <p>8. Jean O’Connell: 0000-0001-7241-8025</p> <p>9. Clare Gilsenan:</p> <p>10. Francis M. Finucane: 0000-0002-5374-7090</p> <p>11. Gráinne O’Donoghue: 0000-0002-9126-2094</p> <p> </p> <p> </p> <p><strong>Project abstract (Protocol): </strong></p> <p><em>Introduction</em>:</p> <p>Pain is prevalent in people living with overweight and obesity. Obesity is associated with increased self-reported pain intensity and pain-related disability, reductions in physical functioning and poorer psychological well-being. People living with obesity tend to respond less well to pain treatments or management compared to people living without obesity. Mechanisms linking obesity and pain are complex and may variously include contributions from and interactions between physiological, behavioural, psychological, socio-cultural, biomechanical, and genetic factors. Our aim is to study the multidimensional pain profiles of people living with obesity, over time, in an attempt to better understand the relationship between obesity and pain.<br> </p> <p><em>Methods and analysis: </em></p> <p>This longitudinal observational cohort study will recruit (n=216) people living with obesity and who are newly attending three weight management services in Ireland. Participants will complete questionnaires that assess their multidimensional biopsychosocial pain experience at baseline and at 3, 6, 12 and 18-months post-recruitment. Quantitative analyses will characterise the multidimensional pain experiences and trajectories of the cohort as a whole and in defined sub-groups.<br> </p> <p><em>Ethics and dissemination: </em></p> <p>The study protocol has been approved by the Ethics and Medical Research Committee of St Vincent’s Healthcare Group, Dublin, Ireland (Reference No.: RS21-059) and the University College Dublin Human Research Ethics Committee (Reference No.: LS-E-22-41-Hinwood-Smart). Findings will be disseminated through peer-reviewed journals, conference presentations, public and patient advocacy groups, and social media.</p>
ScienceDex guides
Understand access before you commit
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.