SARS-CoV-2 NCBI consensus submission protocol: GenBank v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Emma Griffiths ◽  
Lee Katz ◽  
Duncan MacCannell ◽  
Michael Weigand
Keyword(s):  
Large Volume ◽  
Consensus Sequence ◽  
Raw Data ◽  
Data Submission ◽  
Sequence Read Archive ◽  
Specific Protocol ◽  
Set Up ◽  
Laboratory Submission

This is a SARS-CoV-2 specific protocol that covers the steps needed to submit SARS-CoV-2 consensus sequence to GenBank. If you need a pipeline for frequent or large volume submissions, follow Step 1 in the SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. This protocol assumes (and requires) that the user has a BioProject and BioSamples(s) already registered. Complete in order:: 1. Populate your templates first. 2. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort. SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample. Users can modify this protocol to just create a BioSample with no linked raw data. 3. SARS-CoV-2 NCBI consensus submission protocol: GenBank (included protocol) Required: established BioProject and BioSamples Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data. Version history: V3: Direct links provided to download metadata templates (instead of hosting duplicate files). minor edits throughout the protocol.

SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Emma Griffiths ◽  
Duncan MacCannell ◽  
Lee Katz ◽  
Michael Weigand
Keyword(s):  
Large Volume ◽  
Web Interface ◽  
Raw Data ◽  
Data Submission ◽  
Sequence Read Archive ◽  
Specific Protocol ◽  
The Creation ◽  
Set Up ◽  
Laboratory Submission

PURPOSE: This is a SARS-CoV-2 specific protocol that covers the steps needed to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in the SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. These protocols cover submission using NCBI's Submission Portal web-interface. Complete in order:: 1. Populate your templates first. 2. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject (included protocol) Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort. SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample. Users can modify this protocol to just create a BioSample with no linked raw data. 3. SARS-CoV-2 NCBI consensus submission protocol: GenBank Required: established BioProject and BioSamples Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data. Version history: V4: Direct links provided to download metadata templates (instead of hosting duplicate files). Other minor edits throughout the protocol.

Overview of NCBI's SARS-CoV-2 submission process and the metadata required v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Emma Griffiths ◽  
Lee Katz ◽  
Michael Weigand
Keyword(s):  
Raw Data ◽  
Data Submission ◽  
Sequence Read Archive ◽  
Submission Process ◽  
Laboratory Submission

PURPOSE: This protocol explains the metadata requirements for the following two protocols: 1. SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission account and for creating and linking a new BioProject to an existing umbrella effort. SARS-CoV-2 raw data submission to SRA (Sequence Read Archive) and metadata to BioSample. Users can modify this protocol to just create a BioSample with no linked raw data. 2. SARS-CoV-2 NCBI consensus submission protocol: GenBank Required: established BioProject and BioSamples Submit SARS-CoV-2 assemblies to NCBI GenBank, linking to existing BioProject, BioSamples, and raw data. Version history: V4: Updated metadata templates to reflect updated PHA4GE templates (V3) plus minor text edits.

NCBI submission protocol for microbial pathogen surveillance v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey ◽  
Robyn Randolph ◽  
Julie Haendiges ◽  
Sai Laxmi Gubbala Venkata ◽  
...  
Keyword(s):  
Active Surveillance ◽  
Genome Sequence ◽  
Large Volume ◽  
Pathogen Detection ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Web Interface ◽  
Data Submission ◽  
Set Up

PURPOSE: Step-by-step instructions for submitting pathogen whole genome sequence data to NCBI and to the NCBI Pathogen Detection portal. This protocol covers the steps needed to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. SCOPE: for use by any laboratory submitting WGS data for species under active surveillance within NCBI’s Pathogen Detection. (This includes US laboratories in GenomeTrakr, NARMS, Vet-LIRN, PulseNet, and other non-US networks and submitters). For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. This protocol covers submission using NCBI's Submission Portal web-interface. Version history: V5: Linking directly to the metadata template guidance instead of including duplicate copies of the files in this protocol. Updated screenshot for choosing the pathogen template to reflect changes at NCBI. V4: updated screenshots to reflect NCBI submission portal changes. Updated custom BioSample template.

NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject v2

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Large Volume ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Set Up

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API. Version updates: V2: minor edits to the BioSample and SRA templates

NCBI submission protocol for SARS-CoV-2 wastewater data: SRA, BioSample, and BioProject v1

2021 ◽  
Author(s):  
Ruth E Timme ◽  
Maria Balkey
Keyword(s):  
Quality Control ◽  
Food Safety ◽  
Genome Sequencing ◽  
Large Volume ◽  
Rna Extraction ◽  
Data Submission ◽  
Sequencing Quality ◽  
Project Monitoring ◽  
Pandemic Response ◽  
Set Up

PURPOSE: This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr’s pandemic response project, monitoring SARS-CoV-2 variants in wastewater​​. Protocols developed for this project cover wastewater collection, concentration, RNA extraction, RT-qPCR, library prep, genome sequencing, quality control checks, and data submission to NCBI. This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol then walks through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal. For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission. If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact [email protected] to set up an account for submitting through the API.

scholarly journals Comparative membrane proteomics: a technical advancement in the search of renal cell carcinoma biomarkers

2015 ◽  
Vol 11 (6) ◽  
pp. 1708-1716 ◽  
Author(s):  
Francesca Raimondo ◽  
Samuele Corbetta ◽  
Andrea Savoia ◽  
Clizia Chinello ◽  
Marta Cazzaniga ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Membrane Protein ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Protein Analysis ◽  
Comparative Proteomics ◽  
Label Free ◽  
Membrane Proteomics ◽  
Specific Protocol ◽  
Set Up

Set-up of a specific protocol for membrane protein analysis, applied to label free, comparative proteomics of renal cell carcinoma microdomains.

On-Line Industrial 3D Measurement Techniques for Large Volume Objects

2005 ◽  
Vol 295-296 ◽  
pp. 423-430 ◽  
Author(s):  
Ji Gui Zhu ◽  
S.H. Ye ◽  
Xue You Yang ◽  
Xing Hua Qu ◽  
C.J. Liu ◽  
...  
Keyword(s):  
Large Volume ◽  
Measurement Techniques ◽  
Integrated System ◽  
3D Measurement ◽  
Digital Cameras ◽  
Combined Use ◽  
Small Set ◽  
Close Range ◽  
On Line ◽  
Set Up

Rapid progress in modern manufacturing demands for better measurement technique with on-line characteristics. This paper presents a systematic visual solution for on-line industrial 3D measurement. The solution comprises two parts, a multi-sensor visual inspecting station (MSVIS) and a digital close-range visual inspecting station (DCVIS). MSVIS is an integrated system with many sensors. It can meet the requirement of application with sparse measuring points distributed within a large volume. DCVIS only contains two digital cameras with one or more projectors. It has high relative accuracy and a small set up volume and is suitable for applications with dense measuring points. The combined use of MSVIS and DCVIS can provide a general solution for on-line industrial 3D measurement.

scholarly journals Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1488 ◽  
Author(s):  
Chao Zhang ◽  
Jochem Bijlard ◽  
Christine Staiger ◽  
Serena Scollen ◽  
David van Enckevort ◽  
...  
Keyword(s):  
Translational Research ◽  
Data Access ◽  
Data File ◽  
Molecular Profiling ◽  
Study Data ◽  
Test Case ◽  
Data Types ◽  
Raw Data ◽  
Data Volume ◽  
Set Up

The availability of high-throughput molecular profiling techniques has provided more accurate and informative data for regular clinical studies. Nevertheless, complex computational workflows are required to interpret these data. Over the past years, the data volume has been growing explosively, requiring robust human data management to organise and integrate the data efficiently. For this reason, we set up an ELIXIR implementation study, together with the Translational research IT (TraIT) programme, to design a data ecosystem that is able to link raw and interpreted data. In this project, the data from the TraIT Cell Line Use Case (TraIT-CLUC) are used as a test case for this system. Within this ecosystem, we use the European Genome-phenome Archive (EGA) to store raw molecular profiling data; tranSMART to collect interpreted molecular profiling data and clinical data for corresponding samples; and Galaxy to store, run and manage the computational workflows. We can integrate these data by linking their repositories systematically. To showcase our design, we have structured the TraIT-CLUC data, which contain a variety of molecular profiling data types, for storage in both tranSMART and EGA. The metadata provided allows referencing between tranSMART and EGA, fulfilling the cycle of data submission and discovery; we have also designed a data flow from EGA to Galaxy, enabling reanalysis of the raw data in Galaxy. In this way, users can select patient cohorts in tranSMART, trace them back to the raw data and perform (re)analysis in Galaxy. Our conclusion is that the majority of metadata does not necessarily need to be stored (redundantly) in both databases, but that instead FAIR persistent identifiers should be available for well-defined data ontology levels: study, data access committee, physical sample, data sample and raw data file. This approach will pave the way for the stable linkage and reuse of data.

scholarly journals Investigation of thermo-oxidative ageing effects on the fatigue design of automotive anti-vibration parts

2018 ◽  
Vol 165 ◽  
pp. 08004
Author(s):  
Morgane Broudin ◽  
Yann Marco ◽  
Vincent Le Saux ◽  
Pierre Charrier ◽  
Wilfried Hervouet ◽  
...  
Keyword(s):  
Degradation Process ◽  
Fatigue Properties ◽  
Anaerobic Conditions ◽  
Rubber Material ◽  
Fatigue Design ◽  
Specific Protocol ◽  
Wide Range ◽  
Oxygen Conditions ◽  
Set Up ◽  
Oxidative Ageing

Elastomeric parts found in automotive anti-vibration systems are usually massive. Ageing therefore leads to heterogeneous properties, usually induced by several mechanisms due to the availability, or not, of oxygen in the part’s bulk. To better understand the effects of oxygen in the degradation process and on the fatigue properties, this paper aims at studying the ageing of a rubber material (semi-efficient vulcanization system) in aerobic (with oxygen) and anaerobic (without oxygen) conditions for a wide range of temperatures, relevant for under hood applications. The material studied here is a fully formulated compound NR/IR blend reinforced with carbon black. A specific protocol to perform ageing under anaerobic conditions was set up and validated. Numerous tests have been carried out to evaluate the consequences of ageing on monotonic tension and fatigue properties. A comparison of these consequences and of their kinetics is finally presented for ageing with or without oxygen.

scholarly journals Optimization of the scanning protocol in musculoskeletal ultrasound

2020 ◽  
Author(s):  
Alessandroni Maddalena ◽  
Collocola Alessio ◽  
Durante Stefano
Keyword(s):  
Medical Professional ◽  
Musculoskeletal Tissue ◽  
Technical Parameters ◽  
Area Of Interest ◽  
Specific Protocol ◽  
Ultrasound Study ◽  
Set Up ◽  
Time Required ◽  
The Right ◽  
Anatomical Area

The main limit of the ultrasound resides on the fact that it is a strictly operator-dependent method, and, against the growing discrepancy in the execution methods, the application of a specific protocol for the anatomical area of interest has the function of implementing the achievement of the diagnostic result. This experimentation aims to optimize the parameters of the ultrasound equipment, remaining placed in a strictly technical context, without trying to emulate in any way the diagnostic ability of the medical professional. The first step was mainly focused on ultrasound training and in particular on acquiring a good mastership of the technical image parameters. Subsequently there were performed some scans on five volunteer patients in various anatomical areas according to two different orientations of the ultrasound transducer. The images were acquired at first by the use of the presets already placed on the ultrasound equipment since the installation. The next step was to create a new ultrasound protocol for musculoskeletal tissue changing the values of the technical parameters of the image by scanning the five patients previously recruited. The final step concerned the comparison with the medical professional who was required to scan the same five patients in the same anatomical sections and according to the same scan plans previously set. This experimentation compares the three protocols above mentioned, pursuing the aim to set up an execution protocol for the ultrasound study of musculoskeletal tissue by defining the right setting for the main technical image parameters in order to optimize the performance of the exam, to reduce the time required to complete the survey and to obtain good quality images.

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