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.

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.

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.

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 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.

Born Digital? Digitization and the Birth of the Moroccan National Archives

2020 ◽  
Vol 47 ◽  
pp. 195-218
Author(s):  
Nora El Qadim
Keyword(s):  
Public Policy ◽  
Good Governance ◽  
International Standards ◽  
Archival Institution ◽  
National Archives ◽  
The Creation ◽  
Set Up

Abstract:This article examines the digitization policy of Archives du Maroc (AdM), Morocco’s national archival institution, which was set up in 2011 and opened in 2013. Given its recent creation, the AdM lead us to question the particularity of digitization in archiving policies when included from the start rather than retroactively. Through an analysis of the creation and development of AdM as a public policy connected to national efforts at transparency and “good governance,” I argue that digitization has served as a way of performing modernity through technology and international standards, thus reinforcing the legitimacy of a nascent institution.

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.

The Creation of a Multi-Link Load Balancing Mechanism for Planetary Gearing: Part 2 — Optimum Mechanism Selection and Dimension Determination

1992 ◽  
Author(s):  
Zhang Hong ◽  
Wei-qing Cao ◽  
Ting Li Yang ◽  
Jin Kui Chu
Keyword(s):  
Load Balancing ◽  
Arbitrary Number ◽  
Uniform Load ◽  
Topological Structures ◽  
Optimum Load ◽  
New Type ◽  
The Common ◽  
The Creation ◽  
Set Up

Abstract This paper is the second of a series of two papers which designed a new type of load balancing mechanisms for planetary gearings with arbitrary number of planets. In this paper the common expression of the non-uniform load share factor was deduced, and a function parameter:force-arm factor and their solution was given. That makes it possible that the dimensions and the ability of load equilibrium of Multi-Link Load Balancing Mechanisms can be determined. The criteria of optimum load balancing Mechanisms selection were set up with consider of the effects of turning pair clearances, and optimum mechanisms were selected among the 15 candidates obtained in Part 1. Finally, it was demonstrated that the optimum multi-link load balancing mechanisms for arbitrary number of planets had the similar topological structures and same function and performence of load equilibrium.

The 60-Minute MVP

2019 ◽  
Vol 3 (4) ◽  
pp. 371-386
Author(s):  
Doan Winkel ◽  
Justin Wilcox ◽  
Atul Teckchandani
Keyword(s):  
Hypothesis Testing ◽  
Iterative Process ◽  
Technical Expertise ◽  
Start Up ◽  
Starting Point ◽  
The Creation ◽  
Mind Set ◽  
Set Up ◽  
Critical Aspects

The 60-minute minimum viable product (MVP) exercise teaches critical aspects of the entrepreneurial mind-set and lean start-up methodology, namely, the iterative process of hypothesis testing through the creation of MVPs. In 60 minutes, with no prior technical expertise, students will work in teams to design a landing page, create a teaser video, and set up a way to gather information from prospective customers. The resulting low-fidelity MVP can subsequently be shared with prospective customers to gauge interest and be used as a starting point for the hypothesis testing process used in the lean start-up methodology. This is an immersive exercise that activates students, builds confidence, and teaches important entrepreneurial principles.

Music Then and Now: Using Technology to Build a Lyric Animation Module

2019 ◽  
Vol 65 (2) ◽  
pp. 264-276 ◽  
Author(s):  
Wayne Geerling ◽  
G. Dirk Mateer ◽  
Brian O’Roark
Keyword(s):  
Student Group ◽  
Group Project ◽  
The Everyday ◽  
The Creation ◽  
Do It Yourself ◽  
Set Up ◽  
Jel Classifications

This article describes a student group project (Music for Econ) which synthesizes music with economics and is a great way to connect with your audience. We trace the journey of Music for Econ from its inception as a Pop-Up video in the early 2000s through to the creation of a Music for Econ library on Critical Commons. Music for Econ is a pedagogical device which can be used to demonstrate the everyday application of economics and help unlock student creativity. Consequently, we provide the instructor with a do it yourself (DIY) manual, which shows them how to set up the project, customize it depending on the size of their class, and how to avoid common pitfalls. We also include an end of project survey template for reference and future use in an appendix. More broadly, Music for Econ is simply fun to watch if you like music and enjoy leaning about economics. JEL Classifications: A20, A21, A22

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