The Metabolomics workshop on experimental and data analysis training for untargeted metabolomics was hosted by the Proteomics Society of India in December 2019. The Workshop included six tutorial lectures and hands-on data analysis training sessions presented by seven speakers. The tutorials and hands-on data analysis sessions focused on workflows for liquid chromatography-mass spectrometry (LC-MS) based on untargeted metabolomics. We review here three main topics from the workshop which were uniquely identified as bottlenecks for new researchers: a) experimental design, b) quality controls during sample preparation and instrumental analysis and c) data quality evaluation. Our objective here is to present common challenges faced by novice researchers and present possible guidelines and resources to address them. We provide resources and good practices for researchers who are at the initial stage of setting up metabolomics workflows in their labs.

Complete detailed metabolomics/lipidomics protocols are available online at EMBL-MCF protocol including video tutorials.

NOAA Ship Nancy Foster Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Nancy Foster Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Nancy Foster Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Nancy Foster Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.html

NOAA Ship Delaware II Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Delaware II Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Delaware II Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Delaware II Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.html

NOAA Ship Gordon Gunter Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Gordon Gunter Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Gordon Gunter Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Gordon Gunter Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.html

The data provided here are part of a Galaxy Training Network tutorial for reads Quality Control.

PacBio HiFi reads were provided by PacBio - GIAB sample HG002 (https://www.pacb.com/smrt-science/smrt-resources/datasets/) and was downsampled using seqtk (https://github.com/lh3/seqtk)

Nanopore reads were provided by Tim Kahlke as part of "Long-Read, long reach Bioinformatics Tutorials" (https://timkahlke.github.io/LongRead_tutorials/) and was basecalled using Guppy v5.0.2 (dna_r9.4.1_450bps_sup.cfg).

This is the tutorial data for the 'Single-cell quality control with scater' tutorial on the Galaxy Training Network. The data is the same dataset that is used as the inbuilt example dataset within scater, but has been implemented as individual files.

The current dataset includes sequencing data from Arabidopsis thaliana (specifically chromosome 4) to complete the tutorial on quality checks and genome assembly using Illumina, ONT, HiFi, and Hi-C data. This reduced dataset is intended to shorten the overall analysis time. The original dataset was published by Wang et al. in 2021 (see reference below).

NOAA Ship Fairweather Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Fairweather Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Fairweather Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Fairweather Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.html

Hourly contaminant concentrations measured continuously by the Quebec Air Quality Monitoring Network (RSQAQ). To consult the descriptive statistics of these data, look for the RSQAQ-Statistics-Descriptive-Data-Continuous-Data data. If you have any questions about this data, contact the Info-Air department:. These data exclude those measured on Montreal Island. For detailed instructions on how to open and navigate data files to easily find accurate data, see the [RSQAQ: Navigating Air Quality Data] tutorial (https://www.youtube.com/watch?v=3bLBUOmMEFk).

RNA sequencing (RNA-Seq) is a powerful tool that captures information about how organisms respond to stimuli in their environment at the molecular level. A common RNA-Seq approach involves isolating and sequencing all of the messenger RNA (mRNA) in a tissue sample taken from an organism. Researchers can compare patterns observed in RNA-Seq data to understand how individuals respond to the environment over minutes, hours, or days and how populations evolve in response to the environment over millions of years. The materials in this repository will guide users through an analysis of RNA-Seq data collected from two California populations of a copepod crustacean, Tigriopus californicus, that were exposed to different levels of salinity. Users will examine the contents of a fastq file that contains raw RNA-Seq data, determine the quality of the RNA-Seq data using a web-server, and test for significant differences in gene expression between the copepod populations using the R packages DE...

This data product, sourced from the NEON data portal for the purposes of the dataspice tutorial, contains the quality-controlled, native sampling resolution data from in-situ measurements of live and standing dead woody individuals and shrub groups, from all terrestrial NEON sites with qualifying woody vegetation. The exact measurements collected per individual depend on growth form, and these measurements are focused on:

enabling biomass and productivity estimation, estimation of shrub volume and biomass calibration / validation of multiple NEON airborne remote-sensing data products. In general, comparatively large individuals that are visible to remote-sensing instruments are mapped, tagged and measured, and other smaller individuals are tagged and measured but not mapped. Smaller individuals may be subsampled according to a nested subplot approach in order to standardize the per plot sampling effort.

Structure and mapping data are reported per individual per plot; sampling metadata, such as per growth form sampling area, are reported per plot.

Research Ship T. G. Thompson Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~' indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. (Don't include backslashes in your query.) See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlResearch Ship T. G. Thompson Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~' indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. (Don't include backslashes in your query.) See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlResearch Ship T. G. Thompson Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~' indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. (Don't include backslashes in your query.) See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlResearch Ship T. G. Thompson Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~' indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. (Don't include backslashes in your query.) See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.html

This dataset is used in video tutorial here to enhance the quality of imagery: https://youtu.be/FepNl8FTrh4

This dataset contains the data and code necessary to replicate work in the following paper: Narayan, Sneha, Jake Orlowitz, Jonathan Morgan, Benjamin Mako Hill, and Aaron Shaw. 2017. “The Wikipedia Adventure: Field Evaluation of an Interactive Tutorial for New Users.” in Proceedings of the 20th ACM Conference on Computer-Supported Cooperative Work & Social Computing (CSCW '17). New York, New York: ACM Press. http://dx.doi.org/10.1145/2998181.2998307 The published paper contains two studies. Study 1 is a descriptive analysis of a survey of Wikipedia editors who played a gamified tutorial. Study 2 is a field experiment that evaluated the same the tutorial. These data are the data used in the field experiment described in Study 2. Description of Files This dataset contains the following files beyond this README: twa.RData — An RData file that includes all variables used in Study 2. twa_analysis.R — A GNU R script that includes all the code used to generate the tables and plots related to Study 2 in the paper. The RData file contains one variable (d) which is an R dataframe (i.e., table) that includes the following columns: userid (integer): The unique numerical ID representing each user on in our sample. These are 8-digit integers and describe public accounts on Wikipedia. sample.date (date string): The day the user was recruited to the study. Dates are formatted in “YYYY-MM-DD” format. In the case of invitees, it is the date their invitation was sent. For users in the control group, these is the date that they would have been invited to the study. edits.all (integer): The total number of edits made by the user on Wikipedia in the 180 days after they joined the study. Edits to user's user pages, user talk pages and subpages are ignored. edits.ns0 (integer): The total number of edits made by user to article pages on Wikipedia in the 180 days after they joined the study. edits.talk (integer): The total number of edits made by user to talk pages on Wikipedia in the 180 days after they joined the study. Edits to a user's user page, user talk page and subpages are ignored. treat (logical): TRUE if the user was invited, FALSE if the user was in control group. play (logical): TRUE if the user played the game. FALSE if the user did not. All users in control are listed as FALSE because any user who had not been invited to the game but played was removed. twa.level (integer): Takes a value 0 of if the user has not played the game. Ranges from 1 to 7 for those who did, indicating the highest level they reached in the game. quality.score (float). This is the average word persistence (over a 6 revision window) over all edits made by this userid. Our measure of word persistence (persistent word revision per word) is a measure of edit quality developed by Halfaker et al. that tracks how long words in an edit persist after subsequent revisions are made to the wiki-page. For more information on how word persistence is calculated, see the following paper: Halfaker, Aaron, Aniket Kittur, Robert Kraut, and John Riedl. 2009. “A Jury of Your Peers: Quality, Experience and Ownership in Wikipedia.” In Proceedings of the 5th International Symposium on Wikis and Open Collaboration (OpenSym '09), 1–10. New York, New York: ACM Press. doi:10.1145/1641309.1641332. Or this page: https://meta.wikimedia.org/wiki/Research:Content_persistence How we created twa.RData The files twa.RData combines datasets drawn from three places: A dataset created by Wikimedia Foundation staff that tracked the details of the experiment and how far people got in the game. The variables userid, sample.date, treat, play, and twa.level were all generated in a dataset created by WMF staff when The Wikipedia Adventure was deployed. All users in the sample created their accounts within 2 days before the date they were entered into the study. None of them had received a Teahouse invitation, a Level 4 user warning, or been blocked from editing at the time that they entered the study. Additionally, all users made at least one edit after the day they were invited. Users were sorted randomly into treatment and control groups, based on which they either received or did not receive an invite to play The Wikipedia Adventure. Edit and text persistence data drawn from public XML dumps created on May 21st, 2015. We used publicly available XML dumps to generate the outcome variables, namely edits.all, edits.ns0, edits.talk and quality.score. We first extracted all edits made by users in our sample during the six month period since they joined the study, excluding edits made to user pages or user talk pages using. We parsed the XML dumps using the Python based wikiq and MediaWikiUtilities software online at: http://projects.mako.cc/source/?p=mediawiki_dump_tools https://github.com/mediawiki-utilities/python-mediawiki-utilities We o... Visit https://dataone.org/datasets/sha256%3Ab1240bda398e8fa311ac15dbcc04880333d5f3fbe67a7a951786da2d44e33018 for complete metadata about this dataset.

Concentrations of particles and metals measured sequentially by the Quebec Air Quality Monitoring Network (RSQAQ). These data cover the fractions of respirable particles with an aerodynamic diameter equal to or less than 10 µm (PM10) and those of total suspended particles with an aerodynamic diameter equal to or less than 100 µm (PST). If you have any questions about this data, contact the Info-Air department:. These data exclude those sampled on Montreal Island. For detailed instructions on opening and navigating data files and for easily retrieving accurate data, see the [RSQAQ: Navigating Air Quality Data] tutorial (https://www.youtube.com/watch?v=3bLBUOmMEFk).

4-minute concentrations of H2S and SO2 measured continuously by the Quebec Air Quality Monitoring Network (RSQAQ). If you have any questions about this data, contact the Info-Air service: infoair@environnement.gouv.qc.ca. These data exclude those measured on the island of Montreal. For detailed instructions on how to open and navigate data files to easily find accurate data, see the RSQAQ tutorial: Navigating Air Quality Data.

NOAA Ship Pisces Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Pisces Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Pisces Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Pisces Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.html

Abstract

The NIS is the largest publicly available all-payer inpatient healthcare database designed to produce U.S. regional and national estimates of inpatient utilization, access, cost, quality, and outcomes. Unweighted, it contains data from around 7 million hospital stays each year. Weighted, it estimates around 35 million hospitalizations nationally. Developed through a Federal-State-Industry partnership sponsored by the Agency for Healthcare Research and Quality (AHRQ), HCUP data inform decision making at the national, State, and community levels.

Its large sample size is ideal for developing national and regional estimates and enables analyses of rare conditions, uncommon treatments, and special populations.

Usage

IMPORTANT NOTE: Some records are missing from the Severity Measures table for 2017 & 2018, but none are missing from any of the other 2012-2020 data. We are in the process of trying to recover the missing records, and will update this note when we have done so.

Also %3Cu%3EDO NOT%3C/u%3E

use this data without referring to the NIS Database Documentation, which includes:

• Description of NIS Database
• Restrictions on Use

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• Data Elements
• Additional Resources for Data Elements
• ICD-10-CM/PCS Data Included in the NIS Starting with 2015 (More details about this transition available here.)
• Known Data Issues
• NIS Supplemental Files
• HCUP Tools: Labels and Formats
• Obtaining HCUP Data

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Before Manuscript Submission

All manuscripts (and other items you'd like to publish) must be submitted to

phsdatacore@stanford.edu for approval prior to journal submission.

We will check your cell sizes and citations.

For more information about how to cite PHS and PHS datasets, please visit:

https:/phsdocs.developerhub.io/need-help/citing-phs-data-core

HCUP Online Tutorials

For additional assistance, AHRQ has created the HCUP Online Tutorial Series, a series of free, interactive courses which provide training on technical methods for conducting research with HCUP data. Topics include an HCUP Overview Course and these tutorials:

• The HCUP Sampling Design tutorial is designed to help users learn how to account for sample design in their work with HCUP national (nationwide) databases. • The Producing National HCUP Estimates tutorial is designed to help users understand how the three national (nationwide) databases – the NIS, Nationwide Emergency Department Sample (NEDS), and Kids' Inpatient Database (KID) – can be used to produce national and regional estimates. HCUP 2020 NIS (8/22/22) 14 Introduction • The Calculating Standard Errors tutorial shows how to accurately determine the precision of the estimates produced from the HCUP nationwide databases. Users will learn two methods for calculating standard errors for estimates produced from the HCUP national (nationwide) databases. • The HCUP Multi-year Analysis tutorial presents solutions that may be necessary when conducting analyses that span multiple years of HCUP data. • The HCUP Software Tools Tutorial provides instructions on how to apply the AHRQ software tools to HCUP or other administrative databases.

New tutorials are added periodically, and existing tutorials are updated when necessary. The Online Tutorial Series is located on the HCUP-US website at www.hcupus.ahrq.gov/tech_assist/tutorials.jsp.

Important notes about the 2015 data

In 2015, AHRQ restructured the data as described here:

https://hcup-us.ahrq.gov/db/nation/nis/2015HCUPNationalInpatientSample.pdf

Some key points:

• For the 2015 data, all diagnosis and procedure data elements, including any data elements derived from diagnoses and procedures, were moved out of the Core File and into the Diagnosis and Procedure Groups Files.
• Prior to 2015, and for Q1-3 of 2015, the DX1-30 and PR1-15 variables (which use ICD-9 codes) variables were used, but starting in Q4 of 2015, the I10_DX1-30 and I10_PR1-I10-15 (which use ICD-10 codes) were used. The best way to identify discharges for quarter 1-3 or quarter 4 is based on the value of the diagnosis version (DXVER); For quarters 1-3, DXVER has a value of 9; while for quarter 4, DXVER has a value of 10.
• Some other variables also transitioned in Q4 of 2015. Please refer to the link above for more details.
• Starting in 2016, the diagnosis and procedure information returned to the Core file. Additional details about the data in 2016 are available here: https://hcup-us.ahrq.gov/db/nation/nis/NISChangesBeginningDataYr2016.pdf

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NIS Areas of Research and HCUP Publications

NOAA Ship Okeanos Explorer Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Okeanos Explorer Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Okeanos Explorer Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.htmlNOAA Ship Okeanos Explorer Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS) program. IMPORTANT: ALWAYS USE THE QUALITY FLAG DATA! Each data variable's metadata includes a qcindex attribute which indicates a character number in the flag data. ALWAYS check the flag data for each row of data to see which data is good (flag='Z') and which data isn't. For example, to extract just data where time (qcindex=1), latitude (qcindex=2), longitude (qcindex=3), and airTemperature (qcindex=12) are 'good' data, include this constraint in your ERDDAP query: flag=~'ZZZ........Z.* 'in your query. '=~ 'indicates this is a regular expression constraint. The 'Z's are literal characters. In this dataset, 'Z' indicates 'good' data. The '.'s say to match any character. The '*' says to match the previous character 0 or more times. See the tutorial for regular expressions at http://www.vogella.com/tutorials/JavaRegularExpressions/article.html

Galaxy is an open source, web-based platform for data intensive biomedical research. It makes accessible bioinformatics applications to users lacking programming skills, enabling them to easily build analysis workflows for NGS data.

The course "Exome analysis using Galaxy" is aimed at PhD student, biologists, clinicians and researchers who are analysing, or need to analyse in the near future, high throughput exome sequencing data. The aim of the course is to make participants familiarise with the Galaxy platform and prepare them to work independently, using state-of-the art tools for the analysis of exome sequencing data.

The course will be delivered using a mixture of lectures and computer based hands-on practical sessions. Lectures will provide an up-to-date overview of the strategies for the analysis of exome next-generation experiments, starting from the raw sequence data. Analyses include sequence quality control, alignment to a reference genome, refinement of aligned sequences, variant calling, annotation and interpretation, and tools for visual inspection of results. Participants will apply the knowledge gained during the course to the analysis of Illumina’s real exome datasets, and implement workflows to reproduce the complete analysis. After the course, participants will be able to create pipeline for their individual analyses.

Those are the needed datasets for this course.