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Open Source Science

https://github.com/fgcz/qg

MS queue generator

https://github.com/fgcz/qg

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 2 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.2%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

MS queue generator

Basic Info
  • Host: GitHub
  • Owner: fgcz
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 156 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Created over 1 year ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

queueGenerator (qg)

Motivation:

anno 2010

  • fgcz naming convention,
  • injecting bfabric sample IDs and order IDs, ...
  • automatic linking to meta data in bfabric ...
  • on some point we want to have it in bfabric

Challenges

  • ((autoQC_user|QC)) - autoQC01, autoQC03, autoQC4; soon: ((autoQC05)), ((autoQC06)), ((autoQC07)), ((autoQC08))
  • blanc/clean/wash runs
  • plate, e.g., 96WP, / multiplate systems
  • LC systems: .eksigent(), .water(), ..., nanoElute() , .vanquish()
  • instrument control software, e.g., XCalibur, HyStar
  • (block) randomization run order / across plates
  • multi order
  • acquisition of a sample set multiple times (with different methods, eg. pos and neg mode)
  • DIL (metabolomics)
  • ...
  • Legacy code

Workflow/Pipeline

  1. user -> enters samples in bfabric
  2. qg queries bfabric sample of project
  3. ...

Package Organization

  • inst/extdata/instrument.csv - table instrument;area;system;lc
  • R/config.R - general configuration, e.g., Hystar driver, insertSample FUN
  • R/configProteomics.R - configuration for proteomics
  • R/configMetabolomics.R - configuration for metabolomics
  • R/lc-systems.R - LC systems mainly how to write the possitions

See also

  • https://fgcz-intranet.uzh.ch/tiki-index.php?page=sw.queueGenerator
  • runs as virtual machine: http://fgcz-c-072.uzh.ch:4001/extractPlateId/

Sample use cases

cont | instument |LC. | system | position | type | area | test | :------|:-----------|:---------|:---------|:---------|:---------------|:----:|:-----| 36104 | ASTRAL1 | MCLASS | XC SII | 1:A,1 | vial | P | | 35270 | EXPLORIS3 | VANQUISH | | 1:A1 | vial | M |git | 35117 | TIMSTOF1 | EVOSEP | HyStar | 1:A1 | plate | P || 36946 | EXPLORIS2 | EVOSEP. | | 1:A1 | vial | P | | 37142 | EXPLORIS2 | EVOSEP | | 1:A1 | plate 479[34] | P | | 37146 | EXPLORIS2 | EVOSEP | Chronos | 1:A1 | vial | P || 28073 | ASTRAL | VANQUISH | | | | P || xxx | EXPLORIS_2 | MCLASS | XC LCdevs| | vial | P | |

Usage

  1. install python3 bfabricPy package

uv tool install bfabric-scripts

  1. run the SOAP REST Proxy

BFABRICPY_CONFIG_ENV=FGCZSTABLE bfabric_flask.py

3.

set HOME .Renviron

login="$USER" webservicepassword="eXXXe3XXX55dc39eXXXaeb763ec2XXXX" bfabricposturl="http://127.0.0.1:5000/"

4.

install

``` devtools::install_github("fgcz/qg")

```

and use the queue generator ``` shiny::shinyApp(ui = qg::.buildQgUI , server = qg::.buildQgServer) -> qg qg

Have a lot of fun!

```

Read how to use it on the command line:

browserViewer("qg")

Owner

  • Name: Functional Genomics Center UZH|ETH Zurich
  • Login: fgcz
  • Kind: organization
  • Email: protinf@fgcz.ethz.ch
  • Location: Switzerland

proteome informatics FGCZ

GitHub Events

Total
  • Issues event: 3
  • Delete event: 3
  • Issue comment event: 5
  • Push event: 48
  • Pull request event: 6
  • Fork event: 1
  • Create event: 7
Last Year
  • Issues event: 3
  • Delete event: 3
  • Issue comment event: 5
  • Push event: 48
  • Pull request event: 6
  • Fork event: 1
  • Create event: 7

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 99
  • Total Committers: 2
  • Avg Commits per committer: 49.5
  • Development Distribution Score (DDS): 0.01
Past Year
  • Commits: 99
  • Committers: 2
  • Avg Commits per committer: 49.5
  • Development Distribution Score (DDS): 0.01
Top Committers
Name Email Commits
Christian Panse cp@f****h 98
Christian Panse c****e@e****h 1
Committer Domains (Top 20 + Academic)
ethz.ch: 1 fgcz.ethz.ch: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 3
  • Total pull requests: 5
  • Average time to close issues: 4 minutes
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.6
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 5
  • Average time to close issues: 4 minutes
  • Average time to close pull requests: 1 day
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.6
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cpanse (2)
  • leoschwarz (1)
Pull Request Authors
  • leoschwarz (3)
  • cpanse (1)
  • cfortes-fgcz (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 4.4 depends
  • bfabricShiny >= 0.13.2 imports
  • httr * imports
  • jsonlite >= 1.4 imports
  • shiny >= 1.0 imports
  • shinyStore >= 0.1.1 imports
  • stringr * imports
  • DT * suggests
  • RCurl * suggests
  • ggplot2 >= 2.2 suggests
  • kableExtra * suggests
  • protViz >= 0.7 suggests
  • rmarkdown * suggests
  • roxygen2 >= 6.0 suggests
  • testthat * suggests
  • tidyverse * suggests
  • xml2 >= 1.1 suggests