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Open Source Science

https://github.com/fgcz/pyfgcz

Move and Convert Mass Spectrometry Data using BioBeamer and FCC

https://github.com/fgcz/pyfgcz

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords

automation data-processing high-throughput python3 robot staging-algorithm workflow-engine
Last synced: 4 months ago · JSON representation

Repository

Move and Convert Mass Spectrometry Data using BioBeamer and FCC

Basic Info
Statistics
  • Stars: 2
  • Watchers: 4
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Topics
automation data-processing high-throughput python3 robot staging-algorithm workflow-engine
Created over 9 years ago · Last pushed over 5 years ago
Metadata Files
Readme License

README.rst 

PyFGCZ
======

*BioBeamer* helps to collect vast amounts of instrument data (M|G|TBytes).
An example configuration collecting mass spectrometric measurement of more
then a dozen devices can be seen through
http://fgcz-ms.uzh.ch/config/BioBeamer.xml.

*FCC* is a minimalistic workflow engine.
The specification/properties of the program are as follow:

- converting instrument files, e.g., RAW-files to all kinds of formats

- being generic

- follows FGCZ hierarch storage granularity: project, user, instrument, time range

- multi-platform, host, task

- configurable through XML file which means new converter by new tag in XML file NO CODE CHANGE!

- stdout and errout through Syslog

A current configuration can be found through http://fgcz-ms.uzh.ch/config/fcc_config.xml.


Install
-------

::
    pip3 install PyFGCZ

Usage
-----

adapt the following scripts

*Linux*

::
    fcc_run_linux.py --ncpu 1 --hostname fgcz-s-021 --output __runme.bash --exec --loop


*Windows*

::
    C:\\Python37\\python.exe c:\\FGCZ\\fcc\\fcc_run_windows.py --ncpu 1 --exec --loop


See also
--------

- https://github.com/fgcz/BioBeamer

- https://github.com/fgcz/fcc 


References
----------

*FCC - An automated rule-based processing tool for life science data*,
Simon Barkow-Oesterreicher, Can Türker and Christian Panse,
Source Code for Biology and Medicine20138:3 `DOI: 10.1186/1751-0473-8-3`__.

__ http://dx.doi.org/10.1186%2F1751-0473-8-3

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
Last Year

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 45
  • Total Committers: 2
  • Avg Commits per committer: 22.5
  • Development Distribution Score (DDS): 0.333
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Christian Panse cp@f****h 30
Christian Panse c****e 15
Committer Domains (Top 20 + Academic)
fgcz.ethz.ch: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cpanse (2)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 6 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
pypi.org: pyfgcz

PyFGCZ contains BioBeamer and FCC python code.

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 6 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 21.6%
Forks count: 22.6%
Average: 26.6%
Stargazers count: 27.8%
Downloads: 50.8%
Maintainers (1)
cpanse
Last synced: 5 months ago

Dependencies

setup.py pypi
  • PyYAML >=3
  • lxml >=3.4