AltamISA

AltamISA: a Python API for ISA-Tab files - Published in JOSS (2019)

https://github.com/bihealth/altamisa

Science Score: 93.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
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Committers with academic emails
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Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

bioinformatics isa isa-tab

Keywords from Contributors

interpretability parsing mesh interactive

Last synced: 4 months ago · JSON representation

Repository

AltamISA: a Python API for ISA-Tab files

Basic Info

Host: GitHub
Owner: bihealth
License: mit
Language: Python
Default Branch: master
Homepage:
Size: 1000 KB

Statistics

Stars: 5
Watchers: 8
Forks: 2
Open Issues: 30
Releases: 6

Topics

bioinformatics isa isa-tab

Created almost 8 years ago · Last pushed 11 months ago

Metadata Files

Readme Changelog Contributing License Codeowners Authors Codemeta

AltamISA

AltamISA is an alternative implementation of ISA-tools data model and ISA-Tab file format.

also:

Ambrosia peruviana is a species of plant in the family Asteraceae. It occurs from Mexico south to Argentina, being common in the Antilles and the Andes.

In its native range, A. peruviana is used as a medicinal plant with analgesic, antiinflammatory, anthelmintic and antiseptic properties.

-- Ambrosia peruviana, Wikipedia

For the Impatient

```bash $ pip install altamisa

OR

$ conda install altamisa ```

What is ISA and ISA-Tab?

The ISA (Investigation-Study-Assay) defines a data model for describing life science experiments (specification). ISA-Tab defines a file format based on TSV (tab-separated values) for storing of ISA data in files. Shortly, experiments are encoded by DAGs (directed acyclic graphs) of samples being taken from sources (e.g., donor individuals) and then subjected to "operations" (e.g., extraction, assays, transformations) leading to different downstream "materials".

Why AltamISA?

Attempting to use the official isa-api Python package in early 2018 led to quite some frustration. Even the official ISA-tab examples parsed into non-expected graph structures. Attempting bug fixes to isa-api proofed difficult because of not having complete automated tests. Further, the scope of isa-api was much broader (including between ISA-Tab and other formats) such that we expected high maintenance costs (development had apparently stalled).

Quick Facts

Programming Language: Python 3 (with full type annotations)
License: MIT
Test Coverage: >90%
Documentation: see here
Code Style: black, 100 characters/line

Owner

Name: Berlin Institute of Health
Login: bihealth
Kind: organization

Website: https://www.cubi.bihealth.org/
Repositories: 215
Profile: https://github.com/bihealth

BIH Core Unit Bioinformatics & BIH HPC IT

JOSS Publication

AltamISA: a Python API for ISA-Tab files

Published

August 20, 2019

DOI

10.21105/joss.01610

Volume 4, Issue 40, Page 1610

Authors

Mathias Kuhring

Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany, Berlin Institute of Health Metabolomics Platform, Berlin Institute of Health (BIH), Berlin, Germany, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany

Mikko Nieminen

Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany

Jennifer Kirwan

Berlin Institute of Health Metabolomics Platform, Berlin Institute of Health (BIH), Berlin, Germany, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany

Dieter Beule

Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany

Manuel Holtgrewe

Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany, Charité – Universitätsmedizin Berlin, Berlin, Germany

Editor

Lorena Pantano

CodeMeta (codemeta.json)

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      "name": "Mathias Kuhring",
      "affiliation": "Berlin Institute of Health (BIH), Berlin, German"
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    {
      "@id": "https://orcid.org/0000-0002-4180-8810",
      "@type": "Person",
      "email": "mikko.nieminen@bih-charite.de",
      "name": "Mikko Nieminen",
      "affiliation": "Berlin Institute of Health (BIH), Berlin, German"
    },
    {
      "@id": "https://orcid.org/0000-0002-5423-1651",
      "@type": "Person",
      "email": "jennifer.kirwan@bih-charite.de",
      "name": "Jennifer Kirwan",
      "affiliation": "Berlin Institute of Health (BIH), Berlin, German"
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    {
      "@id": "https://orcid.org/0000-0002-3284-0632",
      "@type": "Person",
      "email": "dieter.beule@bih-charite.de",
      "name": "Dieter Beule",
      "affiliation": "Berlin Institute of Health (BIH), Berlin, German"
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    {
      "@id": "https://orcid.org/0000-0002-3051-1763",
      "@type": "Person",
      "email": "manuel.holtgrewe@bih-charite.de",
      "name": "Manuel Holtgrewe",
      "affiliation": "Berlin Institute of Health (BIH), Berlin, German"
    }
  ],
  "identifier": "https://zenodo.org/record/3345950",
  "codeRepository": "https://github.com/bihealth/altamisa",
  "datePublished": "2019-07-25",
  "dateModified": "2019-07-25",
  "dateCreated": "2019-07-25",
  "description": "AltamISA: a Python API for ISA-Tab files",
  "keywords": "ISA-Tab, Python, software library",
  "license": "MIT",
  "title": "AltamISA",
  "version": "v0.2.0"
}

GitHub Events

Total

Create event: 10
Issues event: 2
Release event: 1
Delete event: 9
Issue comment event: 7
Push event: 12
Pull request review event: 1
Pull request event: 19

Last Year

Create event: 10
Issues event: 2
Release event: 1
Delete event: 9
Issue comment event: 7
Push event: 12
Pull request review event: 1
Pull request event: 19

Committers

Last synced: 5 months ago

All Time

Total Commits: 147
Total Committers: 8
Avg Commits per committer: 18.375
Development Distribution Score (DDS): 0.619

Past Year

Commits: 6
Committers: 3
Avg Commits per committer: 2.0
Development Distribution Score (DDS): 0.333

Top Committers

Name	Email	Commits
Manuel Holtgrewe	m**e@b**e	56
Mathias Kuhring	m**g@b**e	36
Mathias Kuhring	m****g	25
sellth	t**l@p**e	15
dependabot[bot]	4****]	12
varfish-bot	1****t	1
Tommaso Leonardi	t**m@i**z	1
Kyle Niemeyer	k**r@g**m	1

Committer Domains (Top 20 + Academic)

bihealth.de: 2 itm6.xyz: 1 posteo.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 52
Total pull requests: 118
Average time to close issues: 2 months
Average time to close pull requests: about 2 months
Total issue authors: 7
Total pull request authors: 8
Average comments per issue: 0.52
Average comments per pull request: 0.88
Merged pull requests: 87
Bot issues: 0
Bot pull requests: 33

Past Year

Issues: 2
Pull requests: 13
Average time to close issues: N/A
Average time to close pull requests: about 2 months
Issue authors: 2
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.46
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 13

View more stats

Top Authors

Issue Authors

mkuhring (23)
holtgrewe (16)
sellth (6)
tleonardi (3)
tbrittoborges (2)
dsurujon (1)
mikkonie (1)

Pull Request Authors

dependabot[bot] (54)
mkuhring (43)
sellth (34)
holtgrewe (25)
varfish-bot (2)
codacy-badger (1)
kyleniemeyer (1)
tleonardi (1)

Top Labels

Issue Labels

enhancement (14) bug (2)

Pull Request Labels

dependencies (54) work in progress (1) autorelease: tagged (1) autorelease: pending (1)

Packages

Total packages: 1
Total downloads:
- pypi 1,009 last-month

Total dependent packages: 0
Total dependent repositories: 5
Total versions: 3
Total maintainers: 2

pypi.org: altamisa

Implementation of ISA-tools data model and ISA-TAB

Homepage: https://github.com/bihealth/altamisa
Documentation: https://altamisa.readthedocs.io/
License: MIT license
Latest release: 0.3.0
published about 1 year ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 5
Downloads: 1,009 Last month

Rankings

Dependent repos count: 6.6%

Downloads: 9.3%

Dependent packages count: 10.1%

Average: 14.0%

Forks count: 19.2%

Stargazers count: 25.1%

Maintainers (2)

Manuel.Holtgrewe mkuhring

Last synced: 4 months ago

Dependencies

requirements/base.txt pypi

attrs *

requirements/develop.txt pypi

Sphinx >=1.7.0 development
m2r * development
pip ==21.1 development
sphinx-rtd-theme >=0.4.3 development
twine * development
watchdog ==0.8.3 development
wheel ==0.30.0 development

requirements/test.txt pypi

codacy-coverage >=1.3.6 test
coverage * test
flake8 >=3.5.0 test
pytest >=3.6.0 test
pytest-cache >=1.0 test
pytest-cov * test
pytest-runner >=2.11.1 test
tox ==2.9.1 test

requirements/test_black.txt pypi

black ==18.9b0 test

requirements.txt pypi

attrs *

.github/workflows/ci.yml actions

AndreMiras/coveralls-python-action develop composite
actions/checkout v2 composite
codacy/codacy-coverage-reporter-action master composite
s-weigand/setup-conda v1 composite

setup.py pypi

AltamISA

Science Score: 93.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

AltamISA

For the Impatient

OR

What is ISA and ISA-Tab?

Why AltamISA?

Quick Facts

Owner

JOSS Publication

AltamISA: a Python API for ISA-Tab files

Authors

Editor

Tags

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

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Top Labels

Issue Labels

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Packages

pypi.org: altamisa

Rankings

Maintainers (2)

Dependencies