openms

The codebase of the OpenMS project

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
91 of 235 committers (38.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.4%) to scientific vocabulary

Keywords

3-clause-bsd algorithms analyses c-plus-plus hacktoberfest linux macos mass-spectrometry metabolomics ms-data openms proteomics windows

Keywords from Contributors

bioinformatics nextflow report nf-core interpretability ecosystem-model genomics pypi standardization autograder

Last synced: 6 months ago · JSON representation

Repository

The codebase of the OpenMS project

Basic Info

Host: GitHub
Owner: OpenMS
License: other
Language: C++
Default Branch: develop
Homepage: https://www.openms.de
Size: 765 MB

Statistics

Stars: 524
Watchers: 29
Forks: 360
Open Issues: 703
Releases: 15

Topics

3-clause-bsd algorithms analyses c-plus-plus hacktoberfest linux macos mass-spectrometry metabolomics ms-data openms proteomics windows

Created about 12 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing Funding License Code of conduct Authors

README

------------------------------
--     OpenMS library       --
------------------------------


This directory contains the source code of OpenMS.
License information can be found in the License.txt file.

If you downloaded a stable release, detailed installation
instructions and other information can be found in the 
documentation (doc/index.html).

If this is a development version obtained via git or as a
nightly snapshot, the documentation is not contained in
this package. Please refer to the OpenMS website for 
installation instructions.

------------------------------
--       TOPP tools         --
------------------------------

In addition to the OpenMS library 'The OpenMS 
PiPeline' (TOPP) is also included in this package.
The installation instructions for OpenMS also 
contain installation instructions for TOPP!

------------------------------
--      Contributing       --
------------------------------

If you would like to contribute to OpenMS, this is how 
to best get started: 

- Familiarize yourself with our online documentation, 
  available at http://www.openms.de/current_doxygen/html/

- Learn how to build OpenMS (by reading the building 
  instructions at the online documentation)

- Start reading the OpenMS tutorial for developers at 
  http://www.openms.de/current_doxygen/html/OpenMS_tutorial.html

- Any questions can be directed at the mailing list, 
  see http://openms.de/support for up-to-date information
  about how to contact the OpenMS developers.

Owner

Name: OpenMS
Login: OpenMS
Kind: organization

Website: https://openms.de
Twitter: OpenMSTeam
Repositories: 29
Profile: https://github.com/OpenMS

OpenMS is an open-source C++ software library for LC-MS data management and analysis

Committers

Last synced: 10 months ago

All Time

Total Commits: 29,352
Total Committers: 235
Avg Commits per committer: 124.902
Development Distribution Score (DDS): 0.866

Past Year

Commits: 506
Committers: 30
Avg Commits per committer: 16.867
Development Distribution Score (DDS): 0.706

Top Committers

Name	Email	Commits
Hannes Roest	r**t@i**h	3,921
Chris Bielow	c**w@f**e	3,648
Timo Sachsenberg	s**b@i**e	2,087
Marc Sturm	m**m@u**t	1,534
jpfeuffer	p**r@i**e	1,230
lars20070	l**e@d**k	1,138
Stephan Aiche	s**e@f**e	1,116
Hendrik Weisser	h**r@s**m	1,043
enetz	e**z@g**m	894
kyowonjeong	k**g@g**m	858
Samuel Wein	s**m@s**m	817
Julianus Pfeuffer	j**r@f**e	715
Andreas Bertsch	a**h@u**t	692
Hendrik Weisser	h**5@s**k	614
timosachsenberg	s**b@a**e	610
oliveralka	r**9@g**t	555
mwalzer	w**r@i**e	469
Clemens Gröpl	g**l@u**t	429
Johannes Veit	d**l@g**m	370
Pasquale Domenico Colaianni	p**m@b**k	357
Eva Lange	e**e@u**t	342
Douglas McCloskey	d**7@g**m	324
Alexandra Zerck	a**k@u**t	272
axelwalter	a**r@u**e	261
Ole Schulz-Trieglaff	o**t@u**t	222
JeeH-K	j**1@g**m	198
Tom Waschischeck	t**k@w**e	195
lukas	l**n@t**e	194
George Rosenberger	g**8@c**u	186
timosachsenberg	s**b@a**e	185
and 205 more...

Committer Domains (Top 20 + Academic)

users.sourceforge.net: 32 informatik.uni-tuebingen.de: 11 fu-berlin.de: 8 zedat.fu-berlin.de: 7 lncrna.imp.fu-berlin.de: 5 abinode06.informatik.uni-tuebingen.de: 4 redwood.imp.fu-berlin.de: 3 uni-tuebingen.de: 3 abinode07.informatik.uni-tuebingen.de: 2 github.com: 2 sequoia.imp.fu-berlin.de: 2 mi.fu-berlin.de: 2 imsb.biol.ethz.ch: 2 sanger.ac.uk: 2 abinode05.informatik.uni-tuebingen.de: 2 abinode03.informatik.uni-tuebingen.de: 2 biosustain.dtu.dk: 2 leons-mbp.fritz.box: 1 abinode02.informatik.uni-tuebingen.de: 1 gmx.de: 1 mednet.ucla.edu: 1 seecs.edu.pk: 1 ibminode02.cs.uni-tuebingen.de: 1 abibuilder2.informatik.uni-tuebingen.de: 1 nero.imp.fu-berlin.de: 1 sonne.informatik.uni-tuebingen.de: 1 id.ethz.ch: 1 ebi.ac.uk: 1 tuebingen.mpg.de: 1 cumc.columbia.edu: 1 mimuw.edu.pl: 1 bu.edu: 1 rwth-aachen.de: 1 bala.imp.fu-berlin.de: 1 u-084-c227.eap.uni-tuebingen.de: 1 u-080-c092.eap.uni-tuebingen.de: 1 u-083-c004.eap.uni-tuebingen.de: 1 ub-haus-10-126-76-254.eduroam-ub-haus.privat: 1 ub-haus-10-126-75-234.eduroam-ub-haus.privat: 1 scg3-ln02.stanford.edu: 1 abinode04.informatik.uni-tuebingen.de: 1 zbh.uni-hamburg.de: 1 microcebus.imp.fu-berlin.de: 1 ibminode06.cs.uni-tuebingen.de: 1 student.uni-tuebingen.de: 1 uni-jena.de: 1 abibuilder2.cs.uni-tuebingen.de: 1 uw.edu: 1 deadtime.informatik.uni-tuebingen.de: 1 u-081-c185.eap.uni-tuebingen.de: 1 u-080-c228.eap.uni-tuebingen.de: 1 u-082-c121.eap.uni-tuebingen.de: 1 arakan.informatik.uni-tuebingen.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 514
Total pull requests: 1,414
Average time to close issues: over 1 year
Average time to close pull requests: about 1 month
Total issue authors: 126
Total pull request authors: 71
Average comments per issue: 3.8
Average comments per pull request: 2.77
Merged pull requests: 965
Bot issues: 0
Bot pull requests: 140

Past Year

Issues: 176
Pull requests: 698
Average time to close issues: 12 days
Average time to close pull requests: 6 days
Issue authors: 62
Pull request authors: 48
Average comments per issue: 2.38
Average comments per pull request: 2.73
Merged pull requests: 435
Bot issues: 0
Bot pull requests: 43

View more stats

Top Authors

Issue Authors

timosachsenberg (111)
jpfeuffer (98)
poshul (38)
cbielow (37)
hroest (9)
lopippo (9)
jonasscheid (7)
mr-c (7)
pjones (7)
bernt-matthias (7)
elrubio (6)
sagitter (6)
JKVISION1101 (5)
eeko-kon (5)
YasinEl (5)

Pull Request Authors

timosachsenberg (476)
poshul (238)
cbielow (168)
dependabot[bot] (95)
jpfeuffer (73)
github-actions[bot] (43)
jcharkow (23)
pjones (23)
t0mdavid-m (18)
singjc (17)
SGSSGene (16)
matteopilz (15)
MaLLLiYA (12)
FreezB11 (10)
radusuciu (9)

Top Labels

Issue Labels

major (33) enhancement (33) blocker (30) sprint candidate (24) minor (21) defect (16) Hacktoberfest (14) TOPPView (13) critical (12) GSoC 2025 (11) beginner tasks (11) good first issue (10) task (10) question (10) first-timers-only (8) OpenMS - library (7) Documentation (7) CI (6) TOPP (6) Performance (6) BinaryPackages (6) Build System (5) bug (4) Projects (4) KNIME (4) pyOpenMS (3) UTILS (3) wontfix (2) usability (2) internal (2)

Pull Request Labels

Review effort [1-5]: 2 (119) dependencies (103) enhancement (102) Review effort [1-5]: 1 (53) Review effort [1-5]: 3 (44) automated pr (31) feature (31) configuration changes (30) NoJenkins (21) Bug fix (20) Documentation (19) Review effort [1-5]: 4 (18) Review effort 1/5 (18) wontfix (13) Review effort 2/5 (11) bug_fix (10) tests (10) submodules (9) Review effort 3/5 (6) Performance (5) pyOpenMS (4) Review effort [1-5]: 5 (4) OpenSwathAlgo (2) ready-post-release (2) hacktoberfest-accepted (2) internal (1) major (1) GSoC 2025 (1) github_actions (1) blocker (1)

Dependencies

.github/workflows/containerdeploy.yml actions

docker/build-push-action v3 composite
docker/login-action v2 composite

.github/workflows/cppcheck.yml actions

actions/checkout v3 composite
deep5050/cppcheck-action main composite

.github/workflows/openms_clang_format.yml actions

DoozyX/clang-format-lint-action v0.15 composite
actions/checkout v3 composite
tj-actions/changed-files v34.6.1 composite

.github/workflows/openms_clang_format_add_and_commit.yml actions

DoozyX/clang-format-lint-action v0.14 composite
actions/checkout v3 composite
tj-actions/changed-files v34.6.1 composite

.github/workflows/pyopenms-wheels.yml actions

actions/checkout v3 composite
actions/download-artifact v3 composite
actions/upload-artifact v3 composite
egor-tensin/vs-shell v2 composite
jurplel/install-qt-action v3 composite
jwlawson/actions-setup-cmake v1.13 composite
pypa/gh-action-pypi-publish release/v1 composite
rokroskar/workflow-run-cleanup-action master composite

src/pyOpenMS/setup.py pypi

numpy *
pandas *

.github/workflows/knime_tests.yml actions

.github/workflows/openms_ci_matrix_full.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/download-artifact v3 composite
actions/setup-java v3 composite
actions/upload-artifact v3 composite
egor-tensin/vs-shell v2 composite
jurplel/install-qt-action v3 composite

.github/workflows/test_pyopenms.yml actions

actions/checkout v3 composite
actions/setup-python v2 composite
juliangruber/read-file-action v1 composite

.github/workflows/update_version_numbers.yml actions

actions/checkout v3 composite
peter-evans/create-pull-request v4 composite

.github/workflows/update_year_number.yml actions

actions/checkout v3 composite
peter-evans/create-pull-request v5 composite

cmake/knime/DESCRIPTION cran

src/openms/thirdparty/nlohmann_json/docs/mkdocs/requirements.txt pypi

Babel ==2.11.0
GitPython ==3.1.29
Jinja2 ==3.1.2
Markdown ==3.3.7
MarkupSafe ==2.1.1
PyYAML ==6.0
Pygments ==2.13.0
certifi ==2022.12.7
charset-normalizer ==2.1.1
click ==8.1.3
csscompressor ==0.9.5
future ==0.18.3
ghp-import ==2.1.0
gitdb ==4.0.10
htmlmin ==0.1.12
httplib2 ==0.21.0
idna ==3.4
importlib-metadata ==5.1.0
joblib ==1.2.0
jsmin ==3.0.1
livereload ==2.6.3
lunr ==0.6.2
markdown-include ==0.8.0
mergedeep ==1.3.4
mkdocs ==1.4.2
mkdocs-git-revision-date-localized-plugin ==1.1.0
mkdocs-material ==8.5.11
mkdocs-material-extensions ==1.1.1
mkdocs-minify-plugin ==0.6.2
mkdocs-redirects ==1.2.0
mkdocs-simple-hooks ==0.1.5
nltk ==3.8
packaging ==22.0
plantuml ==0.3.0
plantuml-markdown ==3.7.3
pymdown-extensions ==9.9
pyparsing ==3.0.9
python-dateutil ==2.8.2
pytz ==2022.7
pyyaml_env_tag ==0.1
regex ==2022.10.31
requests ==2.28.1
six ==1.16.0
smmap ==5.0.0
tornado ==6.2
tqdm ==4.64.1
urllib3 ==1.26.13
watchdog ==2.2.0
zipp ==3.11.0

src/openms/thirdparty/nlohmann_json/tools/serve_header/requirements.txt pypi

PyYAML ==6.0
watchdog ==2.1.7

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

openms

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README

Owner

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies