pathvisio
PathVisio - pathway editor, visualization and analysis software
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 34 committers (8.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary
Repository
PathVisio - pathway editor, visualization and analysis software
Basic Info
- Host: GitHub
- Owner: PathVisio
- License: apache-2.0
- Language: Java
- Default Branch: master
- Homepage: http://www.pathvisio.org
- Size: 181 MB
Statistics
- Stars: 23
- Watchers: 7
- Forks: 22
- Open Issues: 101
- Releases: 5
Metadata Files
readme.md
PROJECT STRUCTURE
| File/Folder | Description | | ------------- | ------------- | | apidoc/ (autogenerated) | contains autogenerated documentation | | build/ (autogenerated) | contains generated class files | | release/ (autogenerated) | output: jnlp, jar and zip package. | | lib/ | contains the external libraries that PathVisio needs. | | example-data/ | mapp and gpml files for quick testing | | modules/ | the java source code for each of the different modules | | pathvisio.sh | shortcut for running PathVisio from the command line (Linux/MacOSX) | | pathvisio.bat | shortcut for running PathVisio from the command line (Windows) | | readme.md | this file | | build.xml | ant build file (see below) | | pathvisio.iss | inno-setup script, to generate installer |
HOW TO IMPORT IN ECLIPSE
For detailed instructions, please see: https://github.com/PathVisio/pathvisio/wiki/PathVisio-setup-in-Eclipse
HOW TO BUILD WITH ANT
Using the ant build file, you can build the project from the command line. You can also use ant to generate the apidocs and to create an executable jar.
It is also possible to set up eclipse to build ant targets.
First make sure ant is set up properly. It comes with eclipse, but you'll have to check if the path is set correctly if you want to run it from the command line.
The ant build file provides the following targets, which you can invoke it from the directory which contains build.xml with
ant <target>
where
compile: just compile all classes
docs: generate all apidocs
exe: generate executable jar file
clean: remove all generated files
dist: generate zip package and windows installer.
The zip package only includes files needed to *run* not compile.
all: clean, then compile, jar, dist and docs.
HOW TO RUN FROM THE TERMINAL
If you have managed to build the classes with ant or with eclipse, you can use pathvisio.bat to start java from the command line.
Owner
- Name: PathVisio
- Login: PathVisio
- Kind: organization
- Website: http://www.pathvisio.org
- Repositories: 27
- Profile: https://github.com/PathVisio
Pathway editor, analysis and visualization software
Citation (CITATION.cff)
cff-version: 1.2.0
title: PathVisio
message: 'If you use this software, please cite it as below.'
type: software
identifiers:
- type: url
value: 'https://github.com/pathvisio/pathvisio'
description: Source code repository for PathVisio
repository-code: 'https://github.com/pathvisio/pathvisio'
url: 'https://pathvisio.org/'
license: Apache-2
preferred-citation:
type: article
authors:
- family-names: Summer-Kutmon
given-names: Martina
- family-names: Iersel
given-names: Martijn P
name-particle: van
- family-names: Bohler
given-names: Anwesha
- family-names: Kelder
given-names: Thomas
- family-names: Nunes
given-names: Nuno
- family-names: Pico
given-names: Alexander R.
- family-names: Evelo
given-names: Chris T.
doi: 10.1371/JOURNAL.PCBI.1004085
journal: 'PLoS Comput Biol'
title: 'PathVisio 3: an extendable pathway analysis toolbox'
issue: 2
volume: 11
year: 2015
GitHub Events
Total
- Issues event: 7
- Watch event: 3
- Issue comment event: 5
- Push event: 2
- Pull request event: 4
- Fork event: 1
Last Year
- Issues event: 7
- Watch event: 3
- Issue comment event: 5
- Push event: 2
- Pull request event: 4
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| martijn | a****n | 1,602 |
| Thomas Kelder | t****r | 1,239 |
| Martina Summer-Kutmon | m****n | 288 |
| Alexander Pico | a****o@g****u | 199 |
| bartvdh565 | b****5@4****6 | 88 |
| Laurens | L****s@4****6 | 64 |
| KristinaHanspers | k****s | 54 |
| Egon Willighagen | e****n@g****m | 42 |
| Anwesha | p****a@g****m | 36 |
| sjoerd | s****d@4****6 | 35 |
| XueminLiu | X****u@4****6 | 30 |
| s051453 | s****3@4****6 | 30 |
| rdeneer | r****r@4****6 | 30 |
| De | d****r@m****l | 26 |
| A.vanAdrichem | A****m@4****6 | 24 |
| Mark Woon | m****n@g****m | 23 |
| mkutmon | m****n@g****m | 22 |
| colin | c****n@4****6 | 22 |
| Egon Willighagen 0000-0001-7542-0286 | e****w | 22 |
| liubing | l****g@4****6 | 21 |
| margriet | m****t@4****6 | 20 |
| rebecca | r****a@4****6 | 17 |
| jmelius | J****S | 14 |
| andra | a****g | 14 |
| nick | n****k@4****6 | 9 |
| www-data | w****a@4****6 | 6 |
| manager | m****r@4****6 | 4 |
| Lars Willighagen | l****n@g****m | 3 |
| meliusjonathan@gmail.com | m****n@g****m | 3 |
| Kutmon | M****n@u****l | 2 |
| and 4 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 5
- Total pull requests: 2
- Average time to close issues: about 2 months
- Average time to close pull requests: 25 days
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 0.2
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 2
- Average time to close issues: about 2 months
- Average time to close pull requests: 25 days
- Issue authors: 3
- Pull request authors: 2
- Average comments per issue: 0.2
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- alexandra-valeanu (3)
- mkutmon (2)
- khanspers (2)
- matthiaskoenig (1)
- egonw (1)
- beekvandaan (1)
- Akshay-gurav-31 (1)
- DeniseSl22 (1)
- Zpapounet (1)
Pull Request Authors
- egonw (2)
- Akshay-gurav-31 (1)
- Finterly (1)
- markwoon (1)