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| Here is an example of an app article from this collection: [[http://f1000research.com/articles/3-152/v2 | WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization]]. | Here is an example of a Cytoscape app published in this collection: [[http://f1000research.com/articles/3-152/v2 | WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization]]. |
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| Another popular avenue for publishing Cytoscape app paper is the "Application Note" format in BMC Bioinformatics. This represents a traditional peer-reviewed publication process. | |
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=== Contents of an app paper === In addition to the requirements on content imposed by the journal publisher, an app article should contain the following: |
Guidelines for submission can be found at [[http://www.oxfordjournals.org/our_journals/bioinformatics/for_authors/general.html | BMC Bioinformatics]]. A few key points from their author guide in regards to Applications Notes are: * Applications Notes are short descriptions of novel software or new algorithm implementations, databases and network services (web servers, and interfaces). * Application Notes are p to 2 pages, approx. 1300 words or 1000 words plus one figure * Software or data must be freely available to non-commercial users. |
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* Implementation: describe any * Availability: describe how and where users can get access to the app |
Here's an example of a Cytoscape app published in BMC Bioinformatics: [[http://bioinformatics.oxfordjournals.org/content/early/2015/01/09/bioinformatics.btu853.long |ENViz: A Cytoscape App for Integrated Statistical Analysis and Visualization of Sample-Matched Data with Multiple Data Types]]. |
Publish your app
Overview
You have developed your app, tested it and announced it to the user community. Now its time to write a paper about your app. This step will provide some ideas and resources for publishing your app in a peer-reviewed journal.
Process
Where to publish
While there are many options for where to submit app articles, there are two that are recommended:
F1000Research
The F1000Research Cytoscape App Collection was first published in July 2014, and is intended to serve as a resource to both researchers and app developers. It is a tailored publication hub for new and updated Cytoscape apps and serves as a resource to help researchers find out more about relevant Cytoscape apps and to provide app developers with useful implementation tips. The collection will grow over time as new Cytoscape apps are developed and published. All Cytoscape apps published in this collection are free and open source.
- New app articles can be submitted at any time to the Cytoscape App Collection
Articles are peer-reviewed after publication. Read more about F1000Research's post-publication peer-review system here.
- Articles can be revised after submission
Article submission guidelines are available here.
Here is an example of a Cytoscape app published in this collection: WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization.
BMC Bioinformatics
Another popular avenue for publishing Cytoscape app paper is the "Application Note" format in BMC Bioinformatics. This represents a traditional peer-reviewed publication process.
Guidelines for submission can be found at [[http://www.oxfordjournals.org/our_journals/bioinformatics/for_authors/general.html
- | BMC Bioinformatics]]. A few key points from their author guide in regards to Applications Notes are:
- Applications Notes are short descriptions of novel software or new algorithm implementations, databases and network services (web servers, and interfaces).
- Application Notes are p to 2 pages, approx. 1300 words or 1000 words plus one figure
- Software or data must be freely available to non-commercial users.
Here's an example of a Cytoscape app published in BMC Bioinformatics: ENViz: A Cytoscape App for Integrated Statistical Analysis and Visualization of Sample-Matched Data with Multiple Data Types.