We plan to eventually release the software as a plugin of the V3D-Neuron package at http://penglab.janelia.org/proj/v3d.org/proj/v3d
This can be done in diverse ways, e.g., in command line mode, as a plugin of CellDesigner, as a gadget in Garuda, etc.
The method was implemented as a plugin for the scientific open source image processing package ImageJ.
The method is implemented as a plugin for the fully open source ImageJ ((Rasband, 2008)) distribution called Fiji that is actively maintained and expanded by an international community of developers ensuring long-term availability and future improvements of the stitching method.
In this work we developed a new approach using a "first biological assignment" strategy and we implemented our method as a Cytoscape plugin, called FunMod.
With this predicted association network, three interesting clusters were found using MCODE, 24 a plugin of Cytoscape 25 (see "Data and methods" section for more detail).
An alternative method adopting the CLFDM principle, that generates a curved-layered printing path, was developed using a single scripting environment called Grasshopper – a plugin of Rhinoceros®.
The prediction of coding potential of transcripts not annotated in the PERNI data set was performed, as described in Salvemini et al., 2014 [ 36], using three independent prediction methods: the Portrait software (performed in this paper as a plugin within the Annocript pipeline) [ 38, 41], the Coding Potential Calculator (CPC) [ 43] and the Coding Potential Assessment Tool (CPAT) [ 42].
As a plugin for the Chrome and Firefox desktop browsers, Adblock Plus has been very popular.
It is designed as a plugin for the Abaqus commercial FE code allowing for fatigue predictions based on the results of Abaqus FE analyses.
