NDEx: A Community Resource for Sharing and Publishing of Biological Networks.

Networks are a powerful and flexible paradigm that facilitate communication and computation about interactions of any type, whether social, economic, or biological. NDEx, the Network Data Exchange, is an online commons to enable new modes of collaboration and publication using biological networks. NDEx creates an access point and interface to a broad range of networks, whether they express molecular interactions, curated relationships from literature, or the outputs of systematic analysis of big data. Research organizations can use NDEx as a distribution channel for networks they generate or curate. Developers of bioinformatic applications can store and query NDEx networks via a common programmatic interface. NDEx can also facilitate the integration of networks as data in electronic publications, thus making a step toward an ecosystem in which networks bearing data, hypotheses, and findings flow seamlessly between scientists.

NDEx, the Network Data Exchange.

Networks are a powerful and flexible methodology for expressing biological knowledge for computation and communication. Network-encoded information can include systematic screens for molecular interactions, biological relationships curated from literature, and outputs from analysis of Big Data. NDEx, the Network Data Exchange (www.ndexbio.org), is an online commons where scientists can upload, share, and publicly distribute networks. Networks in NDEx receive globally unique accession IDs and can be stored for private use, shared in pre-publication collaboration, or released for public access. Standard and novel data formats are accommodated in a flexible storage model. Organizations can use NDEx as a distribution channel for networks they generate or curate. Developers of bioinformatic applications can store and query NDEx networks via a common programmatic interface. NDEx helps expand the role of networks in scientific discourse and facilitates the integration of networks as data in publications. It is a step towards an ecosystem in which networks bearing data, hypotheses, and findings flow easily between scientists.

Porting and using PanGIA for Cytoscape 3: challenges and solutions.

Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which plugins relied changed, requiring a significant porting effort for plugins to work as Cytoscape 3 apps. PanGIA is a Cytoscape add-on (http://apps.cytoscape.org/apps/pangia) designed to analyze and visualize genetic interaction data in light of physical interaction data. In order to convert the PanGIA plugin to an app, various challenges, including those related to a transformed data model, concurrency, and randomization had to be overcome. In the process, the ability to control randomization was added to the GUI, a feature which was not only integral to the porting process, but which also ensures more easily reproducible scientific analysis for PanGIA users. Most authors of Cytoscape 2 plugins will face similar challenges porting their software to work with Cytoscape 3, and this paper gives details of how the PanGIA port addressed them.

The Cytoscape app article collection.

As a network visualization and analysis platform, Cytoscape relies on apps to provide domain-specific features and functions. There are many resources available to support Cytoscape app development and distribution, including the Cytoscape App Store and an online "cookbook" for app developers. This article collection is another 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.

Precision microchannel scaffolds for central and peripheral nervous system repair.

In previous studies, we demonstrated the ability to linearly guide axonal regeneration using scaffolds comprised of precision microchannels 2 mm in length. In this work, we report our efforts to augment the manufacturing process to achieve clinically relevant scaffold dimensions in the centimeter-scale range. By selective etching of multi-component fiber bundles, agarose hydrogel scaffolds with highly ordered, close-packed arrays of microchannels, ranging from 172 to 320 µm, were fabricated with overall dimensions approaching clinically relevant length scales. Cross-sectional analyses determined that the maximum microchannel volume per unit volume of scaffold approached 80%, which is nearly twice that compared to our previously reported study. Statistical analyses at various points along the length of the microchannels also show a significant degree of linearity along the entire length of the scaffold. Two types of multi-component fiber bundle templates were evaluated; polystyrene and poly(methyl methacrylate). The scaffolds consisting of 2 cm long microchannels were fabricated with the poly(methyl methacrylate) fiber-cores exhibited a higher degree of linearity compared to those fabricated using polystyrene fibers. It is believed that the materials process developed in this study is useful for fabricating high aspect ratio microchannels in biocompatible materials with a wide range of geometries for guiding nerve regeneration.