The submatrix of S pertaining to the reactions and metabolites so identified is extracted and saved in appropriate format as a full specification of the subnetwork, which can be further analysed by standard network analysis or FBA software tools.
However, as the basis for our proposed visualization, we need an approach that allows us to explicitly generate a joint coordinate system that can be used to consistently specify coordinates of annotations (and also of experimental data such as mapped sequencing reads or RNAseq expression graphs), which can be used independently from a specific analysis or visualization software.
Even if the raw data are deposited in public archives, the essential analysis intermediaries, scripts or software are frequently not made available, meaning the science is not reproducible.
Sometimes the raw data are deposited in archives, but the essential analysis intermediaries, scripts or software are not available, meaning the results of a study are not reproducible by others.
All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software.
β-III-tubulin immunoreactivity was detected in DRG cultures on coverslips using a fluorescence microscope (Nikon Diaphot, Nikon, Tokyo, Japan) or Olympus BX61 (Olympus), and images were captured using a CCD camera (Hamamatsu Orca, Hamamatsu Photonics, Hamamatsu, Japan) or ColorView Soft Imaging System and Openlab (Improvision, Coventry, UK) or analySIS software.
As both film and electronic images were acquired, manual (light box) or software analysis methods were used to measure displacements.
However, the resulting geometries are modeled as NURBS 3D surfaces and can be imported to other CAD or analysis software via standard exchange protocols.
Therefore, most references to chemical agents in scientific research articles cannot be easily linked to other repositories of scientific knowledge, and are thus not amenable for analysis or searching using cheminformatic software.
The fluorescence can be quantified by fluorescence activated cell sorting (FACS) analysis or by special microscopic software.
