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To see if performance could be improved for aDNA, we have modified the default alignment parameters to improve mapping sensitivity at acceptable run-times.
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For accelerating the power consumption in our simulation, we modify the default values of the NS2 default value [17].
Some methods modify the default versions of these force fields by modifying individual scoring terms or using only a subset of the scoring terms.
The only way to reduce the delay jitter then was to modify the default values of some MAC specific attributes in order to switch off the backoff mechanism.
A configuration file allows to modify the default movie appearance (e.g, resolution, colors) and layout parameters (see the project website).
Upon providing all the above, a user-friendly interface commences allowing the user to modify the default values in a series of optional inputs.
Users can also modify the default behavior of the web service to specify the particular tasks to perform with the parameter task, which can take gner (gene NER), sner (species NER) or gnorm (normalization to Entrez Gene IDs) as arguments.
Drupal Views can be useful for creating custom pages when no programming expertise is available to modify the default Tripal template files, although template files will provide the most flexibility for data display.
However, VCM icons are computer-generated and it should be possible to modify the default colors according to user preferences (e.g. using gray and black rather than red and green for color-blind people).
In the query interface, users can also modify the default parameters of the application, including: search space (all species or restricted to human genes), the number of genes to present per result page, the maximum number of publications supporting each gene returned in the result page and the number of pages to build for each of the algorithm runs.
You may (and most likely will) modify the default behaviors included in this implementation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com