FAQ
Q: Is Newt free to use?
A: Yes, Newt is an open source project, distributed under GNU Lesser General Public License.
Q: Is there anything I need to install to start using Newt?
A: No, Newt is web based and is expected to work on most major browsers with recent releases without any prior installation or set up. If you'd like to run/deploy it locally rather than using the sample deployment however, some services need to be started.
Q: What is the best way to get started with Newt?
A: First, read the tutorials page and watch the associated videos.
Q: What notation is used in Newt to draw biological maps?
A: Newt supports SBGN Process Description (PD) and
Activity Flow (AF), SIF and SBML notations. A quick introduction to SBGN can be found
here.
For those preferring a simplified notation, SIF
would be a good choice. Finally, a notation based on SBML is also supported in Newt.
Users are also allowed mix up notation from these notations by chaning the map type at the cost of disabled validation
checks during creation.
Q: What format does Newt use to save maps?
A: Newt uses a native format (".nwt" file) for all notations supported (which is in fact based on
SBGNML). Thus, "File | Save..." stores maps in
this format and "File | Open..." expects a ".nwt" file as well. Since ".nwt" file is an extension of SBGNML, however,
plain SBGNML (".sbgn") files will be loaded successfully as PD or AF maps depending on the notation specified inside
the file.
Newt can import SIF
or AF files formatted as tab-delimited text. Exporting to a simple tab-delimited format for SIF files is also supported
through "Export | SIF".
Furthermore, Newt supports import from and export to
CellDesigner ,
SBML, and
GPML file formats via various services.
Details on file operations are explained here.
Maps can also be exported as static (raster or vector) images.
Q: Does Newt save styling information (e.g. color, font, custom annotations, etc.)?
A: Yes, any style information per node/edge/map is saved as an extension to standard SBGNML with file extension ".nwt".
Thus, you can restore such information when you load such files back up on Newt but such information might be lost
when imported to other tools (since other tools might not support the style extension to SBGNML). If a tool is having
difficulty importing our files, try exporting in plain SBGNML ("Export | SBGN-ML Plain") with file extension ".sbgn".
Q: How can I create a reversible reaction in Newt?
A: Use of a single process for a reversible reaction is
a controversial issue
since it can lead to ambiguities when the process has modulators. In Newt, if a map's type is PD, it doesn't allow
connecting production edges to both the input and the output ports of a process. However, one can create reversible reactions
using SBGN bricks ("Edit | Add Using SBGN Bricks..."), but the map may no longer pass PD validation checks.
Q: How can I be sure that my map is SBGN compliant?
A: Newt provides both syntactic and semantic (in SBGN PD maps only) validation. As you're creating map objects and interactions, Newt will warn you if they are incompatiable with the current map type. In addition, for SBGN PD maps, we also provide semantic validation with suggestions to fix any problems with your maps with most type of errors in an interactive fashion.
Q: I uniformly use a certain style (map and object properties such as colors) in my maps. Can I simply keep these preferences across sessions?
A: Newt lets you save preferences and load them back in your next session, so the look and feel of your maps could be uniform.
Q: Can I overlay experimental data on my maps in Newt?
A: You can upload and overlay your experiment data (as many sets as desired) using a simple tab-delimited file. The valid range for data values as well as colors to be used for mapping may be customized by the user.
Q: Can I deploy my own Newt instance?
A: Yes, it is rather straightforward to deploy and maintain a local copy of Newt. In addition, Newt is specifically designed to be easily customizable (modify menu and toolbars, and other functionality) and embeddable within your own website.
Q: What if I'd like to contribute to Newt development?
A: We'd love to have more resources. Please contact us privately through this form.