SyBValS

Systems Biology Validation Service (SyBValS) is a web service that validates maps in SBGNML format and produces graphical images of the map with an option to highlight errors. After validating maps, if desired, SyBValS will resolve these errors when possible, reproducing the image after any fixes and returning the corrected SBGN file. During the resolution of errors, the user is also provided with possible choices when applicable, or the errors are resolved with default choices.

Here is a video tutorial:

Please cite the following when you use SyBValS:

  Y.Z. Ozgul, U. Dogrusoz and H. Balci, "SyBValS: a validation and error resolution service for biological pathways", under review, 2024.

Here is an example from our simple demo on a sample deployment. Below is a list of errors found by the service for the map provided by the user upon Validate:

Notice how each error is color-coded both in its text description and in the image, respectively. Also, the user is provided with resolution alternatives when applicable.

Here is the same map after the user applied Resolve Errors:

All problems have now been fixed.

The main capabilities of SyBValS include:

• validate and create an image of a map in SBGNML format, and
• resolve the errors in a map in SBGNML format, recreate an image of the validated map, and produce a corrected version of the input SBGN file.

Backed by these capabilities, SyBValS can be used to validate, resolve, and generate images of SBGN models (e.g., for including in web pages or scientific articles).

SyBValS is distributed under the MIT License.

Here is a sample server deployment along with a simple client-side demo:

Sample maps used in the demo are taken from:

• Systems Biology Graphical Notation: PD Level 1 examples - IFN regulation. https://sbgn.github.io/examples#ifn-regulation.
• McCormick, D.B., Chen, H.: Update on interconversions of vitamin b-6 with its coenzyme. J Nutr. 129(2), 325–7 (1999) https://doi.org/10.1093/jn/129.2.325
• Van Wijk, R., Van Solinge, W.W.: The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis. Blood 106(13), 4034–4042 (2005) https://doi.org/10.1182/blood-2005-04-1622
• Ma, H., Groth, R.D., Cohen, S.M., Emery, J.F., Li, B., Hoedt, E., Zhang, G., Neubert, T.A., Tsien, R.W.: γcamkii shuttles ca2+/cam to the nucleus to trigger creb phosphorylation and gene expression. Cell 159(2), 281–294 (2014) https://doi.org/0.1016/j.cell.2014.09.019
• Systems Biology Graphical Notation: PD Level 1 examples - Neuro-muscular junction. https://sbgn.github.io/examples#neuro-muscular-junction.