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What can Evolvix do for you?

Evolvix can help you think. It shows the consequences you can expect if a certain set of conditions are true for your model. Our current prototype may already help you with some of these modeling needs, but if you expect a polished product, then you may want to wait - unless you want to help us improve by telling us about all the problems you may encounter.

Why not to use a prototype

Prototypes are well known for having all sorts of issues that have not yet been fixed. Evolvix is no difference. Evolvix is currently at a very early embryonic stage and what you can download is a very early prototype. Unless you

  • are curious and willing to overlook the occasional glitch -or-
  • want to help us develop Evolvix -or-
  • want to become an alpha tester -or-
  • have direct access to core developers of Evolvix, 

we recommend:

 

Do not yet use Evolvix at this point in time --- if you want a polished user experience without the need to tell us about problems you encounter.


Oscillating systems are frequent in biology, from molecular circadian clocks to predator-prey systems. This time series is computed as if the system was deterministic, ignoring all possible sources of variability.What Evolvix can do for you now

If you don't mind the warning above and are happy to tell us about any issues you might experience, feel free to start using Evolvix. We welcome anything you send us: use cases or suggestions for new features or ideas for improvements or problems you experience. We recommend that you establish contact with the developers, if you want to use Evolvix for any serious analysis of any type of question that has not been explicitly listed as "production ready" on this website. 

In principle: If you have a computational modeling question of a type that is currently supported by Evolvix, then you can formulate your model and your question in the Evolvix language and have the Evolvix system automatically compute the results. 

Specifically, Evolvix can already help you to:

  • encode global dynamic mass-action kinetics models with fixed rates using an easy to learn syntax that describes the system in terms of parts and actions
  • automatically translate these models into deterministic systems of ordinary differential equations (ODEs) and equivalent differential algebraic equations (DAEs)
  • automatically translate these models into stochastic simulation algorithm models (SSAs)
  • simulate deterministic models using a state of the art solver from the SunDials suite (DAE_IDAS_dense)
  • simulate stochastic models using an Evolvix implementation of the 'Sorting Direct Method' (SSA_SDM)
  • observe a set of predetermined parts to record timeseries of their amounts and net fluxes during a simulation
  • automatically filter the masses of generated timeseries data at the source to only report values that are substantially different from previous values based on some definable criterion (e.g. relative error in %)
  • collect the data needed for pairwise phase diagrams
  • automatically produce pdfs with convenient plots of timeseries or phase diagrams of amounts or fluxes.

So if you need simple simulations of what is essentially a mass-action model, Evolvix may already be useful to you. However, if your simulation needs are more complex (e.g. automatically change parameters, etc) or you need arbitrary kinetcs (e.g. Michaelis-Menten, etc), you have to wait a bit longer.

Current production ready capabilities:  No functionality has been released as "production ready" at this point.

Source code for Evolvix will be open source as soon as proper documentation can be provided. We are working on this.

If there are any questions, please contact us.

 

 For screenshots, see here.