muCell is currently maintained by Dominic Orchard, however this is not my main concern and time is short. We are keen for new contributors and maintainers. Please get in contact if you are interested. Alternatively if you are a student/researcher and want to take up some or all of the project we have the following outlined research proposals. I am happy to supervise or advise any students taking on projects with muCell.

1. muCell could be extended with a richer environment for creating
   experiments that incorporate external stimulus, interactivity, and
   events. SBML already has support for triggers and events, adding them
   to muCell would provide more dynamic simulations with changes to the
   environment caused by external stimulus, not just passive diffusion
   and the cell’s own effects.
2. The task of saving data from a program with such a large and complicated data model is always difficult and is not yet fully complete and tested in muCell. Thus for the software to be practically appliable on a regular basis the saving and loading features need to be completed. Currently the serialization of muCell experiments and simulations is incomplete. In particular extra-cellular model linkages are not saved and some information in simulations is omitted. – You will need to have or acquire skills in dealing with serialization and deserialization of XML, and will need to learn the SBML systems biology format. There is possible work neeed in created an XML standard for muCell.
3. Better error handling of broken SBML models. Linked in to the previous point, some models can crash muCell, particular some hang made models from the BioModels Database. Additionally currently when formulas fail to parse, errors are produced at the console but useful exceptions are not raised and shown to the users. There needs to be better error handling and correction. Skills will be acquired in XML, parsing, math syntax trees, SBML
4. Adding support for saving the 3D spatial simulator output to a video file. Currently the 3D simulation is shown as computed. Ideally it would also be saved as in a standard video format so that it could be watched in the real-time of the simulation as opposed to “as the computation completes”. Programming skills, movie handling skills. A library can probably be found for encoding videos.
5. More parameters for time series. Currently only species, cell populations, and run/tumble times can be handled as values in time series formula. It would be great if also other cell properties like speed, position, and any other state could also be handled. The math AST in the muCell will need to be extended for my types of data. Skills will be acquired in handling syntax trees, parsing, functional-style programming (folding of trees in functions). The handling of trees and functions in muCell is an interesting piece of code that makes use of the functional side to C#. Good for any functional programming enthusiasts.
6. Add better controls to the 3D viewer. Better navigation, individual cell tracking, shiny effects. Skills acquired/needed: OpenGL, graphics programming, algorithms, visual design.

1. Currently the muCell tool is in some ways a proof of concept that spatial behaviours
   can be simulated and explored by interoperation models of signalling with other models of cell structures. The numerical accuracy of measurements within muCell is correct up to the definition of the models but measurements taken from simulations may not match measurements from in vivo experiments. The parameters of models can be tweaked to give data that matches experimental data to an extent, but further collaboration with biologists is required if more realistic measurements are to be achieved.
2. Implementing support for parallel computation (Group project)
3. Making better use of all the features in SBML, i.e. compartments, events, constraints (Group project).
4. Implementing different numerical integrators that can solve stiff problemts better (Single person project)
5. Better graphics tools, with arbitrary axes, maybe even 3D. (Single person)
6. Currently, there are only procedural models for flagella bundles, receptors, and cell bodies (which facilitate cell collisions). This
   set should be extended to include components for modelling further processes such as cell growth, death, mitosis and cytokinesis (cell
   division), haptotaxis, and cell excretion. Furthermore, there should be tools for the user to develop their own procedural models of cell
   components. This may involve some form of synthetic language, or construction tool, that should be sufficiently flexible to allow definition of current and future models. A solution, already applied in existing tools such as CompuCell3D, is to allow modules to be written in a standard programming language that are then compiled and imported into the software.

We have the following larger research proposals already outlined in PDFs:

1. Increased perception via automatic visualisation techniques on metabolic pathways
2. Hybrid Modelling
3. Abstract modelling language for extra-cellular components