FAQ

Introductory Questions

What is transsys?

transsys is a framework for the computational modelling of gene regulatory networks (GRNs).

How is transsys different from other GRN modelling systems?

One of its unique features is its object-oriented structure that facilitates building integrated models that represent the GRNs as well as other levels of biological organisation (e.g. pattern formation, morphogenesis, and others).

Are there some introductory examples?

Yes, please have a look at the tutorial

Installation

Can I install transsys on my computer?

Yes. You need a Linux system on your computer with the gcc and Python development options installed. On any contemporary Linux box with these, you should be able to install transsys by downloading the transsys distribution and configuring, building and installing that.

Can you tell me the commands for installing transsys?

Yes, but please notice this disclaimer first: Executing commands supplied by others on your computer can damage your system. You run this code at your own risk.

With this disclaimer in place, you can try the following commands:

 wget http://www.transsys.net/software/transsys-current.tar.gz
 tar -zxvf transsys-current.tar.gz
 cd transsys-current
 ./configure --prefix=${HOME}
 make
 make install

This will install transsys into your local account. Therefore you can use these without having root privileges. These commands may overwrite an existing transsys build directory. The FAQ author(s) are not aware of any other damage that these commands may cause. You may have to update your PATH and PYTHONPATH environment variables for your transsys installation to work.

Tips and Tricks

My transsys models take very long to equilibrate, what can I do about that?

Notice that the speed of equilibration depends on the smallest decay rate in your transsys program. Therefore, bringing up your decay rates as much as possible will speed up equilibration. However, too high decay rates will result in large numerical artifacts, this typically implies a limit for increasing decay rates.

Can I use mechanisms other than Michaelis-Menten kinetics to model activation and repression?

Yes. You can use arbitrary mathematical expressions with the constitutive promoter element.

Is it possible to model translation?

transsys does not provide any specific mechanism for modelling translation. Gene products, i.e. factors, may be used to either represent mRNAs or proteins, it is up to the modeller to decide what a factor represents. Translation can be simulated by using a "mRNA factor" and a "ribosome" gene like this:

 factor my_mrna { ... }
 factor my_product { ... }
 
 gene my_gene
 {
   promoter { ... }
   product { default: my_mrna; }
 }
 
 gene my_ribosome
 {
   promoter { constitutive: my_mrna; }
   product { default: my_product}
 }

This way, the gene my_gene encodes a mRNA and my_ribosome "translates" the mRNA to synthesise the product my_product.

This technique works reasonably well where distinct modelling of messages and products is required for one or a few genes, but it is not really suitable where this distinction is desired for a larger number of genes.

Translation is really a metabolic process and the transsys core does not model these. Using the Python API it is possible to develop any metabolism simulator.

Can transsys programs be converted to SBML

Yes. There is a script called trsys2sbml included in the transsys software package.

Using the Python API

Please see the the API documentation.