- Version history SYCAMORE - STAPAC/PIPSA (parameter estimation module)
- Version history SYCAMORE - COPASI (time course analysis and paramter estimation)
- General setup
- Load existing model
- Build new model
- View and edit model
- Refine and analyze model
- Save model
- Use case
Sycamore is a system which is meant to support your computational approaches in systems biology. Thus, the system helps you to set up models by guiding you through that process and verifying certain steps.
This implies that it has been tested, but surely will need feedback from the community to become perfectly user-friendly and bug-free. Therefore, we appreciate such feedback from you. Please also don't hesitate if you have any questions regarding the system. Such questions will help us to identify points where the transparency of the system is clearly imperfect.
The GUI for Sycamore is divided in 2 panels. The left one has a tree structure that allows you to navigate through the different tasks. Please note that some tasks might be disabled, if they are not applicable for you specific problem at the moment. The right panel displays the task that is currently activated.
Load existing model:
This task allows you to load a previsouly defined model into Sycamore.
The following is possible:
- The model can be
loaded from your disk. Clicking on this option will display a
facility to browse your disk on the right side and select a
resepective SBML file.
- If the file should
be from a previously started project within Sycamore, you have to
enter your previous registration and project number on the right
- Load an example model provided by us.
Build new model:
This task allows you to build a model from start. The following is possible:
- Clicking on the
option “Sycamore new model” displays a window that
optionally allows you to create a model ID. If you then click on
build new model, a window is displayed which allows you to specify
reactions by clicking on “add reaction” and then
entering the participating species with their respective
stoichiometry, ID and role. Please note that the reaction equations
are automatically generated by the system. Since SBML files are
generated Ids for the models and species are required. In the lower
table you might enter the kinetics and parameters governing the
speed of your particular reaction. When you click on “add
reaction” the system verifies your entry. If it is as complete
as necessary and conforms to the respective standards, the reaction
is integrated in your model. If not, the system tells you what is
missing/wrong etc. You can add as many reactions as you want to
include in the model.
- Building the new model using SABIORK will connect you to the database containing information about biochemical reactions and their kinetics from literature. You can either enter through the homepage or directly via reaction search. There is also detailed documentation about the database available. Please refer to that for learning how to select reactions and their kinetics from the database. Once you have collected all available reactions that you want to include in your computational model, you can chose the option to send the data to Sycamore.
View and edit model:
This tasks allows you to view different levels of information about your loaded or built model and to edit it. The following is possible:
- View the general
model data, like ID, name and comments.
- View global
parameters meaning parameters that are defined not only for one
specific reaction, but for the whole model.
- View your unit
definitions, if there are any.
- View the rules
within the model. Rules might be contained in a previously defined
SBML model and are algebraic equations.
- Display either a list
of compartments or edit the compartment information.
- Have a look at the
table of reactions or each individual reaction seperately and edit
- Finally, it is possible to display a pathway map or graphical representation of your model. Right now, this only works, if your SBML file contained layout information. In the future layout will be generated on the fly. The graph can be tuned by editing the table w.r.t. background color, fonts etc.
Refine and analyze model:
Here, you find tools to analyse and improve your model. The following is possible:
Clicking on this task, Sycamore will check your current model w.r.t. missing parameters or kinetics. The result is displayed on the right side.
This task will tell you how sensitive steady-state concentrations of your system are w.r.t local (small) parameter changes. You can chose those species which concentration should be analysed. If you then click on “perform analysis” a table will be displayed which contains rows associated with each selected species and columns with each parameter of the model. The sensitivities are colorcoded according to the table below. Thus, it should be easy to find those parameters to which the concentrations of interest are most sensitive. These parameters usually should be determined most closely experimentally whereas those with very low sensitivities are less crucial for the models behaviour at this point. However, please verify that this is a local measure only valid for small parameter changes. You will need to perform this analysis again, if you change any of the parameters significantly. Therefore, this can only give you some indications about parameter importance.
- Model simulation:
Right now, you can either use Copasi for a quick simulation of your model which is provided by Sycamore or you can download your model and open it in a locally installed SBML compatible simulation program of your choice. If you want to have a quick glance on your model, press the option Copasi. The panel on the right side will then ask you to specifiy the species in your model that should be displayed as well as a starting and stopping time for your model. Please note that due to size restrictions, no simulation with more than 200 points is possible that way. Once defined that simulation can be carried out and the result will be displayed as a graph and table for the selected species.
Clicking on “General” will give you some information how to faciliate the direct linking of Sycamore to a locally installed simulation engine and will also point you to the links of SBML compatible simulators.
Here, seperate documentation for the parameter computation on protein structure basis is available.
This task allows you to save your model either:
- on your disk
- or as project file within Sycamore.
Here, you are referred to a number of model repositories and relevant databases that might aid you in your setting up and working with a model.
A registration is necessary if you want to either store your projects on the Sycamore server or if you want to use structure based parameter estimation techniques, since these demand more computational time and therefore are commonly not possible while you are connected and online.
Makes this documentation available.
A use case for Sycamore.
Weidemann A, Richter S, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U. (2008) SYCAMORE - a SYstems biology Computational Analysis and MOdeling Research Environment. Bioinformatics 24, 1463-4.
Gabdoulline RR, Stein M, Wade RC. (2007) qPIPSA: Relating enzymatic kinetic parameters and interaction fields. BMC Bioinformatics 8, 373.
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. (2006) COPASI - a COmplex PAthway SImulator. Bioinformatics 22, 3067-74.
(Last updated February 2010)