Questionnaire Modeling and Systems Biology

ATTENTION: We are completing the evaluation of the questionnaires submitted. You still may submit a questionnaire, but it will not show up in the final report.

Remark 1: This questionnaire will be used in the frame of the EU-funded project Yeast Systems Biology Network to get an overview on modeling tools and techniques that are used by the scientific community. Collected data will be published on the YSBN web site and used for a report in an anonymous way. No personal data will be given to third party or used for any other purpose. Data submission is voluntary.

Remark 2: It is not necessary to answer all questions. Even partial information is welcome.

0. Some personal information

Email address (optional, if you wish to receive the report via email)

You consider yourself a

Modeler Experimentalist both

Your main areas of research are:

1. Model types

What types of models do you currently develop or have developed? Add a brief description of what biological problem(s) these models address.

Model Type		Biological problems
Deterministic
Non-deterministic
Probabilistic
Discrete (in time, space, or variable values)
Continuous (in time, space, or variable values)

Modeling Technique		Biological problems
Bayesian networks
Boolean networks
Petri Net Models
State transition systems
Cellular automata
Graphical models
ODE models
PDE models
Stoichiometric models
Stoichiometric steady state models
Other model types

Free text field for comments and additions

2. Analysis methods

Which analysis methods do you perform and for which type of model? Do you use a specific tool?

Method		applied to which model type / comment
Steady state determination
Stability of steady state
Bifurcation analysis
Stoichiometric analysis
Elementary modes/extreme pathways
Flux balance analysis (FBA)
Metabolic control analysis (MCA)
Optimization
Optimal control
Parameter estimation
Parameter sensitivity
Other methods

Free text field for comments and additions

3. Modeling tools and software

Please mark how often you use the tools listed below. Give specific comments below the table, if any.

Legend:
     My favorite one
     Frequent use
     Used previously
     Tested a few times
     Known, but not used
     Never heard of
     Frequent use for specific tasks
     Used only/especially for graphical representation

Tool	Usage (see legend)								Comment
BALSA
BASIS
BIOCHAM
BioCharon
biocyc2SBML
BioGrid
BioModels
BioNetGen
BioPathway Explorer
Bio Sketch Pad
BioSens
BioSPICE Dashboard
BioSpreadsheet
BioTapestry
BioUML
BSTLab
C/C++
CADLIVE
CellDesigner
Cellerator
CellML2SBML
Cellware
CL-SBML
COPASI
Cytoscape
DBsolve
Dizzy
E-CELL
ecellJ
ESS
Excel
FluxAnalyzer
Fluxor
Gepasi
INSILICO discovery
JACOBIAN
Jarnac
JAVA
JDesigner
JigCell
JWS Online
Karyote
KEGG2SBML
Kinsolver
libSBML
Mathematica
MatLab
MathSBML
MesoRD
MetaboLogica
MetaFluxNet
MMT2
Modesto
Moleculizer
Monod
Narrator
NetBuilder
Oscill8
PANTHER Pathway
PathArt
PathScout
PathwayLab
Pathway Tools
PathwayBuilder
PATIKAweb
PaVESy
PNK
Reactome
Perl
Powerpoint
ProcessDB
PROTON
pysbml
PySCeS
Python
R
runSBML
SABIO-RK
SBML ODE Solver
SBMLeditor
SBMLmerge
SBMLR
SBMLSim
SBMLToolbox
SBliD
SBToolbox
SBW
SCIpath
Sigmoid
SigPath
SigTran
SIMBA
SimBiology
Simpathica
SimWiz
SmartCell
SRS Pathway Editor
StochSim
STOCKS
TERANODE Suite
Trelis
Virtual Cell
Visio
WinSCAMP
XPPAUT
others

Please list advantages (or disadvantages, if any) of your favorite tools. What are they good for? Why are they for you superior to other tools?
Think about

Availability (free download, purchase costs)
Graphical representation of the network
Ease of inputting graphs or equations or other relevant data
Clarity of task processing, options (how to??)
Speed of computation
Representation of results
Presence and quality of analysis tools
Communication / model exchange with other tools

Can you provide a ranking of tools with respect to above mentioned properties?

Please add tools that you use (or tested) and that are not on the above lists.

What type of functionality is missing - in your favorite tool or in general?

4. Standards

Is the creation of standards in modeling necessary or desirable?
Yes No

Free text field for comments

4.1 Exchange formats

Do you use standard model exchange formats like the ones given below?

SBML
CellML
Others

If you don't use standard model exchange formats. what prevents you from doing so?

My favorite tool does not support SBML/CellML, etc.
SBML/CellML have missing functionality
The learning curve is too steep/ I am too lazy.
Other reasons?

If you don't use standard model exchange formats: In which format do you store and exchange your models?

4.2. Graphical representation

Do you draw graphical representations ("wiring schemes", "network graphs") according to a well-defined nomenclature?
Yes No

Which one(s)?

4.3. Additional aspects

Looking into the future: Which aspect(s) of modeling need to be standardized?

Looking into the future: Which functionality or tool would you like to have (find for free download on a website)?

Are you aware of MIRIAM, a suggested standard for model annotation?
Yes No

Should scientific journals support development and establishment of standards, e.g. by demanding authors to submit models in certain format?
Yes No

Do you expect recommendations for standards from the YSBN?
Yes No

Responsible for content: Edda Klipp; technical realisation: Anselm Helbig