Presentation given at EclipseCon2010 about the uses of Eclipse in Systems Biology software.
- 1.Eclipse meets Systems BiologyMarch 24th 2010
Richard Adams
Centre for Systems Biology
University of Edinburgh
UK
2. Talk plan
What is Systems Biology?
What computational approaches are used?
How can Eclipse technology help?
3. Biology occurs across many levels
4. ~ 20 000 genes
2x106protein types
> 20 000 metabolites
5. Microscopy
Structural detail
Genetics
Biochemistry
60% metal, 10% wood, 30% plastic
Identify important components:
Steering wheel, lights, etc.,
6. ignition
engine
gears
Steering wheel
Controlled movement
7. Aim toproduce quantitative, predictive, computational
models
of biological processes.
Maths
Biology
Existing knowledge
Static models
Kinetic models
New knowledge
High-throughput data
High-resolution data
8. Example : predicting drug response in breast cancer
Systems biology reveals new strategies for personalizing cancer
medicine and confirms the role PTEN in resistance to
trastuzumab
Faratian et al., Cancer Reseach 2009
9. Systems biology software spectrum
Biopepa
Edinburgh
Pathway Editor
Mathematica
Biology-specific modelling tools
Pathway drawing tools
Text-mining/knowledge DBs
Matlab
1_3_0_RC1_18_3_10
Eclipse RCP ?
10. customizable 11. nice UI for biologists 12. Accessto IDEs
for computational modellers.- Reusable ready-made components
13. Biopepa
Edinburgh
Pathway Editor
14. What is EPE?
A Graphical editor for drawing pathways
Why not just use Powerpoint?
- EPE allows export to common systems biology data formats
- multiple graphical notations
- syntax rules for drawing valid diagrams.
- semantic validation.
Currently developedby Anatoly Sorokin, Stuart Moodie and
Igor Goryanin, Department of Informatics,University of
Edinburgh.
15. 16. Overview of Systems Biology Software Infrastructure
SBSI
clients
SBSI Visual
Desktop application
Upload and edit SBML models
17. Configure optimisations Interact with external
repositories
Visualisation of data and results
SBSI Web
Interface
Command
line
SBSI
Dispatcher
(Task Manager)
18. Submit jobs to HPCRetrieve results
Provide job status
SBSI Numerics
Numerical algorithms and
Frameworks for
-Sensitivity analysis
core
Eddie (ECDF)
SBSI repository
Models (SBML)
Data ( SBSI standard format):
-experimental data
-simulation results
19. Runningparameter optimisations
Step 1 create a newSBSI project
Editor view allows access to files
In the workspace youcan
store models, data, objective functions and results
Data visualization panel
20. Runningparameter optimisations
Step 2 choose models,
data and algorithm type
- multiple datasets can be selected
