Biology

From SC Education

Houston CBBE:

Talk to Houston about content – There was an initial indication of interesting image analysis. Possible interest in databases, archiving, metadata.

Standard CBBE fare Dynamic modeling intro:

 Dynamic modeling background
 Diagramming a system
 Morning chemical kinetics background: rate laws

Hands on:

 Time-course analysis in Excel
 Diagram model of system
 Build model in vensim
 Modeling 

Systems biolgy tools:

 SBGN
 SBML or CellML
 CellDesigner vs. other design tools (look at Matlab SimBiology)
 Simulators

Agent modeling

 Agent sheets or Netlogo

Bioinformatics

 Sequence comparison
 Molecular phylogeny

Structural biology

 PDB – structure, function, molecular motion resources
 BSW – Gromacs interface or NanoHub: NanoGromacs
 VMD structures and trajectories need to be prepared 
   contact Paul and Charlie about possible MD runs to produce trajectory files on cyclin-depenant 
   kinases that could be tied in with cell-cycle control models for systems biology demo

Costa Rica – First look, nanotechnology, biomedical

 Inbio[1]
 Open-source software tools and environments
 Server-based computing
 Innexpensive – thin clients, www.koolu.com, extreme green computer – green computer LX800
 Earth University – they have a relationship with Google
 www.eduteka.org - Spanish translations of Interactivate materials
 Eric says a group in Spain has translated biology workbench materials