Documents

Burgos, E. S., Ho, M. C., Almo, S. C., and Schramm, V. L. (2009) A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT. Proceedings of the National Academy of Sciences of the United States of America 106, 13748-13753

Burgos, E. S., Ho, M. C., Almo, S. C., and Schramm, V. L. (2009) A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT. Proceedings of the National Academy of Sciences of the United States of America 106, 13748-13753

Burgos, E. S., Ho, M. C., Almo, S. C., and Schramm, V. L. (2009) A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT. Proceedings of the National Academy of Sciences of the United States of America 106, 13748-13753

Takahashi, R., Nakamura, S., Nakazawa, T., Minoura, K., Yoshida, T., Nishi, Y., Kobayashi, Y., and Ohkubo, T. (2010) Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase. J Biochem 147, 95-107

Overview of the results obtained from the Simulation Foundry.

Overview of the quality control checks obtained from the Simulation Foundry.

This is a list of errors that can be produced if the Simulation Foundry is not used correctly - the messages are cryptic, hopefully the file is helpful to some.

Manual to Simulation Foundry Version 1.5.

Scripts and Input Files for Analysis V1.5

OPLSAA force field used by GROMACS on the BINAC Supercomputer (chem/gromacs/5.1.4-gnu-4.9, https://wiki.bwhpc.de/e/Category:BwForCluster_BinAC )

Screenshot of the directory structure required for the Simulation Foundry.

fifth worksheet for RStudio-Shiny application, relating to the following pages:

simulation2 concluding question (all pages, simulations, worksheets)

fourth worksheet for RStudio-Shiny application, relating to the following pages:

Therapies and senescence simulation1

third worksheet for RStudio-Shiny application, relating to the following pages:

Senescence in tissue biology

second worksheet for RStudio-Shiny application, relating to the following pages:

Cellular senescence

first worksheet for RStudio-Shiny application, relating to the following pages:

Systems Biology

fifth worksheet for RStudio-Shiny application, relating to the following pages:

simulation2 concluding question (all pages, simulations, worksheets)

fourth worksheet for RStudio-Shiny application, relating to the following pages:

computational modelling simulation1

third worksheet for RStudio-Shiny application, relating to the following pages:

treatment options drug resistance

Second worksheet for RStudio-Shiny application, relating to the following pages:

Risk factors, features and biomarker cancer characteristics

first worksheet for RStudio-Shiny application, relating to the following pages:

what is breast cancer breast cancer types

Detailed programme with organizers' notes.

Slides for the Python Workshop

What is PlaSMo? PlaSMo stands for Plant Systems-biology Modelling; Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

The original PlaSMo project description is included within the attached document.

Our aims

To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost To represent these models in a declarative XML-based ...