Projects being developed under the FURM guidelines |
| ISL |
In Silico (Isolated Perfused Rat) Liver - an ISL experimental apparatus implemented in software.
|
| IS-HIC |
In Silico Hepatic Intrinsic Clearance
|
| EI3 |
We are working on our third hypothetical mechanism for
hepatic enzyme induction. Our first round was
described here.
And our second round (EI2) is described in our
ADS'12
paper | .
| EC2 |
We migrated our analogs to execute in Amazon's EC2 when we
outgrew our 8 node OSCAR cluster. We describe our cross-model
validation from the cluster to the cloud in
our BMC
Systems Biology paper | .
| PtII-Bio |
Ptolemy
II is a co-simulation environment designed for simulating
systems of heterogeneous components. It is mostly
designed for the simulation of engineered systems, both
hardware and software. It's actor-oriented approach
facilitates the graphical construction, quasi-autonomy, and
integration of components based on heterogeneous models of
computation
(so-called Directors)
as well as the semi-automated model-checking of composed
models. Such facilities turn out to be useful for biological
modeling and we have begun designing more biologically
relevant Ptolemy II models and actors. |
| APAP Hepatotoxicity |
Acetominophen (APAP) hepatotoxicity in mice is a reference
model for drug induced liver injury in humans. Because APAP
toxicity involves many positive and negative feedback loops
across many scales and aspects, it is not clear which of those
networks are essential players in the toxicity cascade and
which are mere correlations. This project is a collaborative
effort between the BioSystems Group at UCSF, Neil
Kaplowitz, and Laurie
DeLeve both at USC to build falsifiable mechanistic alternative
models to help decouple the correlations from the causal
influences.
|
Please note that, in
the BioSystems Group at
UCSF, there are several projects that, for various reasons, are
not yet compliant with the FURM method, but the plan is that they all
evolve to do so.
Spin-off projects |
| Glossary |
Many of the issues we cover present the typical inter-disciplinary problem of getting everyone to use a stable lexicon. The glossary is an attempt to hone in on definitions of terms as we would like to see them used. None of these definitions are intended to be universal or authoritative. Indeed, we expect them to change daily. But, presenting them gives some stability to the other work and the communication required for these projects.
Credit goes to Dr. Bernie Zeigler for the inspiration of this glossary and many of the definitions herein. ACIMS Definitions |