def get_all_workspaces(get_latest_exposures=False,
url="http://models.cellml.org/workspace/rest/contents.json"):
"""
List all available CellML models.
:param bool get_latest_exposures: Query models.cellml.org for latest
exposure for each model? This can take several minutes.
:param str url: URL to list of cellml.org workspaces.
:return: Record array with fields "title", "uri", "workspace",
and optionally "exposure", "ew", where the latter can be passed to the
:meth:`Cellmlmodel` constructor.
If you wanted to check out every workspace at cellml.org,
you could run the following in IPython::
from cgp.physmod.cellmlmodels import get_all_workspaces
w = get_all_workspaces()
for uri in w.uri:
!hg clone $uri
"""
d = json.loads(urlcache(url))
w = OrderedDict((k.lower(), v)
for k, v in zip(d["keys"], zip(*d["values"])))
w["workspace"] = [i.split("/")[-1] for i in w["uri"]]
if get_latest_exposures:
m = Cellmlmodel()
w["exposure"] = []
for ws in w["workspace"]:
m.workspace = ws
w["exposure"].append(m.get_latest_exposure())
return dict2rec(w).view(np.recarray)
def __array__(self):
"""
Convert timing to record array.
>>> np.array(Timing()) # ...ellipsis to allow 0 or 0L
array([(0..., nan, nan, nan, nan, nan)],
dtype=[('attempts', '<i8'), ('waiting', '<f8'), ('started', '<f8'),
('finished', '<f8'), ('error', '<f8'), ('seconds', '<f8')])
"""
return dict2rec(self)
def par2ph(par):
"""
Phenotype: Equilibrium expression level of gene 2.
This maps a parameter value to a phenotype value.
"""
model._ReInit_if_required(y=np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.0]))
model.pr[:] = par
_t, y = model.eq(tmax=100, tol=1e-6)
return dict2rec(dict(Y2=y[2] + y[3]))