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Home » Eclipse Projects » Spatiotemporal Epidemiological Modeler (STEM) » Operon Labs Ebola Model (using stem)(Vincent Ruslan from Operon Labs creates Ebola Model with STEM)
Operon Labs Ebola Model (using stem) [message #1434069] Mon, 29 September 2014 16:17 Go to next message
James Kaufman is currently offline James KaufmanFriend
Messages: 194
Registered: July 2009
Senior Member
Dr. Vincent Ruslan from Operon Labs has used STEM to quickly create a model for Ebola.
His model is slightly different from the one to be release on Eclipse but it's still very informative. Please see it here.

http://www.operonlabs.com/?q=node/6

Dr. Ruslan is collaborating with Dr Althaus, author of the excellent Sep 2nd, 2014 PLOS paper "Estimating the Reproduction Number of Ebola Virus (EBOV) During the
2014 Outbreak in West Africa". He is affiliated with the Institute of
Social and Preventive Medicine (ISPM), University of Bern, Switzerland.

Dr Althaus's PLOS Ebola Paper (open access):
http://currents.plos.org/outbreaks/article/estimating-the-reproduction-number-of-zaire-ebolavirus-ebov-during-the-2014-outbreak-in-west-africa/

Dr Althaus (and colleagues) Web Site:
http://www.immuno-epidemiology.ch/
Re: Operon Labs Ebola Model (using stem) [message #1434072 is a reply to message #1434069] Mon, 29 September 2014 16:20 Go to previous message
James Kaufman is currently offline James KaufmanFriend
Messages: 194
Registered: July 2009
Senior Member
a nice note from Dr Ruslan about STEM and the STEM team

Thank you Stefan. If anything is impressive , it's actually how solid
STEM is as an enterprise bioinformatics platform. You guys have done
some great work.

Thank you to Matthew for fixing the bug so quickly. That would have
taken me weeks to fix. I just checked and pulled down the new master
code, and the Map View Logger works perfectly now.

In terms of compiling a new platform, I don't need to do that. It was
more of a curiosity to see if I could build a custom version with alpha
features.

Your existing Jenkins build server is a much cleaner solution, so once I
have something to share , I will send you guys a patch file for review.

As for my Ebola simulation, yes it is a bit concerning. That is why I
started building the models. I'm hoping to get a new simulation going
with peer-reviewed numbers soon, so some reliable STEM-based simulations
can be released to the scientific community and public.

I will share my STEM files with you guys once I resolve the numerical
discrepancies with the generation time and the serial interval.

Regarding any Ebola 'worst case' scenario, I do believe there exist
medical therapies which would work off-the-shelf against Ebola. For
example, Clomiphene (an FDA-approved SERM) reduces murine mortality by
90% at concentrations attainable in human plasma and intracellular
fluid.

I did the pharmacological calculations from Johansen's 2013 study. . .

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955358/

Clomiphene protects 90% of mice against Ebola Zaire at 60mg/kg q.o.d.
via IP injection.

The Clomiphene murine dose is converted to humans by multiplying by the
FDA scaling factor (0.08), which yields a human dose of 4.8mg/kg.
Multiplying by approximate human mass of 65kg yields a human dose of
300mg orally a day. This is in the range of normal Clomiphene
treatment doses (50-150mg per day) in humans, and is well below the
toxic concentration.

So it's plausible Clomiphene could be used for EVD treatment as an
experimental therapy.

However, since primate studies are lacking, the WHO will not recommend
Clomiphene against EVD. Hopefully increased awareness will allow
doctors access to off-label therapies like Clomiphene.

I suppose the good news is that Ebola failed to spread into Nigeria and
Senegal. Furthermore, the fact that your group created STEM will allow
scientists to monitor the progress of the disease over the coming
months, and eventually put a stop to it.

In the meantime, my goal is to improve and share STEM with other
scientists to assist in EVD modelling.

Sincerely,
Vincent
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