date:20130214

[NMusers] Bootstrap, re-using inital model run results

2013-02-14 Thread Lommerse, JPM (Jos)

Hi

I would like to ask to NONMEM community whether it is possible to re-use the 
results of a nonmem model run when starting bootstrapping.
As I understand, a bootstrap run using PsN starts with a single calculation of 
the model of interest and data set as is. Once this initial model run
has completed, the actual bootstrapping starts by sampling from the initial 
data set to the requested number of samples.
However, the initial run often has been carried out already, and the bootstrap 
method this seems to be repeated.

I am dealing with a rather time consuming model / data set. Therefore I was 
wondering whether it is possible the re-use the results of a nonmem
model run and start the bootstrapping directly without repeating this initial 
nonmem model run. I was not able to find any option to do so. Perhaps there
is way around?

Thanks,

Jos

Jos Lommerse
Assoc. Prin. Scientist, Quant. Sciences
Clinical PK-PD
T: +31 412 661456
F: +31 412 662555
jos.lomme...@merck.com

MSD
Molenstraat 110, 5342 CC Oss
PO Box 20, 5340 BH Oss
The Netherlands

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
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RE: [NMusers] Bootstrap, re-using inital model run results

2013-02-14 Thread Mats Karlsson

Dear Jos,

 

If you haven't run the original model (indicated by absence of lst-file with
the same prefix) psn will run it before the bootstrap. If you have run it,
PsN will not rerun it. It will use the results in the corresponding lst
file. If you have run it and called it something else, you could use the
"-out=xxx.yyy" to point to the correct file if that does not follow naming
conventions. If you have  not run it and really don't want to run it, you
could substitute xxx.yyy for some other output file with similar structure.

 

Best regards,

Mats

 

Mats Karlsson, PhD

Professor of Pharmacometrics

 

Dept of Pharmaceutical Biosciences

Faculty of Pharmacy

Uppsala University

Box 591

75124 Uppsala

 

Phone: +46 18 4714105

Fax + 46 18 4714003

 

From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Lommerse, JPM (Jos)
Sent: 14 February 2013 08:29
To: nmusers@globomaxnm.com
Subject: [NMusers] Bootstrap, re-using inital model run results

 

Hi

 

I would like to ask to NONMEM community whether it is possible to re-use the
results of a nonmem model run when starting bootstrapping.

As I understand, a bootstrap run using PsN starts with a single calculation
of the model of interest and data set as is. Once this initial model run

has completed, the actual bootstrapping starts by sampling from the initial
data set to the requested number of samples.

However, the initial run often has been carried out already, and the
bootstrap method this seems to be repeated.

 

I am dealing with a rather time consuming model / data set. Therefore I was
wondering whether it is possible the re-use the results of a nonmem

model run and start the bootstrapping directly without repeating this
initial nonmem model run. I was not able to find any option to do so.
Perhaps there 

is way around?

 

Thanks,

 

Jos

 

Jos Lommerse 
Assoc. Prin. Scientist, Quant. Sciences
Clinical PK-PD
T: +31 412 661456
F: +31 412 662555
  jos.lomme...@merck.com 

MSD
Molenstraat 110, 5342 CC Oss
PO Box 20, 5340 BH Oss
The Netherlands 

 

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system.

RE: [NMusers] Bootstrap, re-using inital model run results

2013-02-14 Thread Anubha_Gupta


Dear Mats

My question is more related to boot strapping itself.

if data set and model I am working with takes long time to run, then during
bootstrap run I only run $EST and skip $COV step. We will get confidence
interval for parameter from bootstrap results.

What is your opinion on that?

Best regards

Anubha

..
Anubha Gupta, PhD
Associate Director,
Modeling and Simulation
Clinical Pharmacology
Scientific and Clinical Support CFU
European Knowledge Centre
Mosquito Way, Hatfield, Herts.
AL10 9SN
United Kingdom




  
  From:   "Mats Karlsson"  
  

  
  To: "'Lommerse, JPM \(Jos\)'" , 


  
  Date:   14/02/2013 08:50  
  

  
  Subject:RE: [NMusers] Bootstrap, re-using inital model run results
  

  
  Sent by:owner-nmus...@globomaxnm.com  
  

  





Dear Jos,

If you haven?t run the original model (indicated by absence of lst-file
with the same prefix) psn will run it before the bootstrap. If you have run
it, PsN will not rerun it. It will use the results in the corresponding lst
file. If you have run it and called it something else, you could use the
?-out=xxx.yyy? to point to the correct file if that does not follow naming
conventions. If you have  not run it and really don?t want to run it, you
could substitute xxx.yyy for some other output file with similar structure.

Best regards,
Mats

Mats Karlsson, PhD
Professor of Pharmacometrics

Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala

Phone: +46 18 4714105
Fax + 46 18 4714003

From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Lommerse, JPM (Jos)
Sent: 14 February 2013 08:29
To: nmusers@globomaxnm.com
Subject: [NMusers] Bootstrap, re-using inital model run results

Hi

I would like to ask to NONMEM community whether it is possible to re-use
the results of a nonmem model run when starting bootstrapping.
As I understand, a bootstrap run using PsN starts with a single calculation
of the model of interest and data set as is. Once this initial model run
has completed, the actual bootstrapping starts by sampling from the initial
data set to the requested number of samples.
However, the initial run often has been carried out already, and the
bootstrap method this seems to be repeated.

I am dealing with a rather time consuming model / data set. Therefore I was
wondering whether it is possible the re-use the results of a nonmem
model run and start the bootstrapping directly without repeating this
initial nonmem model run. I was not able to find any option to do so.
Perhaps there
is way around?

Thanks,

Jos

Jos Lommerse
Assoc. Prin. Scientist, Quant. Sciences
Clinical PK-PD
T: +31 412 661456
F: +31 412 662555
jos.lomme...@merck.com

MSD
Molenstraat 110, 5342 CC Oss
PO Box 20, 5340 BH Oss
The Netherlands



Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.





Eisai Limited
Registered in England No. 2242511
Registered Address: European Knowledge Centre, Mosquito Way, Hatfield, 
Hertfordshire, AL10 9SN
Please note our new telephone no. is +44 (0) 845 676 1400 and the fax is +44 
(0) 845 676 
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RE: [NMusers] Bootstrap, re-using inital model run results

2013-02-14 Thread Mats Karlsson

Hi Anuba,

 

I would agree with your suggestion. That is how I usually do it.

 

Best regards,

Mats

 

Mats Karlsson, PhD

Professor of Pharmacometrics

 

Dept of Pharmaceutical Biosciences

Faculty of Pharmacy

Uppsala University

Box 591

75124 Uppsala

 

Phone: +46 18 4714105

Fax + 46 18 4714003

 

From: anubha_gu...@eisai.net [mailto:anubha_gu...@eisai.net] 
Sent: 14 February 2013 10:07
To: Mats Karlsson
Cc: jos.lomme...@merck.com; nmusers@globomaxnm.com
Subject: RE: [NMusers] Bootstrap, re-using inital model run results

 

Dear Mats

My question is more related to boot strapping itself.

if data set and model I am working with takes long time to run, then during
bootstrap run I only run $EST and skip $COV step. We will get confidence
interval for parameter from bootstrap results. 

What is your opinion on that?

Best regards

Anubha

...
Anubha Gupta, PhD
Associate Director,
Modeling and Simulation 
Clinical Pharmacology
Scientific and Clinical Support CFU
European Knowledge Centre
Mosquito Way, Hatfield, Herts.
AL10 9SN
United Kingdom


Inactive hide details for "Mats Karlsson" ---14/02/2013 08:50:29---Dear
Jos,"Mats Karlsson" ---14/02/2013 08:50:29---Dear Jos,




From:


"Mats Karlsson" 




To:


"'Lommerse, JPM \(Jos\)'" , 




Date:


14/02/2013 08:50




Subject:


RE: [NMusers] Bootstrap, re-using inital model run results




Sent by:


owner-nmus...@globomaxnm.com



Eisai Limited
Registered in England No. 2242511
Registered Address: European Knowledge Centre, Mosquito Way, Hatfield,
Hertfordshire, AL10 9SN
Please note our new telephone no. is +44 (0) 845 676 1400 and the fax is +44
(0) 845 676 1401 

  _  




Dear Jos,
 
If you haven't run the original model (indicated by absence of lst-file with
the same prefix) psn will run it before the bootstrap. If you have run it,
PsN will not rerun it. It will use the results in the corresponding lst
file. If you have run it and called it something else, you could use the
"-out=xxx.yyy" to point to the correct file if that does not follow naming
conventions. If you have  not run it and really don't want to run it, you
could substitute xxx.yyy for some other output file with similar structure.
 
Best regards,
Mats
 
Mats Karlsson, PhD
Professor of Pharmacometrics
 
Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala
 
Phone: +46 18 4714105
Fax + 46 18 4714003
 
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] On
Behalf Of Lommerse, JPM (Jos)
Sent: 14 February 2013 08:29
To: nmusers@globomaxnm.com
Subject: [NMusers] Bootstrap, re-using inital model run results
 
Hi
 
I would like to ask to NONMEM community whether it is possible to re-use the
results of a nonmem model run when starting bootstrapping.
As I understand, a bootstrap run using PsN starts with a single calculation
of the model of interest and data set as is. Once this initial model run
has completed, the actual bootstrapping starts by sampling from the initial
data set to the requested number of samples.
However, the initial run often has been carried out already, and the
bootstrap method this seems to be repeated.
 
I am dealing with a rather time consuming model / data set. Therefore I was
wondering whether it is possible the re-use the results of a nonmem
model run and start the bootstrapping directly without repeating this
initial nonmem model run. I was not able to find any option to do so.
Perhaps there 
is way around?
 
Thanks,
 
Jos
 
Jos Lommerse 
Assoc. Prin. Scientist, Quant. Sciences
Clinical PK-PD
T: +31 412 661456
F: +31 412 662555
  jos.lomme...@merck.com 

MSD
Molenstraat 110, 5342 CC Oss
PO Box 20, 5340 BH Oss
The Netherlands 
  

Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system. 


__
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com
__ 


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If you are not the intended recipient you are notified that any disclosure,
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RE: [NMusers] Bootstrap, re-using inital model run results

2013-02-14 Thread pascal . girard

Dear Anuhbia,

Since bootstrap is performed to replace the estimation of precision that 
is performed in the $COV step, you definitively do not need the $COV 
option when you do a bootstrap. 

Then CI are obtained based on the quantiles of the bootstrap estimates.

Kind regards, 

Pascal Girard, PhD
pascal.gir...@merckgroup.com
Head of Modeling & Simulation - Oncology
Global Exploratory Medicine
Merck Serono S.A. · Geneva
Tel:  +41.22.414.3549
Cell: +41.79.508.7898




From:   
To: "Mats Karlsson" 
Cc: , 
Date:   14/02/2013 10:33
Subject:RE: [NMusers] Bootstrap, re-using inital model run results
Sent by:owner-nmus...@globomaxnm.com



Dear Mats

My question is more related to boot strapping itself.

if data set and model I am working with takes long time to run, then 
during bootstrap run I only run $EST and skip $COV step. We will get 
confidence interval for parameter from bootstrap results. 

What is your opinion on that?

Best regards

Anubha

...
Anubha Gupta, PhD
Associate Director,
Modeling and Simulation 
Clinical Pharmacology
Scientific and Clinical Support CFU
European Knowledge Centre
Mosquito Way, Hatfield, Herts.
AL10 9SN
United Kingdom


"Mats Karlsson" ---14/02/2013 08:50:29---Dear Jos,


From:

"Mats Karlsson" 

To:

"'Lommerse, JPM \(Jos\)'" , 


Date:

14/02/2013 08:50

Subject:

RE: [NMusers] Bootstrap, re-using inital model run results

Sent by:

owner-nmus...@globomaxnm.com


Eisai Limited
Registered in England No. 2242511
Registered Address: European Knowledge Centre, Mosquito Way, Hatfield, 
Hertfordshire, AL10 9SN
Please note our new telephone no. is +44 (0) 845 676 1400 and the fax is 
+44 (0) 845 676 1401 


Dear Jos,
 
If you haven’t run the original model (indicated by absence of lst-file 
with the same prefix) psn will run it before the bootstrap. If you have 
run it, PsN will not rerun it. It will use the results in the 
corresponding lst file. If you have run it and called it something else, 
you could use the “-out=xxx.yyy” to point to the correct file if that does 
not follow naming conventions. If you have  not run it and really don’t 
want to run it, you could substitute xxx.yyy for some other output file 
with similar structure.
 
Best regards,
Mats
 
Mats Karlsson, PhD
Professor of Pharmacometrics
 
Dept of Pharmaceutical Biosciences
Faculty of Pharmacy
Uppsala University
Box 591
75124 Uppsala
 
Phone: +46 18 4714105
Fax + 46 18 4714003
 
From: owner-nmus...@globomaxnm.com [mailto:owner-nmus...@globomaxnm.com] 
On Behalf Of Lommerse, JPM (Jos)
Sent: 14 February 2013 08:29
To: nmusers@globomaxnm.com
Subject: [NMusers] Bootstrap, re-using inital model run results
 
Hi
 
I would like to ask to NONMEM community whether it is possible to re-use 
the results of a nonmem model run when starting bootstrapping.
As I understand, a bootstrap run using PsN starts with a single 
calculation of the model of interest and data set as is. Once this initial 
model run
has completed, the actual bootstrapping starts by sampling from the 
initial data set to the requested number of samples.
However, the initial run often has been carried out already, and the 
bootstrap method this seems to be repeated.
 
I am dealing with a rather time consuming model / data set. Therefore I 
was wondering whether it is possible the re-use the results of a nonmem
model run and start the bootstrapping directly without repeating this 
initial nonmem model run. I was not able to find any option to do so. 
Perhaps there 
is way around?
 
Thanks,
 
Jos
 
Jos Lommerse 
Assoc. Prin. Scientist, Quant. Sciences
Clinical PK-PD
T: +31 412 661456
F: +31 412 662555
jos.lomme...@merck.com 

MSD
Molenstraat 110, 5342 CC Oss
PO Box 20, 5340 BH Oss
The Netherlands 
  
Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at 
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from 
your system. 

__
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com
__ 

THIS EMAIL AND ANY ATTACHED FILES ARE CONFIDENTIAL. 
If you are not the intended recipient you are notified that any 
disclosure, reproduction,copying, distribution, or action taken in 
reliance on the contents of this information is strictly prohibited. If 
you have received this transmission in error please notify

[NMusers] Dose-response-time modeling: PhD/Early Stage Research Studentship

2013-02-14 Thread Mats Jirstrand

PhD/early stage research studentship available in a Marie Curie 
EU-funded joint project by University of Warwick, AstraZeneca, 
Fraunhofer-Chalmers Research Centre for Industrial Mathematics, and 
Swedish University of Agricultural Sciences on Modelling Dose Response 
Time Outcome Relationships.


Application deadline: 22nd February 2013

Start date: 1st June 2013

Duration: Three years

The project addresses the development and improvement of methodologies 
for analyzing dose-response-time data when systemic (plasma) exposure is 
sparse or lacking. Extending and applying tools and techniques from 
systems and control theory and in particular nonlinear estimation such 
as Kalman filtering will be central to developing methodology for this 
situation. Dose-response-time data analysis (DRT) enables us to more 
efficiently (quantitatively) analyze and draw conclusions about the 
underlying rate processes where traditional single-point assessment or 
area under the response-time curve approach generally fail. Hopefully, 
this also allows a more robust design tool for future pharmacodynamic 
experiments in both animals and man. The candidate student should have a 
strong background (MSc or equivalent) in biological 
engineering/numerical techniques/computing science/chemical engineering, 
and life science courses. A track record in pharmacokinetics/dynamics 
would also be beneficial.



(Closing date: Feb 22, 2013)

For further details and online application see 
. 



Questions can be directed to Mats Jirstrand (ma...@fcc.chalmers.se) or 
Johan Gabrielsson (johan.gabriels...@slu.se).


--
___
Mats Jirstrand, PhD, Assoc Prof
Head of Department Systems and Data Analysis

Fraunhofer-Chalmers Research Centre
for Industrial Mathematics   Phone: +46-(0)31-7724250
Chalmers Science ParkFax:   +46-(0)31-7724260
SE-412 88 Göteborg   Email: ma...@fcc.chalmers.se
SWEDEN   Web:   www.fcc.chalmers.se/sys

[NMusers] Bootstrap, re-using inital model run results

RE: [NMusers] Bootstrap, re-using inital model run results

RE: [NMusers] Bootstrap, re-using inital model run results

RE: [NMusers] Bootstrap, re-using inital model run results

RE: [NMusers] Bootstrap, re-using inital model run results

[NMusers] Dose-response-time modeling: PhD/Early Stage Research Studentship

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