NONMEM FTP Repository
NONMEM Topic 21
Keywords: NONMEM, FTP, Internet, File Archive
Topic started by: Steven Shafer (steven.shafer@forsythe.stanford.edu)
- 7 October 94
To: NONMEM Users Group
Re: The NONMEM Repository
From: Steven L. Shafer, M.D.
Jaap Mandema, Ph.D.
We have now opened an FTP server here at Stanford to function as a repository
for files and information for the NONMEM community. We intend to build up the
content of the repository over the next year as we add NONMEM projects of
interest (e.g., PREDS, control streams, sample data sets, installation
techniques, etc). We encourage the NONMEM community to consider this
repository a shared resource.
For example, if you have PREDS that you have written and find useful, please
put them into the repository so we can all use them. We all know that that
installation of NONMEM can be very tricky. Many of us have written batch files
to automate the installation for our computing environment. If you could share
your installation batch files, that would help others who work in the same
environment install NONMEM. Another possibility is bench marking routines,
which you could upload to the repository so that interested individuals could
calibrate NONMEM execution speed on their computers against other machines.
To access the repository, please FTP to pkpd.palo-alto.med.va.gov. Sorry about
the long name, but it is US Government issue. That name is still propagating
around the domain name server network, and so you might get an .unknown host.
message. In that case, FTP to 198.31.34.225. Log in as .anonymous. and give
your e-mail address as the password. You will be greeted by a series of readme
files. If you are using a character-based FTP system, and aren.t sure about
FTP commands, try FTP HELP or FTP ? to see how to use FTP.
The repository is fairly spacious: over 1 GB of disk space. Thus, there is
lots of room for you to share your NONMEM tool box, data sets, etc with others.
Over the next few months we plan to add: 1) dial-up modem service, for those of
you for whom FTP is not really feasible, 2) a listserver service, so you can
get files from the repository using e-mail, and 3) full world-wide web
integration, so you can access the repository using Mosaic or another web
browser. These steps will take some time, so please be patient.
Also, we encourage you to also spend time browsing the repository installed and
maintained by David Bourne at OUHSC College of Pharmacy in Oklahoma City. You
can reach the NONMEM discussion topics set up at OUHSC at:
http://157.142.72.77/common/anonymous/nm/t_index.html
or by ftp or gopher to 157.142.72.77.
We have discussed with David linking these repositories via the WWW. As we
work to integrate NONMEM user support with the INTERNET, we will keep the
NMUSERS group posted on our progress.
We are just starting up this repository. Please access it, browse through the
readme files, and see if it makes sense. Do you feel welcome? Is it clear how
to find files? How to download files? How to set up your own directories and
upload files? Is our FTP site adequately responsive, or is it too slow?
We look forward to providing the NONMEM community with this new resource, and
hope it helps you with your modeling efforts.
Response from: lewis@c255.ucsf.EDU (L. Sheiner) - 11 Oct 94
I have put the following directories in the master directory NONMEM on
PKPD.ICON.PALO-ALTO.MED.VA.GOV where they can be accessed by anonymous
FTP:
PKPD.DIR: Various control file(s) that implement PK/PD modeling
(+/- tolerance).
Simultaneous: fit Y{PK,PD} = PKPD-Model(X|theta{PK,P{D}))
Sequential: 1. fit Y{PK} = PK(X|theta{PK}), then
2. fit Y{PD} = PD(X,theta{PK}|theta{PD}).
LOGIST.DIR: Control file(s) for rpt'd measures logistic regression -
g(p(y{ij}=1|X)) = f(X{ij},theta) + eta{i} + eps{ij},
where y{ij} = 0 (no event), or 1 (event) in indiv i at occas j.
Control files here implement
f(X,theta) = gamma.log(dose) - gamma.log(D50),
which yields p(y=1|Dose) = Sigmoid Emax model.
Response from: Steven Shafer (steven.shafer@forsythe.stanford.edu)
- 18 Dec 94
NMUSERS:
Several individuals have observed that the PKPD Repository was
unavailable last Wednesday and Thursday. It is now up and running again.
Because of the demand, I switched the system over to the Windows NT file
system. This will improved access time, provide more flexible security,
and offer greater reliability. Also, the system now gives UNIX style
listings rather than MS-DOS style listings. This will make it work better
with Web browsers and similar programs.
Even locally, I find that I often have to access the service
"pkpd.icon.palo-alto.med.va.gov" more than once to connect. This seems
to be a local internet problem, and not related to the PKPD server per
se. I'm working with our local internet provider to fix this. However,
as a reminder, if you have difficulty getting access using the name,
the IP address itself appears to be 100% reliable. The IP address is
198.31.34.225
Response from: Joachim Grevel (73532.1742@compuserve.com) - 24 Jan 95
I am lost in my efforts to "FTP to pkpd.icon.palo-alto.med.va.gov....or to
198.31.34.225" No matter what I try, what INTERNET Provider I use, I always get
"unknown host". Are you out there?
Has anyone experience with access from outside the Bay Area?
Response from: Joachim Grevel (73532.1742@compuserve.com) - 25 Jan 95
yesterday (01/24/94) I had tried again unsuccessfully to reach the NONMEM
Repository, and I posted a message on the NONMEM User Net.
Today (01/25/94) I could reach pkpd.icon.palo-alto.med.va.gov for the first time
with FTP through my CompuServe account.
The lesson: persistence works on the "information super highway"
Thanks to Steve Shafer!
Response from: Steven Shafer (steven.shafer@forsythe.stanford.edu)
- 26 Jan 95
Thanks for the notes. I'm been quite frustrated by the difficulty of
accessing the repository via "pkpd.icon.palo-alto.med.va.gov."
Even from my own desktop computer, which is separated from the repository by
about 5 feet of ethernet cable, I frequently get the "Unknown host" message!
However, I've been able to log in via 198.31.34.225 from around the United
States, and have heard from others around the world who have been successful
as well, both with the IP number and the machine address.
I'm starting to suspect that the problem is the name itself, both its
length (only 1 character less than the absolute limit on FTP servers) and
possibly the presence of the dash in palo-alto". Needless to say, my local
IRMS people, when I can reach them at all, are clueless on this one. I'm
trying to get an answer from our service provider, Barrnet. However, if I
can't resolve it here, I'll just pick up the entire repository and move it
to a computer at Stanford. Stanford has installed a new system to provide
internet host services (FTP, WWW, etc) to students and faculty for exactly
this sort of thing, so that should solve the access problems.
I complement you on your persistence. I hope it was worth the effort.
Response from: Steven Shafer (steven.shafer@forsythe.stanford.edu)
- 17 Apr 95
The NONMEM Repository / PKPD Server at the Palo Alto VA
has been upgraded:
1) The problems with "host not found" have been tracked down
and fixed. There should be no need to use the IP number
any more. The name remains the cumbersome:
pkpd.icon.palo-alto.med.va.gov
but that is beyond my control (US Gov't issue).
2) I've added a WWW front-end to the server, so you can reach
it via Mosaic/Netscape or any other Web browser. The
server doesn't do much more than drop you into FTP mode, but
it at least provides a starting point for more complete
integration with the WWW when we find the time.
Please let me know how this works. Many of you have sent me
messages on performance issues, and those have been very helpful
in tracking down the problems with the system. Also, please
contribute those models, programs, control streams, and sample
data sets that you think others might find helpful.
Response from: Steven Shafer (steven.shafer@forsythe.stanford.edu)
- 19 Apr 95
Some e-mail I have received suggests continued questions about
logging into the Repository. When using NETSCAPE/MOSAIC or another
WWW browser, the repository can be accessed with either of the
following URLS:
http://pkpd.icon.palo-alto.med.va.gov or
ftp://pkpd.icon.palo-alto.med.va.gov/public/
Attempting to access the repository using:
ftp://pkpd.icon.palo-alto.med.va.gov
does not work because it requires access to the root directory,
which is not accessible for security reasons.
End of Topic - 9 June 1995