Bioequivalence and Bioavailability Forum

intel07 ● 2009-12-04 02:10 (5486 d 10:51 ago) Posting: # 4426 Views: 17,904	Deconvolution using SAS or PCDCON [Software] Post reply
	Hello Everyone, I am trying to apply numerical deconvolution to PK data using SAS program codes or using an existing noncommercial software, e.g. PCDCON. Would someone be kind enough to send me a copy of the PCDCON software? I was not able to find/download a copy of PCDCON from the internet. Thank you very much for your help!

Helmut
★★★

Vienna, Austria,
2009-12-04 03:17
(5486 d 09:45 ago)

@ intel07
Posting: # 4427
Views: 15,387

Deconvolution using SAS or PCDCON

Post reply

Dear intel07 (WT),

I suggested you already ivivc for R at David’s PKPD-list; see also this thread.
I tried myself a couple of times in the last years to find a source of PCDCON on the net, but to no avail. :-(

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

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Helmut
★★★

Vienna, Austria,
2009-12-04 15:03
(5485 d 21:58 ago)

@ intel07
Posting: # 4432
Views: 16,073

PCDCON, PBPK (Java)

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Dear all!

I received a copy of PCDCON 1.1 (William R. Gillespie, 1992) from Yung-jin Lee (THX!). I checked it on Windows XP Pro SP3, it works. Quoting Pcdcon.pdf:

Installation
PCDCON requires an IBM-PC-compatible computer with ≥640K of RAM and a monitor with CGA, EGA, VGA or Hercules graphics capabilities. The current version of PCDCON is not copy-protected. There are no restrictions on the distribution of the software. In fact, distribution to colleagues is encouraged. The author only requests appropriate citation in publications presenting results obtained with PCDCON.
Installation of PCDCON is accomplished by simply copying the file PCDCON.EXE from the distribution diskette to any desired directory on a hard disk or a diskette. Some files containing example data are also included on the distribution diskette and may be copied if desired.

Files are virus-free (Symantec Antivirus 9.0.0.338, Engine 91.2.1.10, Definition files 03.12.2009 rev.4). The software may be downloaded as a zip-file (MD5-checksum 442c7adc789437d1254e50ddc857cbba).
Note that PCDCON is not constrained so the input function can go un-physiologically negative.

Another free software for deconvolution is PBPK from PKQuest (zip-file). You will need a current Java Runtime Environment (JRE) on your machine (download).

Edit: David Bourne brought an interesting article by David Levitt (author of PKQuest) to my attention:

DG Levitt
The use of a physiologically based pharmacokinetic model to evaluate deconvolution measurements of systemic absorption
BMC Clinical Pharmacology 3:1 (2003)
DOI: 10.1186/1472-6904-3-1
free online resource

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

yjlee168
★★★

Kaohsiung, Taiwan,
2012-07-30 02:03
(4517 d 11:58 ago)

@ Helmut
Posting: # 8990
Views: 13,302

PCDCON is for 32-bit Win OS only!

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Dear all,

Recently I have been asked from a user of pcdcon about how to run pcdcon.exe, although I am not the original author of PCDCON (Dr. William R. Gillespie, Ph.D.). Then I accidentally find that pcdcon.exe is ONLY running under a 32-bit Win OS. I do not notice this before since I use a 32-bit Win OS for a long time until recently. Due to more and more PCs are 64-bit machines running with 64-bit Vista/Win7/Win8 (later) Win OS when they ship from PC manufactures, I like to explain how to run pcdcon.exe it if you have a 64-bit WIN OS here.

* Software and documents (ore ref.) you need

you can download PCDCON.ZIP from this Forum (read this thread carefully); Helmut post a very detailed and great comment for it.
Unzip the zip file to any directory or folder you like;
The zip file downloaded from this Forum contains complete files as original author provided many years ago, even including all Fortran source codes (how nice!)
If you need more details about PCDOCN, please read pcdcon.txt and *.pdf for examples bundled with PCDCON.ZIP. These are all original documents.
Just run pcdcon.exe under a dos-command window or the file manager of WINDOWS. No installation is required. Then you should place your data in the same directory/folder as pcdcon.exe for easy operation. To edit or view data file (ascii text file), any text editor will do, such as notepad.exe or wordpad.exe under Windows. Since pcdcon.exe is a dos-command line program, no menu or window-type GUI is provided at all.

* Hardware/Operation System (OS) required

as long as with a 32-bit Win OS.

* How do I know my Win OS is a 32-bit one? Very easy. Just run pcdcon.exe directly. If you get the error message such as '...this program is not compatible with Windows version... You will need a x86 (32 bits) or x64 (64 bits) program.. blablabla...' (I translated this from my Chinese Win OS; it should be something like that in English), then your Win OS is a 64-bit one. No doubt about it.

* How can I run pcdcon.exe with 64-bit Win OS or iMac (iOS) or Linux PC (such as Ubuntu)?

The most easy way is to borrow a 32-bit Win OS PC from a friend, if you just want to run pcdcon.exe for couple time only. If it can be done like that, ignore the following text.
If you will run pcdcon.exe for a long time, you may consider how to run it under a 64-bit Win OS PC. The most smart way is to install a virtual machine under a 64-bit Win OS. I will not recommend that you should re-install a 32-bit Win OS. After all, the 64-bit Win OS is much better than a 32-bit.
I prefer Oracle VM VirtualBox (VB) for virtual machine. It is totally freeware and very user-friendly. iOS/Linux PC (Ubuntu) machine is also able to install. Browse the website to see how to install VirtualBox and use it. Then You need to install a 32-bit WinXP/Vista/Win7 OS on VB. So you can run any 32-bit PC program from it.Note that you will need to know how to assess PC files or programs from VB. You can find it from VB user's guide. Read p.57-58 (Guest Additions for Windows). If you still don't know how to setup VB after reading VB user's guide, you can find great videos from Youtube. Here is a great one. Remember to expand your monitor as full screen for better view/effect. This one is English version. You may find a Spanish or quiet-mode (just sit and watch) version, if you like. YouTube searching keyword: 'virtualbox guest addition'.

Please post your question here if there is any question about how to run PCDCON and VB. Thanks and have a nice day.

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

sally ☆ Egypt, 2012-07-30 02:39 (4517 d 11:22 ago) @ yjlee168 Posting: # 8991 Views: 13,097	PCDCON is for 32-bit Win OS only! Post reply
	Dear Dr. Yung-jin: Thank you sooooo much for your cooperation Edit: Full quote removed. Please delete anything from the text of the original poster which is not necessary in understanding your answer; see also this post! [Helmut]

yjlee168 ★★★ Kaohsiung, Taiwan, 2012-07-30 02:51 (4517 d 11:10 ago) @ sally Posting: # 8992 Views: 13,199	PCDCON is for 32-bit Win OS only! Post reply
	Dear Sally, You are welcome. But you may edit your post again by cutting 'full quote.' — All the best, -- Yung-jin Lee bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee Kaohsiung, Taiwan https://www.pkpd168.com/bear Download link (updated) -> here

Helmut
★★★

Vienna, Austria,
2012-07-30 16:12
(4516 d 21:49 ago)

@ yjlee168
Posting: # 8995
Views: 13,159

Compile sources to get 32(64)bit exe?

Post reply

Dear Yung-jin & Sally,

PCDCON is actually 16bit code.

An alternatice would be to compile the FORTRAN77-sources with GNU Fortran (which supports legacy F77 code) in order to get a native 32bit (or even 64bit) executable.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

yjlee168
★★★

Kaohsiung, Taiwan,
2012-07-31 02:53
(4516 d 11:08 ago)

@ Helmut
Posting: # 8998
Views: 13,126

Compile sources to get 32(64)bit exe?

Post reply

Dear Helmut,

Great idea. Unfortunately, the source codes included in original PCDCON.zip are not as complete as we expect at all. Dr. Gillespie said [quoted from PCDCON.TXT]'...PCDCON, an interactive deconvolution program for PC-compatibles, as well as a few other convolution and deconvolution programs...' That means only some major Fortran subroutines were included, I guess. No way to re-compile PCDCON with g77 or gfortran.

❝ An alternatice would be to compile the FORTRAN77-sources with GNU Fortran (which supports legacy F77 code) in order to get a native 32bit (or even 64bit) executable.

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

ElMaestro
★★★

Denmark,
2012-07-31 12:24
(4516 d 01:37 ago)

@ Helmut
Posting: # 8999
Views: 13,052

Compile sources to get 32(64)bit exe?

Post reply

Hi HS,

❝ An alternatice would be to compile the FORTRAN77-sources with GNU Fortran (which supports legacy F77 code) in order to get a native 32bit (or even 64bit) executable.

How about installing it on a single appropriate machine which is connected 24/7 to the www and setting up an ASP interface etc with three basic functions:

Receipt of dataset from user (possibly also with run instructions)
Shell-execution of the program on the local machine
Shipment of result to user via email.

– this is pretty much like the NIH's sequence alignment tools worked for years.

—
Pass or fail!
ElMaestro

yjlee168
★★★

Kaohsiung, Taiwan,
2012-07-31 23:13
(4515 d 14:48 ago)

(edited on 2012-08-01 00:18)
@ ElMaestro
Posting: # 9009
Views: 13,138

Porting PCDCON to R?

Post reply

Dear ElMaestro,

Another great idea. However, PCDCON was designed as a kind of interactive program. Unless we know what choice is for each step from user after dataset is uploaded, shell-execution of the program on local machine seems impossible to implement (your Step 2).

How about this way: Porting PCDCON to R. Since PCDCON has included major FORTRAN subroutines (codes), it seems possible to convert these FORTRAN subroutines into DLL as one of R libraries (packages). Then user can easily call/assess these PCDCON functions from R script. However, I wonder we can do that, unless we can get permission from Dr. Gillespie first. Bad idea, uh? Never mind.
ref.:

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

sandeepdahiya
☆

India,
2013-07-02 20:13
(4179 d 17:48 ago)

@ yjlee168
Posting: # 10915
Views: 11,722

PCDCON is for 32-bit Win OS only!

Post reply

Dear All,

I don't know whether the question has been solved by now?
Some users may have moved to other programs, some may have installed 'Virtual OS'...

I found this solution, by which one can run 16x bit program on 64x bit Win 7 or Win 8.

DOSBox – is a free free opensource DOS & X86 Emulator for Windows & Linux.

The instructions to use can be found here –
http://www.windowsreference.com/free-utilities/dosbox-free-opensource-dos-x86-emulator-for-windows-linux/

I tried it and PCDCON is working in my Win 7 x64 system.

As this is my first reply on forum, excuse me if i have missed any guideline for posting.

Regards,
Sandeep Dahiya.

yjlee168
★★★

Kaohsiung, Taiwan,
2013-07-03 04:45
(4179 d 09:17 ago)

@ sandeepdahiya
Posting: # 10916
Views: 11,712

PCDCON is for 32-bit Win OS only!

Post reply

Dear Sandeep,

Glad to know one more options. Looks like DOSBox requires less resources (1.2 MB?) and much easier to install/use. PCDCON is a 16-bit application as Helmut said. Can you open .eps (the format of PCDCON plot files) from DOSBox? or you have to exit first and return to Win7 to open .eps file?

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

sandeepdahiya ☆ India, 2013-07-03 15:46 (4178 d 22:15 ago) @ yjlee168 Posting: # 10928 Views: 11,519	PCDCON is for 32-bit Win OS only! Post reply
	Dear Yung-jin, I would like to thank you and Helmut for providing the program here. i have not tried opening the .eps plot file via DOSBox. but as far as i understand, .eps should open normally in windows (both x86 and x64). and we can use both DOSBox and 'Native Windows Programs' at same time. DOSBox just provides an environment in which x16 programs can be run. Regards, Sandeep.

intel07 ● 2009-12-04 19:12 (5485 d 17:50 ago) @ intel07 Posting: # 4433 Views: 15,063	Deconvolution using SAS or PCDCON Post reply
	Thank you for the prompt reply and for the alternative resources! I am glad that PCDCON is "live" again on the internet.

Deconvolution using SAS or PCDCON [Software]

Deconvolution using SAS or PCDCON

PCDCON, PBPK (Java)

PCDCON is for 32-bit Win OS only!

PCDCON is for 32-bit Win OS only!

PCDCON is for 32-bit Win OS only!

Compile sources to get 32(64)bit exe?

Compile sources to get 32(64)bit exe?

Compile sources to get 32(64)bit exe?

Porting PCDCON to R?

PCDCON is for 32-bit Win OS only!

PCDCON is for 32-bit Win OS only!

PCDCON is for 32-bit Win OS only!

Deconvolution using SAS or PCDCON