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*************************************************************************************TALK
ABOUT PRESIDENT  Geroge W. Bush and John F Kerry **YOUR  POLITICAL
CHAT  LINE**FLOW JO MARKETING.*******MARIO ROEDERER
mac vs. pc
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From: Mario Roederer <roede...@drmr.com>
Date: Wed Aug 25 2004 - 15:10:25 EST
I have only one comment to make on this debate:
George W. Bush ("nuculer") uses a PC.
John F. Kerry uses a Mac (<http://www.macminute.com/2004/07/14/
kerry>).
Hmm.
mr
Received on Thu Aug 26 13:18:00 2004
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**************************************************************************************COMMERCIAL
MARKETING THROUGH LIST BLATENT      VERITY HOUSE SOFTWARE
Analysis Software
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From: VSH - Tech Support <t...@vsh.com>
Date: Wed Jun 30 2004 - 12:08:14 EST
David
At the risk of sounding commercial, WinList can do what you want.  I
have
attached a few pictures showing the WinList Region Array feature.
With this
you can tell the program exactly how you want the regions created and
how
many.  If you would like to try it for yourself you can download a
trial
version from our web site www.vsh.com.
Please let me know if you have any questions.
Best regards
Don
Donald J. Herbert
Technical Support Manager
Verity Software House, Inc.
PO Box 247
45A Augusta Road
Topsham, ME, USA  04086
Phone: (207) 729-6767 ext.190
Fax:   (207) 729-5443
email:  t...@vsh.com
web: www.vsh.com
Verity Software House Has a Connected Search Engine attached selling
all software.

WHY DOES VERITY REQUEST ARTICLES TO BE DELETED AFTER READING?

WHY MAIL LIST IS DOWN THESE LINK ARE NOT ACTIVE

**************************************************************************************
Purdue Cytometry Mailing List: Re: DNA analysis software
... J. Herbert > Technical Support Manager > Verity Software
House ...
sender immediately by return e-mail, delete this e-mail and destroy
any copies. Any ...
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26 May 07
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¬-----
Purdue Cytometry Mailing List: DNA analysis software
... a conversion at no charge. I invite you to contact Verity
Software
House directly with any specific questions or issues. Best
regards ...
issues. Best regards, Don Donald J. Herbert Technical Support Manager
Verity Software House ...
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Purdue Cytometry Mailing List: Re: DNA analysis software
... J. Herbert > Technical Support Manager > Verity Software
House ...
sender immediately by return e-mail, delete this e-mail and destroy
any copies. Any ...
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Purdue Cytometry Mailing List: RE: DNA analysis software
... Purdue Cytometry Mailing List: RE: DNA analysis software ... J.
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... Purdue Cytometry Mailing List: RE: DNA analysis software ... J.
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Purdue Cytometry Mailing List: RE: FL2H in PI cell cycle analysis
... From: Verity Software House <ver...@vsh.com> Date: Fri Sep 07
2007
- 17:30:59 EDT ... Verity Software House ...
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ANTI Commercial posting **NOTICE HOW THEY ADD A SMILEY
FACE**********FCS PRESS RAY HICKS
**************************************************************************************
anti) Commercial Posting:)
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From: Ray Hicks <rh...@cam.ac.uk>
Date: Wed Oct 13 2004 - 08:43:13 EST
Just a quick nopte to let people know that FCSPress is now shareware
(no time restrictions or feature reductions for free use, though if
you feel like like paying for it you can using paypal). It also now
works with Diva export files and runs ok under classic on OS 10.2 and
10.3.  I've discontinued FCS Assistant, which has fallen behind
FCSPress remarkably, and which failed to run as shareware on some
systems (it insisted you buy it or refused to run - FCSPress doesn't
even have a nag screen now - pesky things).
FCSPress is available from www.fcspress.com
Enjoy!
Ray
Received on Wed Oct 13 14:38:00 2004
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Mr. Apple WEB IS Mario OWNER OF FLOW JO **MORE MARKETING
**************************************************************************************
Re: mr on Apple web site
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From: Robin Barclay <Robin.Barc...@ed.ac.uk>
Date: Wed Aug 25 2004 - 04:17:52 EST
Well .... some of us PC afficianados hate Macs just as much -
personally I
have hated them since they first made it difficult to access their
DOS
and
write programs in any language (especially for accessing/controlling
lab
apparatus) - back in the '70's when there were several different
options -
not just PC's.  I am glad that the "PC" became a standard (there were
too
many diferent systems) and that IBM did not hang on to it the way
Apple kept
the Mac in house (you get more for your money with a PC because many
different people make them).  You don't often get PC people knocking
Macs
the way that the Mac people knock PCs - there seems to be a lot of
Microsoft
paranoia.  In my opinion PCs are much more common and versatile in
labs than
Macs - especially outside the USA - and will eventually become the
standard
for interfacing with lab equipment..... and they can "look cool" if
you shop
around for the right case if that's important to you.
Robin Barclay
Beverly Barton **STEERING COMMITY FOR* SCIENCE ADVISORY BOARD*****
Kanecki Associates Inc Discussion of FCS QUICK FACS 11 DELETED OFF THE
SITE!
MORE FLOW JO
**************************************************************************************
----- Original Message -----
From: "Beverly Barton" <barto...@UMDNJ.EDU>
To: cyto-inbox
Sent: Monday, August 23, 2004 10:09 PM
Subject: Re: mr on Apple web site

Received on Wed Aug 25 13:58:00 2004
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***THE MENTION OF BD CYTOMETERS AND MORE MARKETING FOR FLOW JO **
MARIO

Randy T. Fischer**********
NIH/NIAMS

Mr. APPLE WEB SITE FLOW JO
**************************************************************************************
RE: mr on Apple web site
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[ Maybe in
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From: Fischer, Randy (NIH/NIAMS) <fisch...@mail.nih.gov>
Date: Mon Aug 23 2004 - 16:18:55 EST
Paul,
I know that for a long time, anyone who used a BD flow cytometer had
***************
little
choice but to use a MAC-data acquisition required it.  And, one of
the
best
third party software packages was FlowJo which only ran on a MAC.
*******************
Mario,
being a FlowJock, naturally was heavily exposed to this atmosphere.
However, most of our other laboratory instrumentation appears to run
on the
IBM clone type of PC-ELISA reader, luminometer, ELISpot reader, and
AFFYMETRIX machine to name the first ones that come to mind.  Of
course,
because Flow is such a key component and FlowJo works so well, we
have
MACs
(and associated cinema displays) at all of our desks.  So, Mario is
probably
pretty close as I guess we now run about 50% MAC, and for most things
they
do run better than our PCs for similar applications, but mostly the
two
platforms tend to be used for very disparate applications and we need
both.
Wish more science companies would move to MAC, but as Microsoft
probably
owns a minority share in most companies, that will not likely happen
in our
lifetimes.
Haven't read the article yet, but hopefully Mario remembered to cite
you for
all the work on the Flow website/mailing list.
Randy T. Fischer
NIH/NIAMS
Building 10, Room 6D50
9000 Rockville Pike
Bethesda, MD 20892
(301) 594-3537
fisch...@mail.nih.gov

Received on Tue Aug 24 16:18:00 2004
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PRISIDENT OF ISAC AND HEAD OF PURDUE CYTOMETRY DEPT J PAUL ROBINSON
PROVIDES MANY GRANTS TO TREESTAR. GRANTS INFORMATION WILL BE PROVIDED
AT END…
****READ DO NOT WET YOUR POCKET PROTECTORS***ADDED LINKS TO WEBSITES
FOR FLOW JO

J.Paul Robinson, PhD                PH:(765)4940757

Received on Tue Aug 24 16:18:00 2004
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***************************************************************************-
******************************************
I know that for a long time, anyone who used a BD flow cytometer had
little
choice but to use a MAC-data acquisition required it.  And, one of
the
best
third party software packages was FlowJo which only ran on a MAC.
Mario,
being a FlowJock, naturally was heavily exposed to this atmosphere
***************************************************************************-
***************************************
For all of the mr groupies out there in cytometry cyberspace. Don't
wet

***************************************************************************-
********************************************

***************************************************************************-
**********************************************
CYTOMETRY SOFTWARE***PURDUE**Links to flow cytometry sites in the USA
and Canada (home of Mario Roederer and Steve Perfetto) home of J.
Paul
Robinson and ...
Perfetto, Steve (NIH/VRC) <perfe...@mail.nih.gov>
***************************************************************************¬*
GRANTS TROUGH *****PURDUE AND THE GOV. NIH FOR FLOW JO By J.Paul
Robinson
PRESIDENT OF ISAC 2007 -2008 AND BOARD MEMBER FOR A LONG TIME********
The Daily Dongle: - 2 visits - Nov 25
Rant about FlowJo's goings-on. ... NIH Funding. Another thread from
Purdue worth posting: .... I saw this question on Purdue mailing list
earlier today. ...
flowjo.typepad.com/the_daily_dongle/2007/06/index.html - 33k - Cached
- Similar pages - Note this
The Daily Dongle: Current Affairs
Rant about FlowJo's goings-on. ... NIH Funding. Another thread from
Purdue worth posting:. We are calling upon you again during this
Independence Day ...
flowjo.typepad.com/the_daily_dongle/current_affairs/index.html - 27k
-
Cached - Similar pages - Note this
[ More results from flowjo.typepad.com ]
This page under construction
http://www.cyto.purdue.edu/hmarchiv/cytomail.htm. Flow cytometry
analysis software: ... http://www.niaid.nih.gov/reposit/tetramer/index.html.
Ebioscience ...
www.immunology.utoronto.ca/research/resources/msb/fc.htm - 27k -
Cached - Similar pages - Note this
The Daily Dongle: - 2 visits - Nov 25Rant about FlowJo's goings-
on. ... -the impact of cuts to grants already funded .... I saw this
question on Purdue mailing list earlier today. Since FlowJo ...
flowjo.typepad.com/the_daily_dongle/2007/06/index.html - 33k - Cached
- Similar pages - Note this
The Daily Dongle: Current Affairs - 12:10amRant about FlowJo's
goings-
on. ... For those of you not on Purdue, Joao Loureiro from Portugal
wrote: ... -the impact of cuts to grants already funded ...
flowjo.typepad.com/the_daily_dongle/current_affairs/index.html - 27k
-
Cached - Similar pages - Note this
Purdue Cytometry Mailing List: By Date - Nov 25Re: Physical
exhaustion
and immune system FlowJo Technical Support - Maciej Simm (Wed Mar 14
2007 - 17:41:46 ..... Travel grants for young investigators, ...
www.cyto.purdue.edu/hmarchiv/Current/thread.htm - 288k - Cached -
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Purdue Cytometry Mailing List: By Date - 2 visits - Nov 25Re: Using
DIVA Exp Files in Flojo FlowJo Technical Support - Maciej Simm ......
Travel grants for young investigators, ImmunoRio2007
gharago...@sums.ac.ir ...
www.cyto.purdue.edu/hmarchiv/current/index.htm - 318k - Cached -
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[ More results from www.cyto.purdue.edu ]
The Whitaker Foundation 1996 Annual Report - Grants ApprovedRESEARCH
GRANTS Auburn University Thomas S. Denney, Jr., .... State
University)
Becky Jo Ficek Rice University (B.S. Purdue University) Anne Marie
Findlay ...
www.bmes.org/WhitakerArchives/96_annual_report/grantsap.html - 33k -
Cached - Similar pages - Note this
Vision now reality in Purdue's Discovery ParkThe park's Birck Center
has awarded $2.4 million in start-up grants for nine of those new
faculty .... V. Jo Davisson, (7865) 494-5238, davis...@purdue.edu ...
www.purdue.edu/UNS/html3month/2004/040919.Rutledge.dispark.html - 28k
- Cached - Similar pages - Note this
Testimony of JO ANNE GOODNIGHTThe development of the miniaturized
flow
probe marks the first time that anyone has ... Funding provided by an
STTR Phase I grant funding resulted in the ...
www.hhs.gov/asl/testify/t010621.html - 26k - Cached - Similar pages -
Note this
This page under constructionFlow cytometry users: useful sites.
Scripps Research Institute Flow Cytometry Core Facility http://facs.scripps.edu/.
Purdue University Cytometry ...
www.immunology.utoronto.ca/research/resources/msb/fc.htm - 27k -
Cached - Similar pages - Note this
FACS Flow Cytometry FacilityUse of stand-alone workstation with
CellQuest and FlowJo software for data analysis ... Flow cytometry
users: useful sites http://facs.scripps.edu/. Purdue ...
www.immunology.utoronto.ca/CellSorter.htm - 23k - Cached - Similar
pages - Note this
ISAC Homepage - ISAC E-News -- June, 2007 - 15 visits - Dec 9
Best wishes. J. Paul Robinson, President ..... Adam Treister
introduced possibilities of integrating these with FlowJo. ...
www.isac-net.org/content/view/593/119/ - 53k - Cached - Similar pages
THE PAGE ABOVE IS NOT ACTIVE DUE TO INVESTIGATION OF PURDUE CYTOMETRY
MAIL LIST (LINK)
**********************************************************************************************************

NON READABLE FCS 3 FILES COULTER FC 500 Flow Jo Discussion on Software
ERRORS and QUOTING FROM PAUL J ROBINSON HE DOES NOT KNOW IF THEY ARE
GOING TO FIX THE PROBLEM OVER THE MAIL LIST>>  FLOW JO DISCUSSES
****NEW BUILD OF SOFTWARE FOR CYTOMETRS
DOES COULTER KNOW? THIS IS COULTERS SOFTWARE USED IN THE FC 500
CYTOMETER?
************************************************************************************

RE: Nonreadable FCS 3 files from Coulter FC 500 cytometer
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From: J. Paul Robinson <j...@flowcyt.cyto.purdue.edu>
Date: Fri Jun 04 2004 - 21:02:48 EST
We notified Coulter of the error in their software a
long time ago. I dont know if htey are going to fix it.
regards
paul robinson
On 3 Jun 2004 at 16:55, maciej simm wrote:

- Hide quoted text -

J.Paul Robinson, PhD             PH:(765)4940757 ***********
Professor of Immunopharmacology
Professor of Biomedical Engineering
Purdue University          FAX:(765)4940517
EMAIL:j...@flowcyt.cyto.purdue.edu
WEB: http://www.cyto.purdue.edu
Have you seen our new HCS webpage? ***************
http://www.cyto.purdue.edu/hcs
Received on Mon Jun 7 14:18:00 2004
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                        FLOW JO AND MARKET SHARE DISCUSSION VS BD
MARKET SHARE
*****************************MARKET SHARE DISCUSSION DOES BD KNOW?
***********
************************************************************************************************************************
Of course, what started this thread was the assertion in the piece
about
Mario on Apple's web site that there were 15,000 to 20,000 Mac-based
flow
cytometers out there. The best estimates I had from industry people
in
early 2003 when I was finishing up the 4th Edition of PFC was that
the
total number of systems from all manufacturers in use was under
20,000. If
that's correct, BD would need a 75% market share to account for the
low end
estimate of 15,000 Mac-based machines. I'd be interested to know
where
the
15,000 to 20,000 figure came from.
***************************************************************************¬***********************************************
Re: mr on Apple web site
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From: Howard Shapiro <h...@shapirolab.com>
Date: Wed Aug 25 2004 - 18:15:38 EST
Robin Barclay wrote:

I can't pass up the opportunity to get into the PC/Mac battle - I
hate
them
both, but there aren't really alternatives (yes, I know, there's
Linux, but
it's probably even harder to hook up a Linux system to hardware than
it is
to hook a Mac up to hardware).
Of course, what started this thread was the assertion in the piece
about
Mario on Apple's web site that there were 15,000 to 20,000 Mac-based
flow
cytometers out there. The best estimates I had from industry people
in
early 2003 when I was finishing up the 4th Edition of PFC was that
the
total number of systems from all manufacturers in use was under
20,000. If
that's correct, BD would need a 75% market share to account for the
low end
estimate of 15,000 Mac-based machines. I'd be interested to know
where
the
15,000 to 20,000 figure came from.
The old (68000 series and possibly early PowerPC) Macs were
difficult,
but
not impossible to connect to hardware; it was easier to work with the
PC's
ISA bus, which, while slow, was perfectly adequate to do most flow
cytometric data acquisition and analysis. There were decent versions
of
Forth, which was one of the first and best languages designed for
controlling hardware from mini- and microcomputers, for both PC (DOS)
and
the Mac (Forth was the first Mac programming language made
commercially
available, at a time when the only other option was buying the very
expensive Lisa from Apple on which to develop Mac software). I found
MacForth easier to program with than the Windows Forths (or other
Windows
languages, e.g., Delphi), but my old Macs used to crash all the time.
So what makes me unhappy with both Windows [and Windows machines] and
the
Mac in their current incarnations? It is now significantly harder for
mere
mortals to write software to get hardware to communicate with either
PCs or
Macs; the gain in complexity associated with the PCI bus, USB/USB2,
FireWire(IEEE 1394), etc. is greater than the gain in speed and
convenience. Also, in making the operating systems more stable (and
Win XP,
despite its security issues, is almost as stable as Mac's Unix-based
OS X),
both Microsoft and Apple elected to eliminate the ability of their
computer
hardware to respond rapidly to interrupts (latencies are now in the
tens of
thousands of instruction cycles), meaning that any really fast
hardware
attachment for either a PC or a Mac now needs to have a DSP in it,
whereas
if the fast interrupt response had been preserved, the hardware
attachments
could have been made much simpler and cheaper. Linux also takes fast
interrupt response off the table, so it doesn't represent a viable
alternative. If you go to Apple's web site and look at what data
acquisition hardware is available for Macs, particularly for Macs
running
OS X, there isn't much, and many of the companies that supported the
Mac in
that area have dropped Mac support for their newer products. That is
undoubtedly one big reason why BD's newer digital pulse processing
cytometers are running on the PC platform.
That doesn't stop anybody from analyzing FCS files on Macs. FlowJo is
well-conceived flow cytometry software; one reason it is as good as
it
is
is that it was written by people who do a lot of flow cytometry, and
cutting edge flow cytometry at that. But there are other people who
do
a
lot of good flow cytometry who have written good software, for PCs as
well
as for Macs.
For the record, I have a G4 PowerBook, which I use mostly for the
iLife
applications, which are slick. It doesn't crash more than once every
couple
of months, but the same is true of my Windows 2000 and XP systems. OS
X can
be as infuriating as Windows when one or another aspect of it goes
counter
to your intuition or to what you have gotten used to. Macs, while
somewhat
more expensive, are much better made than many PCs, and they are
certainly
aesthetically pleasing. If there were a reasonable alternative to
Microsoft's Office applications for the Mac, I might consider
switching.
The 12.1" PowerBook is a nice portable, but it's over a pound heavier
than
the Fujitsu laptop I now use, which has pretty much the same speed,
memory,
and drive capabilities (OK, not DVD-R, but I don't burn a lot of
DVDs).
However, I really wish Apple had stuck with the plan they had a few
years
back of writing a Mac operating system for Intel hardware. I think
that
died when Microsoft bailed Apple out with a few hundred mil. If it
were
possible to run OS X and XP mano a mano on the same hardware, there'd
be a
more rational basis for comparison. But, as may be the case for the
November election, minds, once made up, are not easily changed.
-Howard
Received on Thu Aug 26 16:38:00 2004
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HOW TO DEVELOP SOFTWARE? YOU CAN USE EXISTING COMMERCIAL PROGRAMS?
RESPONSE WITH FLOW JO ***ADAM TRIESTER    TREESTAR/FLOW JO
************************************************************************************************************************
You can use existing commercial programs (Aabel & JMP are nice
Mac 3D applications, and I'm sure there are others), or write it
yourself in OpenGL.  I think OpenGL would be a better choice than C+
+.
OpenGL is a higher level graphics language, and knows how to access
the
specialized accelerators in the graphics cards, which are actually
faster for this stuff than the G5.  That's how the dungeon games do
the
3D shading and rendering.
I'll be happy to donate a considerable amount of code that I've done
in
this effort (most was taken from an old freeware program called
Rotator, which I no longer could find with Google, but I have
somewhere
in my archives), but we decided this was pretty much a dead end.
Rotator was in C, and quite unreadable. For the investment this task
would take, I think it'd be better to start over in OpenGL.  It's
cross-platform too, which is important, as you'll find you want to
port
it to a Cray.
I'd still think you want to use FlowJo to read the DiVa files,
compensate them, transform them, gate them, and then export desired
subpopulations to the 3D viewer.   If it were any other instrument,
you
could probably read the files yourself, with R or our free Java
libraries, but the DiVa files  are a unique format, and almost always
require compensation and transformation to a lin/log scale, so
there's
a lot of work before you even get to viewing them.
***************************************************************************-
***********************************************
Re: 3D Graphics for flow data display
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From: Adam Treister <a...@treestar.com>
Date: Sun Jan 04 2004 - 13:48:24 EST
David,
We've tried on a couple of occasions to add a "spatial" 3D module to
FlowJo, and it has never turned out well enough to make it into a
release.  We've found that using time as the third dimension, as in
our
"data movies," or using several 2D graphs, as in our "multi-graph
overlay" to be more practical solutions.
If you want smoothing or density coloring, that requires binning the
data. Even working at low resolution, you're looking at 256 times as
much time and memory to take the plot into an additional dimension.
You might get a tenfold performance increase with the G5 (which I
think
is quite optimistic, because the G5 adds fast floating point
processing, but binning is a integer operation), but even with that
that, adjusting a gate goes from taking perhaps a second to almost a
half minute.  That would make using FlowJo feel like using CellQuest
(just kidding ;)   At the full resolution of DiVa files, you're
looking
at another thousand fold increase over the 2D version, or a billion
times (1000 ^ 3)  as long as we take to do it now.   So, as best I
can
figure it, we can only support 3D at the cost of losing interactivity
with the data (ie, we can make the views, but changing gates or
parameters won't immediately change the 3D visualization).
It would be tough to have contours in 3D as each layer would obscure
the ones inside it.  Contours would have to have varying opacity,
which
not only increases the computational time and complexity, but would
make it hard to differentiate populations.  And the user interface
for
gating in space would be a real challenge.  You could chop thru space
with planes, but that's 1D gating, which doesn't give you more
capability to define populations than you have now.  So we'd have to
invent polyhedral gating.
If all you want to do is look at already-gated populations in 3D,
there
are options that exist.  Expo32 has this feature, if you can figure
out
how to use Beckman Coulter (actually, ACS wrote it) software to view
BD
files.  You can use existing commercial programs (Aabel & JMP are
nice
Mac 3D applications, and I'm sure there are others), or write it
yourself in OpenGL.  I think OpenGL would be a better choice than C+
+.
OpenGL is a higher level graphics language, and knows how to access
the
specialized accelerators in the graphics cards, which are actually
faster for this stuff than the G5.  That's how the dungeon games do
the
3D shading and rendering.
I'll be happy to donate a considerable amount of code that I've done
in
this effort (most was taken from an old freeware program called
Rotator, which I no longer could find with Google, but I have
somewhere
in my archives), but we decided this was pretty much a dead end.
Rotator was in C, and quite unreadable. For the investment this task
would take, I think it'd be better to start over in OpenGL.  It's
cross-platform too, which is important, as you'll find you want to
port
it to a Cray.
I'd still think you want to use FlowJo to read the DiVa files,
compensate them, transform them, gate them, and then export desired
subpopulations to the 3D viewer.   If it were any other instrument,
you
could probably read the files yourself, with R or our free Java
libraries, but the DiVa files  are a unique format, and almost always
require compensation and transformation to a lin/log scale, so
there's
a lot of work before you even get to viewing them.
I've promised you 3D graphs in FlowJo in the past, and I've done my
best to deliver them, but the results have been pretty
disappointing.
And the benefit of them has never been demonstrated.  If you can show
us how 3D views provide more interpretable data than our current
"compromise solutions,"  that would help.   If you want to pick a
data
file, we'll make you get a spinning, stereoscopic, 3D view of it.  If
we find that other scientists are able to make conclusions about the
data better than they can from our existing visualizations, that will
go a long way towards bumping it up on the FlowJo future feature
list.
I hope that helps.
Adam
On Dec 31, 2003, at 8:38 AM, David Dombkowski wrote:
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VERITY SOFTWARE HOUSE INC. MARKITING AND SALES ON LIST
**************************************************************************************
Re: DNA analysis software
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From: Xiaoping Wu <xiaopi...@psbc.org>
Date: Thu May 24 2007 - 17:04:13 EDT
We have Modfit 3.0 and our computer is installed with both OS 9 and
OS
X. We did not find problem with printing.
On May 23, 2007, at 2:33 PM, Turbov, Jane wrote:

- Hide quoted text -

Xiaoping Wu, Ph.D.
Flow Cytometry Laboratory
Research Division of the Puget Sound Blood Center
1201 Ninth Avenue
Seattle, Washington 98101
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03:12:00 EST
VERITY SOFTWARE HOUSE COMPARES SOFTWARE NOT RELEASED WITH BD SOFTWARE
**************************************************************************************
Purdue Cytometry Mailing List: Analysis software for the Mac
... Purdue Cytometry Mailing List: Analysis software for the Mac ...
programs divide into two price categories, the expensive (CellQuest,
MacLAS, FCAP List, and Verity's WinList for the Mac, not yet
released)
and the relatively ...
http://www.cyto.purdue.edu/hmarchiv/1997/2083.htm - 5.8KB  57%

08 Sep 97
Find Similar
Highlight

EVERY SOFTWARE DEVELOPER AND CORPORATE OWNER ON THE MAIL LIST ABOVE
HAS LICENSE AGREEMENTS ON SOFTWARE…ALL SOFTWARE MUST BE LICENSED….
I DO NOT KNOW IF PURDUE GETS ROYALTIES FROM ALL THE PROVIDERS ABOVE
BUT THE MAIL LIST WAS UNDER TIGHT PROTECTION BY PAUL J. ROBINSON ISAC
PRESIDENT HEAD OF PURDUE CYTOMETRY
************************************************************************************

KANECKI ASSOCIATES INC. INTRODUCED A NEW CYTOMETRY SOFTWARE WITH NO
LICENSE FEE AT A LOW COST TO HELP STUDENTS AND PROGRESS… THE SOFTWARE
IS THE ONLY SOFTWARE THAT DOES NOT USE COMPENSTAION AND CAN PROCESS 10
MILLION EVENT FILES BY 40 PARAMETERS.
*************NO LICENSE FEES AND ONLY $150.00 FOR STUDNETS!
*************

HERE IS HOW THE DISCOVERY OF THE MAIL LIST CAME ABOUT…

FLOW CYTOMETRY SOFTWARE DEVELOPER KANECKI ASSOCIATES INC. WAS CALLED
A
SCAM BY PERDUE J PAUL ROBINSON...THE STORY AND COVER UP THAT IS
WITHIN
THE SYSTEM..WILL THE TRUTH COME OUT?
KANECKI ASSOCIATES INC.INTRODUCES NEW FCS CYTOPRO QUICK FACS 11 TO
PERDUE UNIVERSITY ONLY TO BE INSULTED WITHOUT REASON... UNCOVER THE
SCANDLE THAT IS WITHIN THE SYSTEM AND SEE IF THERE IS A CHANCE FOR
REFORM? WILL IT EVER CHANGE? IT MUST COME TO A END
Nov 22, 2007 16:38
Flow Cytometry Software Developer Kanecki Associates Inc. Gets Called
A SCAM by PERDUE's J PAUL ROBINSON
Posted by cytometryuser
Kanecki Associates Inc. Was SHOCKED when J.Paul Robinson from PERDUE
called them SCAMMERS after being Questioned from the University about
the Response about his prior comment of them sending JUNK MAIL to his
Mail List...THE MAIL LIST seemed to be a very sensitive spot for Mr.
Robinson....
After a email was sent by a undisclosed source with a link providing
a
link to the MAIL LIST everything was uncovered FAST....The link was a
open door to a list of MAIL FROM a group of HIGH POWER
INDIVIDUALS...MOST...SOFTWARE PROGRAMMERS THAT DEVELOPED SOFTWARE
WHILE GETTING EDUCATED THROUGH PURDUE...
KANECKI ASSOCIATES INC. WOULD LIKE TO STATE THEY ARE NOT SCAMMERS NOR
DID THEY EVER ATTEMPT TO GET ON THE PERDUE MAIL LIST...They have
never
sent mail through the list but just tried to introduce the NEW
software that is distributed through C/net, Best Buy, Circuit City,
Simtel, and may other Major Down load sites.
To view the software JUST       GOOGLE:  FCS CYTOPRO QUICK FACS 11.
KANECKI ASSOCIATES INC. RELEASED THE NEW FCS CYTOPRO JAVA 6.0 FOR
DOWNLOAD TOO.
**********************WITH NO LICENSE
FEES******************************** AND REASONABLE PRICES THEY
DELIVER A SUPERIOR PRODUCT THAT PROCESS 10 MILLION EVENT FILES...FCS
3.0
THEY DO NOT USE COMPENSATION LIKE OTHER SOFTWARE PROVIDERS SO THERE
IS
NO OVER COMPENSATION ISSUES........Further More there is NO MENUE BAR
which makes for USER FRIENDLY SOFTWARE...VERY EASY TO USE....JUST
PICK
AND CLICK.................................
SO TO PROVIDE THE TRUTH ALL POST THAT WILL BE SHOWN CAME DIRECTLY
FROM
SAVED EMAIL SENT TO PURDUE...IT WAS NOT SENT TO THE LIST BUT TO THE
HEAD OF  PURDUE..
NOT MR.ROBINSON HE RECEIVED A CC...THEN RESPONDED BU CALLING IT JUNK
MAIL!
ORIGINAL MESSAGE SENT      :    TO ROBERT MURPHY  WITH LINKS FOR
DOWNLOAD AND ALL INFORMATION PERTAINING TO FCS CYTORPO QUICK FACS 11
SOME HOW IT WAS FOWARDED TO: J PAUL ROBINSON...MAYBE FOR REVIEW...?
Fw: NEW FLOWCYTOMETRY SOFTWARE FOR ALL BD and Beckman/Coulter
Flow Cytometers CAN PROCESS 24,000 SAMPLES PER HOUR
Standard
Header|Full Message
View
mitchell haynes <buybro...@yahoo.com>
ViewFriday,
September 28, 2007 1:36:36 AM
To:j...@flowcyt.cyto.purdue.edu
Cc:da...@kanecki2.com
Cytopro
quick facs savings analysis.doc (82KB); Setup-Quick
Facs 11 Demo.exe (7854KB); FCS
CYTOPRO BENIFITS.doc (25KB)
Find:
Dear Robert Murphy
NEW
FLOWCYTOMETRY SOFTWARE FOR ALL BD and Beckman/Coulter Flow Cytometers
CAN
PROCESS 24,000-42,000 SAMPLES PER HOUR.
FLOW CYTOMETRY    FCS CYTO PRO QUICK FACS
http://www.kanecki.com/flow.html
Increased quality and productivity. With 10,000,000 event files, you
can process 24,000 samples/hour, and maintain quality up to Sigma 5
or
better. Compare this to having your research technologist performing
only 100 samples/hour analysis.
Increased laboratory utilization by 3X because you can perform the
analysis off-lab and free laboratory time for reading samples. This
was achieved when I developed the program, and we had a program
project grant from 1992 to 1998 of $8M.
Works with FCS 3.0 in all data modes as floating point, integer*4,
and
ASCII.
Works with BD and Beckman/Coulter Flow Cytometers and Cell Sorters
Backwards compatible with FCS 2.0 files and Flow Cytometers and Cell
Sorters.
Can read FCS 3.0 files up to 10M events with 20 parameters.
Easy to Use, three step process. Load initial file, set gate, specify
file list to process. That's it.
Collaboration tools to allow you to cut and paste image results to
results.
Statistical analysis results imprinted on histogram plots directly as
mean, mode, and median with the ability to present results in log
mode
or linear mode, depending on the detector used.
Plain vanilla coding for easy update and maintenance to allow for the
greatest user and software quality.
One time purchase fee, no yearly renewal fees as with others.
Proven tract record in FACS, Fluorescent Activated Cell Sorter
Laboratory. The laboratory was rated the best laboratory in the
Midwest USA in 1990.
This application is designed for large-scale fluorescent activated
cell sorter
analysis. The program can read up to FCS 3.0 files and has been
tested
to run on Becton Dickinson and CoulterOrtho based flow cytometers and
cell sorters. The main advantage of this program is that you can have
the computer perform the analysis for you after you have selected the
region to analyze. The result is that up to 24,000 samples per hour
can be analyzed on a 1.4 GHz speed computer.
This program is designed for researcher and technologist use. It uses
rectangular gating, and is intuitive to use. To use this program, the
FCS must have the extension, *.bin as "54203023.bin" as an example.
The *.bin extension is what the computer uses to locate the files on
the computer.
THANK YOU FOR YOU TIME
MITCHELL HAYNES
VP
SALES
KANECKI
ASSOCIATES
832-347-1669
THIS WAS J PAUL ROBINSON RESPONSE TO THE INFORMATION SENT
Re: Fw: NEW FLOWCYTOMETRY SOFTWARE FOR ALL BD and Beckman/Coulter
Flow
Cytometers CAN PROCESS 24,000 SAMPLES PER HOUR...Standard Header|Full
Message View J. Paul Robinson J. Paul Robinson ... ViewFriday,
September 28, 2007 9:37:32 AM To:mitchell haynes
Cc:da...@kanecki2.com; skel...@flowcyt.cyto.purdue.edu
Steve
what is this email - it came to me with Bob Murphy's name associated
with it. It seems to be an advertisement, this junk mail, and it
seems
to have been modified by you ...
So I guess I am confused. was this sent to the list, or do you have
an
details about it - i am concerned about these junk messages going out
to
our members, - if they are using our lists, I will deal with them
appropriately, but I am not happy about this - any info you can give
me
appreciated
thanks
paul
WHILE BEING SHOCKED BY THIS MAIL...MITCHELL HAYNES VP.KANECKI
ASSOCIATES INC....WROTE BACK

- Hide quoted text -

<!--[if !supportLineBreakNewLine]-->
AFTER THAT MESSAGE J PAUL ROBINSON RESPONDED WITH OUT REASON!

- Hide quoted text -

----- Original Message ----
From: "j...@flowcyt.cyto.purdue.edu"
<j...@flowcyt.cyto.purdue.edu>
To: mitchell haynes <buybro...@yahoo.com>
Cc: j...@flowcyt.cyto.purdue.edu
Sent: Friday, September 28, 2007 2:26:51 PM
Subject: Re: Fw: NOT A JUNCK MAIL STEVE WAS JUST FOWARDING
INFORMATION
TO
PROPER CHANNELS
Sorry, I think it is junk mail
regards
paul robinson
After this message Kanecki Associates Inc. JOINED many Forums in
which
the MESSAGES WITH THE NAME OF THE SOFTWARE AS RELAYED.....JUST ABOUT
ALL FORUMS DELETED INFORMATION POSTED ABOUT THE
SOFTWARE...FURTHERMOORE...BEING REMOVED AND BANNED FROM FORUMS....
VERY CONFUSED ABOUT ALL THE TALK OF OTHER SOFTWARE THE LAUNCHED
QUESTIONS ON YAHOO..?
WHY DO FORUMS ALLOW THE CONVERSATION OF ONE SOFTWARE AND NOT
ANOTHER..
WHY DO FLOW CYTOMETRY COMPANIES CHARGE LICENSE FEES?
THEN SOMEONE SENT A LINK TO THE PURDUE MAIL LIST BUT IT WAS NOT TO
THE
FRONT BUT BACK ROUTE..WHEN  VIEWED ALL THE REASONS WERE EASY TO
SEE...........
J PAUL ROBINSON HAD A LOT OF POWER AND INFLUENCE IN THE FLOW
COMMUNITY...
FURTHER MOORE EVERY PROGRAMMER THAT HAS SOFTWARE ON THE MARKET WENT
TROUGH THE MAIL LIST SINCE 1992 AND ALL HAD THEIR OWN SOFTWARE FOR
SALE ON THE PERDUE SITE.....THE POST IN THE MAIL LIST ARE UNFILTERED
AND WERE******* NOT WHAT THE REST OF THE LIST HAD ACCESS TO...ONCE
POST STARTED GOING UP THE SITE WAS BLOCKED... SINCE THEN BOTH SITES
HAVE BEEN UP AND DOWN FOR THE MAIL LIST!
WITH THE MARKET BEING VERY SMALL IN FLOW SOFTWARE IT IS EASY TO
CONTROL....
KANECKI ASSOCIATES POSTED A BLOG  WITH THE LINK TO THE BACK ROUTE TO
THE MAIL LIST AND GOT IMMEDIATE RESPONCE...
WHEN MITCHELL HAYNES DISCOVERED THE LINK HE STARTED POSTING THE
DISCOVERY UP ON MIS.HEALTH AIDS THROUGH :::GOOGLE::: AS FOR*****
GOOGLE*****IS THE ONLY SITE NOT FILTERING THE MAIL....
FINALLY A THE MESSAGES WERE SEEN AND SINCE THEY CAME FROM THE MAIL
LIST POSTINGS  THEY WERE NOT PRETTY....
ALL FILES WERE DOWNLOADED
WHAT CAN KANECKI ASSOCIATES INC FCS CYTOPRO JAVA  6.0 DO? NO LICENSE
FEE
0NLY $150.00 FOR STUDENTS 250.00 USD EVERYONE ELSE
*********************************************************************************************************************
POSTED BY MITCHELL HAYNES
IT IS NOT A SCAM OR JUNK MAIL PLEASE READ!
Written by David Kanecki, MBA, ACS, Bio. Sci.
November 25, 2007
Fcs cytopro quick Facs 6.0 java  14
       The FCS Cytopro Quick Facs 6.0 Java allows the performance of
flow
cytometry analysis on computers or PC. This new technology allows for
utilization on Mac, Linux,
Solaris, and Windows with the same functionality and processing
speed.
It is designed to minimize the learning curve by doing away with a
confusing menu bar.
This new easy navigation process allows for any level of student,
technologist or researcher to perform flow cytometry analysis with
ease. The utilization time can be used   inside or outside of the
lab.
Easy operation allows for greater efficiency and quality. This
translates into decrease in time and cost.
About  27% overall savings in flow cytometry experiments. So,Just
pick, click and go!
This program can read three of the four most common modes of the FCS
3.O  files, and is
Backward compatible with FCS 2.O and 1.O files
Equipped with advanced processing speeds allows rapid results, no
need to wait for your computer to think. When performing a batch mode
analysis, you can analyze about 24 to 42,000 samples per hour with
FCS
2.0 files, and about 4,000 samples per hour with 1 million event by 9
parameters for FCS 3.O files. Also 10 million event by 25 parameter
FCS 3.0 file or a 10 million event  FCS 2.0 and 1.0 files.
This FCS Cytopro Quick Facs Java 6.O is for large-scale and rare-
event analysis.
There is no Dongle, License fees, or restrictions for using the
software. The user can process the analysis where ever and whenever
necessary.
There are various features this program has to offer consisting of
analyzing dot plots, dual histograms , and descriptive statistics.
Easy to use just copy and paste the items into your report or paper.
This shows the result of a du
al, histogram analysis along with dual, descriptive statistical
analysis. The first histogram is in red, and the second is in blue.
The first, descriptive
analysis gives the information for the red histogram, and the second
descriptive analysis,
below the first, gives the information for the blue histogram. Also,
in the result box, see the two files listed along with their
checksums. The checksum is a measure that allows you to monitor the
correctness of a file. If a file is the same as the last time, its'
checksum will be the same. If the file is different, same size, but
different data, then its' checksum will be different:
Conclusion
Without a dongle, license fees and excessive time wasted educating
to
on software usage,  Kanecki Associates Inc will save the world
millions.
There will be no need for large seminars and wasted time on how to
utilize software and more time to study important issues. Students
can
learn without fear of being able to afford the software. For only one
hundred and fifty dollars USD. for students. Yes you can own it.
There
is no license fees.
If you are not a student the cost is only two hundred and fifty
dollars USD .So why lease your software from the lab at thirty
dollars
per hour?  Within five hours of leasing software from you lab at 30
dollars per hour you could be at home relaxing and working on you PC.
If you are not a student the cost is only two hundred and fifty
dollars.  Never a license fee or dongle. You can take it or leave it,
where ever  you like!
       The FCS Cytopro Java 6.0 program allows you to analyze large
sample
sets
quickly, easily, and with high-quality and precision.  In addition,
it
can analyze large data
set files of up to 10 million events and 25 parameters for use in
rare-
event analysis or
kinetic  based experiments. This program is designed so that it is
easy to use, and this ease
of use and accuracy translates into high productivity and cost
savings, about 27% overall
in flow cytometry cost.
New technology breaking down the walls developed by Dr. David
Kanecki,
No it is not a Scam or Junk mail! It is  high tech software at a
reasonable price.
Free trial down load so there is nothing to loose
http://www.kanecki.com
http://www.flowcytometrysoftware.com
direct download link for free trial
http://www.flowcytometrysoftware.com/order.html
FCS Cytopro Java 6.0 Script (c) 2007 By D. Kanecki, All Rights
Reserved
Mi...@Kanecki.com
WHAT PEOPLE SAY ON THE MAIL LIST ABOUT THE PRICE AND LICENSE FEES FOR
SOFTWARE!
FACS-software
   * This message: [ Message body ] [ More options ]
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in thread ] [ Replies ]
From: Yuecel, Raif <Raif.Yue...@pmintl.com>
Date: Wed Nov 02 2005 - 06:32:42 EST
Dear FACS-experts,
I need the opinion of the specialist:
I need FACS-software for PC and had decided for FlowJO. I know the
mac-version of FlowJO. Indeed, this is very expensive.
Now, I was asked to get a comparative offer. Therefore, I thought
about
WinList. This is much cheaper. But I have no experience with WinList.
My question to the experts:
1.      What are the advantages and disadvantages of both software?
Question of the business & finance department, which are also
entitled:
1.      Why is FlowJo so expensive, if you need several licence?
2.      Why FlowJo and not WinList, because WinList much cheaper?
Thanks very much for the help !
Best regards
Raif
-----------------------------
Dr. Raif Yuecel
PHILIP MORRIS Research Laboratories GmbH
Fuggerstrasse 3
D-51149 Koeln
Germany
Phone    +49 2203 303 486
Fax         +49 2203 303 362
=====================
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and may
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or distribution is prohibited. If you are not the intended recipient,
please
contact the sender by reply e-mail and destroy all copies of the
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***************************************************************************-
***********************************************
THIS REPLY FROM MITCHELL HAYNES KANECKI ASSOCIATES INC.
WHAT PURDUE DID NOT WANT YOU TO KNOW....
FCS CYTOPRO JAVA 6.0 FREE TRIAL DOWN LOAD
$150.00 STUDENTS
NO LICENSE FEES
FCS 3.0
http://www.kanecki.com/flowF.html
http://www.flowcytometrysoftware.com
**************************************************************************************WHAT
DO THE STUDENTS HAVE TO DEAL WITH AND SAY?
Purdue University Cytometry Laboratories - Flow cytometry
confocal ...... please go to the rippoff website above and make your
complaint and register. ... J. Paul Robinson, Ph.D., Director PUCL,
1203 W. State St., Purdue ...
www.cyto.purdue.edu/flowcyt/rebates.htm?institutionId=694&meetingId=218
- 8k - Cached - Similar pages - Note this
STUDENT CONTRACT THROUGHT PURDUE FOR SOFTWARE THEY SHOULD HAVE
A  LAWYER READ BEFORE THEY SIGN***POLARIS AGREEMENT
"POLARIS" SOFTWARE LICENSE AGREEMENT
(INCLUDING LIMITED NON-COMMERCIAL DISTRIBUTION RIGHTS)
UNIVERSITY OF ILLINOIS
        Under this Agreement, The Board of Trustees of the
University
of Illinois ("University"), a body corporate and politic of the State
of Illinois with its principal offices at 506 South Wright Street,
Urbana, Illinois 61801, U.S.A., on behalf of its Department of
Computer Science on the Urbana-Champaign Campus, provides the
"POLARIS" software ("Software") described in Appendix A, attached
hereto and incorporated, to Purdue University ("Licensee") subject to
the following terms and conditions:
1.       The parties acknowledge that Licensee currently has a
license
that restricts its use of the Software to internal use, and Licensee
has requested the University to grant certain distribution and
sublicensing rights for the Software and derivative works thereof.
Accordingly, upon execution of this Agreement by Licensee below, the
University grants, and Licensee accepts, a royalty-free, non-
exclusive, non-transferable license:
A.     To use, display, install, copy and distribute unlimited copies
of the Software for its own internal academic and research purposes.
B.      To make derivative works of the Software.  However, if
Licensee distributes any derivative work based on or derived from the
Software, then Licensee will (1) notify the University (c/o Professor
David Padua, e-mail:  pa...@uiuc.edu) regarding its distribution of
the derivative work and provide a copy of the modified Software to
the
University, if requested by the University, and (2) clearly notify
users that such derivative work is a modified version and not the
original Software distributed by the University.
C.     To redistribute (sublicense) the Software or derivative works
based on the Software, in whole or in part, to third parties provided
that (1) the University's copyright notice and any accompanying
legends or proprietary notices are reproduced on all copies that
include the University's original code, (2) no royalty is charged for
such copies, and (3) third parties are restricted to using the
Software for academic and research purposes only.
         No license is granted herein that would permit Licensee or
its sublicensees to incorporate the Software into a commercial
product, or to otherwise commercially exploit the Software.   Should
Licensee or its sublicensees wish to make commercial use of the
Software, such Licensee or sublicensee should contact the University,
c/o its Office of Technology Management (o...@uiuc.edu; Telephone
(217)333-7862) to negotiate an appropriate license for such
commercial
use.
2.      THE UNIVERSITY GIVES NO WARRANTIES, EITHER EXPRESSED OR
IMPLIED, FOR THE SOFTWARE AND/OR ASSOCIATED MATERIALS PROVIDED UNDER
THIS AGREEMENT, INCLUDING, WITHOUT LIMITATION, WARRANTY OF
MERCHANTABILITY AND WARRANTY OF FITNESS FOR A PARTICULAR PURPOSE.
        Licensee understands the Software is a research tool for
which no warranties as to capabilities or accuracy are made, and
Licensee accepts the Software "as is¡±, without maintenance,
debugging, support or improvement.  Licensee assumes the entire risk
as to the results and performance of the Software and/or associated
materials.  Licensee agrees that University shall not be held liable
for any direct, indirect, consequential, or incidental damages with
respect to any claim by Licensee or any third party on account of or
arising from this Agreement or use of the Software and/or associated
materials.
3.      Licensee understands the Software is proprietary to the
University.  Licensee will take all reasonable steps to insure that
the source code is protected and secured from unauthorized
disclosure,
use, or release and will treat it with at least the same level of
care
as Licensee would use to protect and secure its own proprietary
computer programs and/or information, but using no less than
reasonable care.
4.      In the event that Licensee shall be in default in the
performance of any material obligations under this Agreement, and if
the default has not been remedied within sixty (60) days after the
date of notice in writing of such default, University may terminate
this Agreement by written notice.  In the event of termination,
Licensee shall promptly:  (i) return to University all copies of
licensed Software and derivative works thereof in tangible or
electronic form that are in Licensee's possession or control; or (ii)
permanently destroy or disable all copies of the Software in
Licensee's possession or control, except as specifically permitted by
the University in writing; and (iii) provide University with a
written
statement certifying that Licensee has complied with the foregoing
obligations.  All rights and licenses granted to Licensee shall
terminate upon such termination.  In the event of any termination of
this Agreement, any and all sublicenses granted by Licensee to third
parties pursuant to this Agreement (as permitted by this Agreement)
prior to the date of such termination shall nevertheless remain in
full force and effect.
5.      In all uses of the Software, where appropriate, Licensee will
credit the origins of the Software, or derivative works based
thereon,
to the creator(s) and the University of Illinois for their role in
the
development of the Software.
6.      This Agreement shall be construed and interpreted in
accordance with the laws of the State of Illinois, U.S.A..
7.      This Agreement shall be subject to all United States
Government laws and regulations now and hereafter applicable to the
subject matter of this Agreement, including specifically the Export
Law provisions of the Departments of Commerce and State.  Licensee
will not export or re-export the Software without the appropriate
United States or foreign government license.
Appendix A:  Software Identification
Form Approved by University Counsel, M.A.R., _1/5/98_
USER DIRECTORIES:vcr:stipswor:Software Lic:distlpol
APPENDIX A
to
"POLARIS" SOFTWARE LICENSE AGREEMENT
(INCLUDING LIMITED NON-COMMERCIAL DISTRIBUTION RIGHTS)
UNIVERSITY OF ILLINOIS
Identification of Licensed Software
Title:  POLARIS
Version Number:   All versions provided to Licensee under license
from
the University
Creator(s):  David Padua, Jay Hoeflinger, Paul Petersen, Rudolf
Eigenmann, William Blume, Keith Faigin, Peng Tu, and Steven
Weatherford
Responsible Unit(s):   Department of Computer Science (formerly
Center
for Supercomputing Research and Development)
Description :  Polaris is a source-to-source Fortran restructurer. It
parses Fortran programs and represents them internally using a
hierarchy of classes.  Polaris contains analysis modules to identify
dependences, private data, reductions, and induction variables.  It
also contains a code generation phase that targets parallel Fortran
extensions used by shared-memory machines.
***************************************************************************-
*************************** GUIDE TO INTERNET RESOURCES
Note from archiver<at>cs.uu.nl: This page is part of a big collection
of Usenet postings, archived here for your convenience. For matters
concerning the content of this page, please contact its author(s); use
the source, if all else fails. For matters concerning the archive as a
whole, please refer to the archive description or contact the
archiver.

________________________________________
Subject: A Biologist's Guide to Internet Resources (2 of 6)
This article was archived around: Thu, 11 Nov 1993 01:44:17 GMT
All FAQs in Directory: biology/guide
All FAQs posted in: sci.bio
Source: Usenet Version
________________________________________
Archive-name: biology/guide/part2
Last-modified: 10 November 1993
________________________________________

-*- 2. Networking

   The Internet has become an excellent place in which to look for
academic
   and professional job announcements, conference announcements and
calls
   for papers, and important notices about recent events in many
fields of
   biology.  Generally, notices of all forms appear on the Internet
well in
   advance of traditional journals and newsletters.  Scientific
interest
   groups, both formal and informal ones, maintain electronic
discussion
   groups, directories, digests and newsletters.  These resources are
   distributed in three principal ways:  via Usenet newsgroups,
(automated)
   listserver mailing lists, and mailing lists administered by real
people.
   Increasingly, the two forms of mailing list have "gateways"
connecting
   them with Usenet newsgroups.

-*- 2.1. Netiquette

   The professionally-oriented newsgroups and mailing lists follow
certain
   conventions of etiquette.  These are none other than those used by
most
   people at public events such as academic conferences.  In fact,
most of
   the science-related newsgroups (and mailing lists) are very much
like
   mid-sized meetings of any professional society, except that they
never
   end.  The participants come and go as they please, but the
discussion
   and exchange of ideas and information continues.

   Submitted articles tend to be of the following types:

   - Discussions on topics of general interest.  Discussions on
specific
     topics, techniques, or organisms are also frequent.

   - Announcements of upcoming conferences or other events, calls for
papers
     or grant proposal deadlines.  In Usenet, announcements can be
set to
     expire (and thus disappear from the list of current articles),
and may
     be limited in their distribution so that they are seen only by
readers
     in the appropriate organization or geographical area (Beware,
this
     feature is often leaky;  see section 2.2, Usenet).

   - Academic and professional job announcements, including many
graduate
     fellowships.  These are generally posted in newsgroups/mailing
lists
     reserved for such notices, often in advance of publication
elsewhere.

   - Reports or comments on new books, papers, methods or software.
Full
     citation of sources is always appropriate and appreciated.
Requests
     for references or comments are also welcome and, when posed as
specific
     questions of general interest, often lead to interesting
discussions.

   Unacceptable articles include:

   - Commercial advertizements, political lobbying messages, and
anything
     not pertaining directly to the topic or purview of the newsgroup
or
     mailing list.  Discussions about some commercial products,
especially
     books and software, are generally allowed as long as they do not
     constitute advertisements.

   - Requests by students for explicit answers to homework and exam
or essay
     questions are generally not welcome.  Requests for help
understanding
     problems in biology are welcome, but the requester should
demonstrate
     at least a basic understanding of the question.

   Some helpful suggestions:

   - Read before you post (look before you leap)

   Before posting an article for the first time, read the discussions
for
   a week or so.  Look for an "FAQ" document that covers frequently
asked
   questions (thus the name) before you make the mistake of asking
one
   yourself.  FAQs are an excellent way to learn a great deal about
the
   culture and resources of the Internet, plus a great deal more.
FAQs
   about resources are updated often (usually monthly), to stay
current.
   (They are far more current than traditionally published books
listing
   Internet resources!)  Each newsgroup or mailing list has its own
unique
   character, that is built from the shared experience of loyal and
active
   participants exchanging ideas and information over the course of
years.

   - Always include your full name and e-mail address

   Put these at the end of your message, with your usual signature.
You
   might want to use a .signature file (standard on most Unix
systems, also
   implemented for Usenet and e-mail readers under VM/CMS) to make
this
   automatic. This is necessary because strange things often happen
to
   headers in e-mail or Usenet articles sent from one network to
another.
   You may want to include your affiliation and/or mailing address,
so that
   others can send you re-prints, and to help in networking outside
of the
   Internet.  Traditionally, people do not indicate their status;
whether
   student or professor, Ph.D. or not, etc.  It is generally believed
that
   the text-only nature of communication via the Internet allows
people to
   form opinions of one another that are based more on intellectual
merit
   than on other, perhaps more superficial qualities.  Either way,
you have
   an unusual degree of control over what others can know about you,
and it
   is to your advantage to use a .signature file that reflects you
well.

   - Send private replies whenever appropriate

   Answers to very esoteric questions are often best sent directly to
the
   person who asked for help, rather than to the newsgroup;  the
choice of
   whether to post a (public) reply or send (private) e-mail is a
personal
   decision.  If you send a reply by e-mail, and would prefer that it
be
   kept private, you should say so in your note, because otherwise
the other
   person may share your comments with others.  If the original
poster
   promises to post a summary at the outset, then all replies should
be
   sent by e-mail, unless they constitute an important re-direction
of the
   original question.

   - Summarize the replies to your article

   Whenever a question or request for information results in many
replies,
   it is expected that the person who posted the original article
will
   compile and post a summary of the responses.

   - Use care when writing summaries

     - The "best" answers should come first.
     - All answers should be separated clearly, and nicely formatted.
     - Redundant, irrelevant or verbose comments, and errors of fact
or
       spelling should be edited out.  It is appropriate to use
square
       brackets and dots to indicate editing [...].
     - Exercise discretion and tact, to ensure a fair and accurate
summary.
     - Unless they asked that their names be withheld, the
contributors of
       each answer should be named and thanked, individually or as a
group.

   - Avoid starting nasty arguments or "flame wars"

     - Be generous when interpreting the arguments of others.
     - Avoid jargon;  write as though addressing an educated lay
audience.
     - Avoid personal attacks on the honor or character of others.
     - Remember, the exercise will be good for you.

   If something you read angers you, save it for a few hours while
you do
   something else (don't reply on an empty stomach).  Go back to it
when
   you are calm and relaxed (and you have thought of a good
rebuttal!).
   If you simply must say something highly critical that is not
confined
   to the subject under discussion (i.e., strays from intellectual
argument
   into the realm of personal insult), consider sending it privately
via
   e-mail, rather than posting or mailing to the group.  And if you
read
   something insulting to you, do not respond immediately;  give
yourself
   time to cool off and think of a tactful (but also devastating)
response.
   E-mail can be a powerful tool, but only if you use it well.

   - Be careful about quotations, citations and copyrights

   The Internet has grown to the point where it has become reasonable
to
   cite documents that exist officially only in an electronic version
on
   the Internet.  And the issue of authenticity and version control
has
   become extremely important.  Thus, it has become appropriate to
express
   copyrights, and to specify within documents how they may or may
not be
   used, both within the Internet and in print.  Please respect these
   restrictions, which are often very generous, and send the author e-
mail
   if you have any doubts about the intended use of any Internet
document.

   As a rule of thumb, you may freely cite or quote anything posted
to a
   newsgroup or mailing list in that forum *only*.  For citations or
quotes
   elsewhere, it is hoped, even expected, that you will first request
express
   permission from the author, which is easy, given the author's e-
mail
   address.  Although there has been a trend to cite specific
articles posted
   in Usenet, it is generally satisfactory to use the "personal
communication"
   formula, but for this reason you should request a specific,
personal
   statement from the author that is directly relevant to and given
in the
   context of the issue that you wish to address.

-*- 2.2. Usenet

   Usenet is a convention, in every sense of the word.

   Usenet is a system of organized "newsgroups" sharing many features
with
   traditional newsletters, mailing lists and focused scientific
societies.
   Usenet is Internet-based (although before the Internet existed it
was
   distributed via UUCP), and strongly developed so that end users
need
   know only how to interact with the particular Usenet "reader"
program
   on their computers.  Features of Usenet that make it far superior
to the
   two types of mailing lists generally include the sorting or
"threading"
   of all articles on a related topic, control of the distribution of
   posted articles to hierarchical levels (e.g., the author's
university,
   state, country, or continent--but this feature may "leak"), the
ability
   to cancel an article even after it has been distributed, and
automatic
   expiration of dated articles.  To test any of these features,
especially
   the distribution control, try posting an article to misc.test;
your
   article will receive "echoes" from other sites that receive it.

   Usenet is "free", but not cheap;  because it requires a lot of
computer
   disk space, and a certain amount of installation and regular
maintenance
   work by a system administrator, not all computer systems carry
Usenet.
   If Usenet is carried locally, it may still be necessary to prod
the local
   Usenet administrator to add the bionet and bit.listserv newsgroups
to the
   local "feed".  Usenet was created by two Duke University graduate
students
   in 1979:  see Spafford (1993) for the definitive history of Usenet
and a
   list of Usenet software for virtually every type of computer.

   To paraphrase Spafford and Salzenberg (1992):  Usenet is *not* a
network.
   Usenet is an anarchy, with no laws and no one in charge.  No one
has any
   real control outside of their own site.  Computer system
administrators
   who distribute Usenet "feeds" to other sites gain some authority
by virtue
   of being "upstream";  that is, they have some say over what
newsgroups
   their "downstream" neighbors can receive.  Usenet feeds are stored
at each
   site in "spools";  it is common for universities to have Usenet
spools on
   one or two computers, and to allow everyone at the university to
read
   Usenet news via "client" programs that connect to the remote "news
server".

   The particular configuration of the Usenet feed to your university
or
   organization determines whether the distribution control feature
of most
   Usenet posting programs will work properly for you.  For example,
the
   mailing lists for the bionet.* newsgroups are gated on the west
coast of
   North America, and you might think that it is safe to post local
items
   in a bionet.* newsgroup if you live elsewhere.  But many sites get
their
   feed of bionet.* groups directly from the machine that runs the
mailing
   lists, which is definitely outside your geographic area.  So your
article
   will be distributed at your site, but will not be propagated from
your
   site to any other site in your area if it must pass out of your
region
   and then return through a separate feed to a university in the
next city.
   Furthermore, it is a more efficient use of network resources to
get as
   much Usenet traffic as possible from the nearest site available.
It is
   important, therefore, to do a little research on Usenet feeds in
your area
   before asking your Usenet administrator to add one of the
newsgroup
   hierarchies listed in section 2.2.2, Special Usenet Hierarchies
and Gated
   Mailing Lists.

   Usenet etiquette:

     - New users should read the Usenet FAQs posted in
news.announce.newusers.

     -    Use the misc.test newsgroup for posting test articles.  Be
sure to
       test the distribution feature here.  Do not post test articles
to
       other newsgroups.

     -    Use the expiration feature for job and conference
announcments.

     -    When posting to more than one newsgroup, use the cross-posting
feature
    so only one copy of your article goes out, but is seen by many
people.

     -    Post (and cross-post) sparingly to groups that have associated
mailing
    lists, to give a break to people who must read the groups via e-mail.

   The cross-posting of articles to more than one gated newsgroup is
strongly
   discouraged, since the e-mail subscribers will get multiple copies
of any
   cross-posted articles.  Usenet readers should be aware of proper
etiquette
   for mailing lists when posting to gated newsgroups.

-*- 2.2.1. Newsgroups of Special Interest

   An "F" after the newsgroup name indicates an FAQ is available.
"M" means
   that the newsgroup is moderated.  "G" means that the newsgroup has
a
   gateway to a parallel mailing list:  see section 2.2.2, Special
Usenet
   Hierarchies and Gated Mailing Lists, for details.

   alt.agriculture.*           [2 groups]
   alt.bbs.internet             F  Announcements of new Internet
services
   alt.cyb-sys                     Cybernetics and Systems
   alt.internet.access.wanted   F  Help getting full Internet access
   alt.internet.services        F  Announcements of new Internet
resources
   alt.native                      Indigenous peoples
   alt.sci.*               [6 groups]
|  alt.earth_summit                Discussion of the recent Earth
Summit
   alt.sustainable.agriculture  G  Sustainable agriculture

   bionet.agroforestry          G  Agroforestry research
   bionet.announce            FGM  Announcements
   bionet.biology.computational GM Comp. and math. applications in
biology
   bionet.biology.n2-fixation   G  Biological nitrogen fixation
   bionet.biology.tropical      G  Tropical biology and ecology
   bionet.chlamydomonas    G  Chlamydomonas discussion
   bionet.cellbio        G  Cell biology discussion
   bionet.drosophila        G  Drosophila discussion
   bionet.general              FG  General discussion
   bionet.genome.*              G  [3 groups:  Arabidopsis and
chromosomes]
   bionet.immunology            G  Research in immunology
   bionet.info-theory          FG  Information theory applied to
biology
   bionet.jobs                  G  Job opportunities in biology
   bionet.journals.contents    GM  Biological journal TOCs
   bionet.journals.note         G  Publication issues in biology
   bionet.metabolic-reg    G  Metabolic regulation and thermodynamics
   bionet.molbio.ageing         G  Cellular and organismal ageing
   bionet.molbio.bio-matrix     G  Computer searches of biological
databases
   bionet.molbio.embldatabank   G  Info about the EMBL Nucleic acid
database
   bionet.molbio.evolution      G  Evolution, especially molecular
   bionet.molbio.gdb            G  The GDB database
   bionet.molbio.genbank        G  The GenBank nucleic acid database
   bionet.molbio.gene-linkage   G  Genetic linkage analysis.
   bionet.molbio.genome-program G  Human Genome Program issues
   bionet.molbio.methds-reagnts G  Tips on lab techniques and
materials
   bionet.molbio.hiv            G  The molecular biology of HIV
   bionet.molbio.proteins       G  Proteins and protein database
searches
   bionet.molbio.rapd           G  Randomly Amplified Polymorphic DNA
   bionet.molbio.yeast        G  Yeast researchers' discussion
   bionet.mycology              G  Mycological research discussion
   bionet.neuroscience          G  Research issues in the
neurosciences
   bionet.photosynthesis    G  Photosynthesis research
   bionet.plants                G  Plant biology, inc. genetics and
ecology
   bionet.population-bio        G  Population biology, especially
theory
   bionet.sci-resources        GM  Information about funding
agencies, etc.
   bionet.software              G  Software for biology, esp. free/
shareware
   bionet.software.*            G  [3 groups:  acedb, gcg, and
sources]
   bionet.users.addresses       G  Help locating biologists who use e-
mail
   bionet.virology              G  Research in virology
   bionet.women-in-bio          G  Discussion by and about women in
biology
   bionet.xtallography          G  Protein crystallography

   bit.listserv.biosph-l        G  Biosphere, ecology, Discussion
List
   bit.listserv.devel-l         G  Tech. Transfer in Internat.
Development
   bit.listserv.ethology        G  Ethology List
|  bit.listserv.geograph    G  Geography List
   bit.listserv.medforum    MG  Medical Students Discussion
   bit.listserv.uigis-l         G  User Interface for GIS
   bit.listserv.vpiej-l         G  Electronic Publishing Discussion
List
   bit.org.peace-corps        G  International Volunteers Discussion Group

   comp.infosystems.gis        FG  Geograpical Information Systems
   comp.infosystems.gopher      F  The Internet gopher access tool
   comp.infosystems.wais        F  The Internet WAIS access tool
   comp.infosystems.www       The Internet WWW access tool
   comp.soft-sys.sas            G  SAS Discussion
   comp.soft-sys.spss        G  SPSS Statistical Discussion
   comp.text.tex                F  TeX, LaTeX and related text format
systems
   comp.theory.cell-automata    G  Cellular automata research
   comp.theory.dynamic-sys      G  Ergodic theory and dynamic systems
   comp.theory.self-org-sys     G  Topics related to self-
organization

   embnet.news.admin        G  EMBnet news helpline for administrators
   embnet.general        G  General discussion
   embnet.net-dev           Network development discussion
   embnet.rpc               Technical discussion of data transfers

   info.grass.programmer       GM  GRASS GIS programmer issues
   info.grass.user             GM  GRASS GIS user issues
   info.ietf            GM  Internet Engineering Task Force
   info.nsf.grants        GM  NSF grants announcements
   info.wisenet                 G  Women in Science and Engineering
Network

   news.announce.newusers      FM  FAQs for new users of Usenet
   news.answers                FM  All FAQ documents
   news.lists                  FM  Statistics and data about Usenet

   sci.answers                GFM  FAQs pertaining to science
   sci.anthropology           Anthropology discussion
   sci.archaeology           Archaeology discussion
   sci.bio                      F  General biology discussion
   sci.bio.ecology        G  Ecological research (sponsored by ESA)
   sci.bio.technology           G  Any topic relating to
biotechnology
   sci.environment           Discussion of environmental issues
   sci.geo.*               [3 newsgroups]
   sci.image.processing    F  Scientific image processing
   sci.nonlinear                   Nonlinear dynamical systems
   sci.research.careers       Discussion of research careers in science
   sci.stat.consult        G  Statistical consulting
   sci.stat.edu        G  Journal of Statistics Education List
   sci.stat.math           Mathematical statistics
|  sci.techniques.xtallography     Crystallography techniques
   sci.*               [60 other newsgroups]

-*- 2.2.2. Special Usenet Hierarchies and Gated Mailing Lists

   There has been a growing trend in the past few years to set up
transparent
   "gateways" between mailing lists and newsgroups, and to create
Usenet
   newsgroup hierarchies that are outside the "main stream".  Both
being new,
   these two trends often go together.

   None of the Usenet newsgroup hierarchies mentioned below are main-
stream
   ones;  that is, they do not conform to all Usenet conventions, and
   consequently are carried by no more than 30-50% of Usenet sites.
This is
   not necessarily a bad thing, since few or no readers at most sites
are
   biologists, and e-mail subscriptions are available for many
groups.  If
   your site carries Usenet, but not these hierarcies, a simple
request to
   your Usenet administrator might be all that's needed to get them
too.
   But see the first part of section 2.2, Usenet, for details about
what to
   ask for.

   bionet.*

   Each of these newsgroups has two gateways to mailing lists, to
save on
   trans-Atlantic transmission costs.  For an e-mail subscription to
any

Rim,

`help' (leave the

elsewhere,

Brief
   descriptions of some of these groups are given in the BIOSCI FAQ,
posted
   in bionet.announce and available on net.bio.net in the directory
   /pub/BIOSCI/ or by e-mail from the BIOSCI staff at
biosci@net.bio.net.

   bit.listserv.*

   As their names imply, the bit.listserv newsgroups started out as
(and
   remain) automated mailing lists.  Most of these mailing lists
became
   so successful that gateways to Usenet were added by popular
demand.
   The Appendix includes 100 or so other mailing lists, most run via
the
   LISTSERV program, of interest to biologists;  those mailing lists
with
   Usenet gateways are listed in section 2.3.3, Gateways to Usenet.
   Charters for each of these groups can be obtained from the
listserver
   that administers each one.  See sections 2.3, Mailing Lists Using
   LISTSERV, and 2.3.1, Commands, for details about e-mail
subscriptions and
   commands for interacting with listserver programs.

   comp.theory.*

   Send e-mail to Erik Fair, fair@apple.com, or see the list of
mailing
   lists posted in news.answers for details about e-mail
subscriptions.

   embnet.*

   The European Molecular Biology Network (EMBnet) runs a group of
Usenet
   newsgroups that are distributed in Europe.  E-mail subscriptions
are
   available from nethelp@embl-heidelberg.de, and these newsgroups
can be
|  read and searched via gopher and WAIS on nic.switch.ch.  Send
general
   e-mail queries to embnet@comp.bioz.unibas.ch.

   info.*

   These groups are mailing lists with gateways to Usenet at the
University
   of Illinois.  See section 2.4, Other Mailing Lists, for e-mail
subscription
   information, or ask your local Usenet administrator to get these
groups.

-*- 2.2.3. Usenet FAQs about Usenet

   You are strongly encouraged to read the following introductory and
   etiquette FAQs before posting any messages to any newsgroup.  They
are
   what might be considered the "mandatory course" for new users, and
   are posted frequently in the Usenet newsgroup
news.newusers.announce.

   See section 4, Useful and Important FAQs, for a list of additional
FAQs
   of general use or interest to biologists, section 4.1, What's an
FAQ and
   where can I get one?, and sections 3.6.2 and 3.6.3 for
instructions on
   how to get copies by anonymous FTP or e-mail if you don't have
access
   to a Usenet reader.

              Title                            Archive filename

--------------------------------------------------------------------

        Introductory information (recommended reading)

   What is Usenet?                             what-is-usenet/part1
   Answers to Frequently Asked Questions       usenet-faq/part1
       about Usenet
   Introduction to news.announce        news-announce-intro/part1

        Etiquette (strongly recommended reading)

   A Primer on How to Work With the            usenet-primer/part1
       Usenet Community
   Emily Postnews Answers Your Questions       emily-postnews/part1
       on Netiquette
   Hints on writing style for Usenet           usenet-writing-style/
part1
   Rules for posting to Usenet                 posting-rules/part1

            Technical issues

   How to Create a New Usenet Newsgroup        creating-newsgroups/
part1
   USENET Software:  History and Sources       usenet-software/part1
   How to become a USENET site                 site-setup
   NetNews/Listserv Gateway Policy             bit/policy
   UNIX BBS Software FAQ with Answers          unix-faq/bbs-software
   Introduction to the news.answers        news-answers/introduction
       newsgroup
   Instructions for posting to news.answers    news-answers/guidelines

            Resource listings

   Mailing Lists Available in Usenet        mail/news-gateways/part1
   Publicly Accessible Mailing Lists        mail/mailing-lists/part[1-6]
   List of Periodic Information Postings    periodic-postings/part[1-6]
   List of Active Newsgroups            active-newsgroups/part[1-2]
   Alternative Newsgroup Hierarchies        alt-hierarchies/part[1-2]

-*- 2.2.4. Usenet by E-mail

|  Many people who do not have direct access to Usenet do have
Internet
|  access, and can read Usenet newsgroups via gopher (see section
3.6.4
|  below for an explanation of gopher).  Gopher is fine for reading