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PURDUE CYTOMETRY CONTROLS SOFTWARE MARKET AND FILTERS MAIL LIST

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Mitch Haynes - 17 Jan 2008 16:20 GMT
THE PROOF IS BEING DYSTROYED AS THE ARCHIVES ARE REMOVED!

From: J. Paul Robinson <j...@flowcyt.cyto.purdue.edu>
Date: Fri Dec 28 2007 - 13:43:46 EST
Beware, the end is nigh!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

PUCL- DELETES OR DIABLES  LINKS THAT ARE EVIDENCE OF EXCLUSIVE
VENDORS
AND PROOF OF FILTERING OUT VENDORS!

From : J. Paul Robinson <j...@flowcyt.cyto.purdue.edu> ... I will
probably get into seriuous trouble for what I am about to say, but
what the heck, ...

www.cyto.purdue.edu/hmarchiv/2005/0587.htm - 14k - Cached - Similar
pages - Note this
[ More results from www.cyto.purdue.edu ]

http://index.cc.purdue.edu:8765/query.html?col=pumerge&qt=purdue+cytometry+mail+
LIST+SOFTWARE&charset=iso-8859-1&si=0


ALL INFORMATION MUST BE TAKEN FROM VERITYHOUSE SOFTWARE SERVER

SAC Homepage - How do I join the Purdue Cytometry Discussion Group? -
8 visits - 2:01pm
Answer: The Purdue Cytometry discussion group is strictly for
discussion of scientific issues relating to the fields in which ISAC
is generally involved. ...
www.isac-net.org/content/view/16/78/ - 14k - Cached - Similar pages -
Note this

Re: [Fwd: flow cytometry
software will you trust Purdue..Lets play MONOPOLY]

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

Larry, we have about 3000 people on the Purdue discussion list which
is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.

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

Larry, we have about 3000 people on the Purdue discussion list which
is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.

Standard
Header|Full
Message View

J. Paul Robinson
<j...@flowcyt.cyto.purdue.edu>

ViewMonday, November 19, 2007 2:14:38 PM

To:Larry Farrell <farrl...@isu.edu>; mitchell haynes
<buybro...@yahoo.com>;
skel...@flowcyt.cyto.purdue.edu; Bartek Rajwa
ra...@flowcyt.cyto.purdue.edu

****Larry, we have about 3000 people on the Purdue discussion list
which is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.
***************************************************************************-
******************************************************

Larry

Sorry you are experiencing a problem

From the header - This is apparently coming from a Mitchel Haynes

mitchell haynes <buybro...@yahoo.com>
- is this correct?

I initially thought messages coming from this person were a scam and

challenged them when they started posting to our list as well. I had

someone do a check on them. it is apparent that they have written
some

software and they think its ants-pants. They have tried to post
things

on the Purdue list, they have used every possible website and email

discussion group to get cross listed to boost their ratings on
Google.

Basically I view their behavior as very tenuous and from the message
you

sent me, it appears that it is not appropriate to do what they are
doing...

I have taken the following action:

1. Steve Kelley has been instructed to remove their email and any

postings on the Purdue list. They are now banned

2. I am going to Copying Bartek Rajwa the editor of the ISAC site to

beware of them

3. I am contacting Google and other sites to let
them know that these

people are self-propagating links.

4. If I see any message that in any way impunes Purdue or our

reputation, I will go after them with every possible legal recourse
at

my disposal. We will not allow our reputation to suffer because of

commercial abuse.

5. You should ban this address, and basically indicate to your
members

that this is a scam. While they claim to be legitimate, they are
acting

exactly as any scam artist...I already told them that they were
acting

as scammers and they got upset with me...well, if they don't desist,

they will find out how much influence we actually have...

I will check the message

> Subject: flow cytometry software will you trust Purdue..Lets play

MONOPOLY

> Date: Mon, 19 Nov 2007 09:38:56 -0800 (PST)
> Organization: http://groups.google.com

and see if this is actually libelous - it appears to be - and if it
is,

I will close this person down really, really fast!!! (Steve please
check

out this message and make a copy)

Larry, we have about 3000 people on the Purdue discussion list which
is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.

I am sorry you are experiencing this problem, and we are happy to
help

in any way we can.

regards

paul Robinson

Professor, Purdue

*****************************************Larry, we have about 3000
people on the Purdue discussion list which is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.
***************************************************************************-
************

WITH EVERY INTERNATIONAL OUTLET THE MAIL LIST HAS WHY????WHY????WHY

3,000 PEOPLE ON THE LIST...

DOES IT SAY......THEY MUST HAVE TO GOT THROUGH WHO?

ONLY 3,000 PEOPLE?

IT IS INTERNATIONAL~!

***************************************************************************-
***********************************************
2007 End of year message from Purdue
*       This message: [ Message body ] [ More options ]
*       Related messages: [ Next message ] [ Previous message ]
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in
thread ] [ Replies ]
From: J. Paul Robinson <j...@flowcyt.cyto.purdue.edu>
Date: Fri Dec 28 2007 - 13:43:46 EST
Beware, the end is nigh!
No, not an apocalyptic prediction - but 2007 is definitely coming to
an
end. Not before time I would say - it s been a busy year. But I have
some strong words to end the year and I am going to say them!! Of
course
you don t have to read them!

Cytometry is now 40 years old and it s been sort of decaying a bit.
What
do I mean? I am amazed at how conservative and frankly boring the
field
has become. Why? It s time to move to the 21st century folks. I'm
getting older and frankly, its time to kick some butt as my younger
colleagues often say. We talk so much like it is the same old
cytometry
it has always been. Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!
True we need to do the core work and do it well, but lets not forget
that fundamental tools of cell analysis are changing and if we don't
keep ourselves up-to-date and educated on what's happening....before
we
know it, a new field will emerge and we will be like the old electron
microscopists who are still wondering what happened ......

I know most of us work in the field and like what we do, but I think
its
time to open up a little and try to do some serious integration of
our
field. It s not happening very effectively on the most part I would
say.
Cytometry is about integration of the tools of the field into the
vast
reaches of biological problems that we can contribute to solving.
Cytometry is about advancement of the field, that means always
looking
ahead. ISAC will soon be the International Society for Advancement of
Cytometry   a 21st century Society not a 20th century Society.

Cytometry is not flow cytometry!! Let s not kid ourselves about this
folks. Cytometry is about measuring cells - however you do it - and
flow
cytometry is just one component of many. I understand that it may be
the
only tool some of you use - I don t want to take away from that or
de-emphasize its value or importance. But, we so often hear people
talk
about our field only in context of just flow cytometry. Recently,
when
we polled the ISAC community on changing our name from "analytical
Cytology" to Advancement of Cytometry" we received comments like "hey
I
don t do flow cytometry, so why are you reducing the breadth of the
field?" Ouch - they think "cytometry" means "flow cytometry". We have
a
long way to go before we convince the community that we cover all
aspects of cytometry. And let s also remember the growing membership
in
India and China   (that s half the worlds population right there)
it
s
high time we paid much more attention to these countries as a field.
Awtar Krishan can t be the only person to drive cytometry training
and
education for 1.2 billion Indians can he? Well he has been up to now.
Who is taking on the mantle of training and education of cytometry in
China?

So here's the scoop. That's one of the reasons why the Purdue Web
portal
is going to change. We tried to make the change this past year, but
there were too many other things happening here to achieve it. But
come
middle of 2008, I am resolved that you will see a huge difference in
the
Purdue site. It s been the default cytometry communication portal now
for many, many years. We have focused on good clean fun with
cytometry
-
quality, timely, simple - no spam. Many people like that actually.
The
portal is almost overwhelming for us   22,000 daily page requests
with
over 2 Gigs daily download. In 2007 alone, downloads of 208,000
powerpoint files, 233,000 PDF files, 8800 movies, 38,000 word
document
files. The education pages and the Cytometry Discussion Archive are
the
most hit for sure. Over 125,000 distinct files from our portal were
accessed in 2007.

But all good things must come to an end. Come July 2008, the usual
Purdue web portal may well be no more. It will be replaced with
something entirely new. Hopefully most will find it more useful and
relevant - some will not like it. Maybe we will be able to make
everyone
happy....ha!..C'est la vie. Some of you will be beta testers and
advisers I hope.

So my best wishes to all in the cytometry field for 2008. Regarding
the
past year on the discussion list, its been lively, with an average of
7
messages per day with 754 different individuals submitting at least
one
message. 139 messages had at least 6 responses.  There were 1205
unique
subject lines. Subscribers came from 64 top level domains. The usual
bunch of suspects answered lots of messages and Marty Bigos seems to
have too much time as he answered the most (thanks Marty!!).
Tragically,
the second most prolific responder was Randy Fisher who passed away
on
December 5.  Randy's responses were always short, to the point and
accurate. It hurts to lose one of our own, particularly when it's one
of
our most active members. But that s the point isn't it. For many
years
to come, we have the value of Randy's hundreds of suggestions over
the
years archived for the many new people who enter our field. Many of
you
probably never actually met Randy - but I bet most of you feel you
knew
him. One of the mysteries of the web I suppose. Our condolences to
Randy's family - perhaps they didn't know how many people knew Randy
"electronically" - but we all did. You know we are a small field when
it
comes to the big world of science so when we lose one person, the
entire
field morns.

To end 2007, let me make a big plug for a program we began at the
2006
ISAC congress. Gary Durack from iCyt and myself started a small
not-for-profit charity called "Cytometry for Life" in response to
Stephen Lewis' compelling plea for some low cost CD4 devices. Our
field
has done a lot of talking about this, but only a few people have
really
tried to do anything practical. Well, folks we have all been doing
cytometry for a very long time - it's time to do something.
"Cytometry
for life" (http://www.cytometryforlife.org) is working hard. We have
made tremendous progress in just one year. It would be great if you
all
decided to jump on board and play a small part. You can give money,
advice, moral support, talk to your politicians, community health-
care,
charities, whatever. But get involved as be recognized as the
cytometry
community to solve this problem of bringing low cost, portable
devices
to the 65% or more of African's who don t live in the cities and
towns
where current CD4 technologies are available. Our goal is to work in
areas not being served by current technologies. We have heard these
calls before, but folks we have to deal with this problem - it's your
problem if you call yourself a "cytometry" person. Email me if you
can
help - consider donating to the program, let's make it work. By the
end
of 2008, I want to be telling you that the program is getting to
people
who need this desperately. Help us achieve that for 2008.

I hope many of you got hold of a copy of our new double DVD set
Cytometry   60 years of Innovation    if not ask your local rep from
virtually any company in our field. It might give you a good sense of
how strong the foundation in our field really is. I will see many of
you
at the 2008 congress in Budapest. I know some of you think its going
to
be expensive so I took several hours myself and created a webpage for
the cheap ones out there so you have no excuses not to go...
(http://www.cyto.purdue.edu/flowcyt/cheapflights1.htm).

It's been a privilege to serve for the past 19 months as President of
ISAC. I will gladly pass that hat to Bob Murphy in May. ISAC is alive
and well  - membership is growing daily. I would not be surprised to
see
us top 2000 by the end of the Congress in May. I know that about 60%
of
the members of this list are NOT ISAC members. Perhaps you should
consider joining the Society that keeps many of you in business?
http://www.isac-net.org/

My best wishes for you all in 2008 from Purdue
Paul

--
J. Paul Robinson
SVM Professor of Cytomics
Professor of Immunopharmacology & Biomedical Engineering
Director, Purdue University Cytometry Laboratories
President, International Society for Analytical Cytology

***************************************************************************-
**************************************************
From: J. Paul Robinson <j...@flowcyt.cyto.purdue.edu>
Date: Fri Dec 28 2007 - 13:43:46 EST
Beware, the end is nigh!
No, not an apocalyptic prediction - but 2007 is definitely coming to
an
end. Not before time I would say - it s been a busy year. But I have
some strong words to end the year and I am going to say them!! Of
course
you don t have to read them!

Cytometry is now 40 years old and it s been sort of decaying a bit.

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!

Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!
***************************************************************************-
****************************************************
IS J PAUL ROBINSON TALKING ABOUT KANECKI ASSOCIATES INC?

WHY DID HE CALL KANECKI ASSOCIATES INC SCAMMERS FOR SENDING SOFTWARE?

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...?
***************************************************************************-
*************************************************
SO HOW COULD SO MANY SALES AND DOWNLOADS GO UNDETECTED BY OTHER SMALL
COMPANIES
AND HOW DO YOU GET ON THE PURDUE CYTOMETRY MAIL LIST?
***************************************************************************-
****************************************************..
Wake up people - times are changing - look at all
these new small companies trying to stick their noses in "our" field!
***************************************************************************-
*****************************************************
Re: [Fwd: flow cytometry
software will you trust Purdue..Lets play MONOPOLY]

Standard
Header|Full
Message View

J. Paul Robinson
<j...@flowcyt.cyto.purdue.edu>

ViewMonday, November 19, 2007 2:14:38 PM

To:Larry Farrell <farrl...@isu.edu>; mitchell haynes
<buybro...@yahoo.com>;
skel...@flowcyt.cyto.purdue.edu; Bartek Rajwa
ra...@flowcyt.cyto.purdue.edu

Larry

Sorry you are experiencing a problem

From the header - This is apparently coming from a Mitchel Haynes

mitchell haynes <buybro...@yahoo.com>
- is this correct?

I initially thought messages coming from this person were a scam and

challenged them when they started posting to our list as well. I had

someone do a check on them. it is apparent that they have written
some

software and they think its ants-pants. They have tried to post
things

on the Purdue list, they have used every possible website and email

discussion group to get cross listed to boost their ratings on
Google.

Basically I view their behavior as very tenuous and from the message
you

sent me, it appears that it is not appropriate to do what they are
doing...

I have taken the following action:

1. Steve Kelley has been instructed to remove their email and any

postings on the Purdue list. They are now banned

2. I am going to Copying Bartek Rajwa the editor of the ISAC site to

beware of them

3. I am contacting Google and other sites to let
them know that these

people are self-propagating links.

4. If I see any message that in any way impunes Purdue or our

reputation, I will go after them with every possible legal recourse
at

my disposal. We will not allow our reputation to suffer because of

commercial abuse.

5. You should ban this address, and basically indicate to your
members

that this is a scam. While they claim to be legitimate, they are
acting

exactly as any scam artist...I already told them that they were
acting

as scammers and they got upset with me...well, if they don't desist,

they will find out how much influence we actually have...

I will check the message

> Subject: flow cytometry software will you trust Purdue..Lets play

MONOPOLY

> Date: Mon, 19 Nov 2007 09:38:56 -0800 (PST)
> Organization: http://groups.google.com

and see if this is actually libelous - it appears to be - and if it
is,

I will close this person down really, really fast!!! (Steve please
check

out this message and make a copy)

Larry, we have about 3000 people on the Purdue discussion list which
is

primarily about cytometry - and a lot of flow cytometry - to join,

people actually have to go through me, and we review every person who

comes on.

I am sorry you are experiencing this problem, and we are happy to
help

in any way we can.

regards

paul Robinson

Professor, Purdue
***************************************************************************-
**************************************************
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28 Mar 07
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Purdue Cytometry Mailing List: Applications Specialist - iCyt -
... Northwest Cytometry Users Group and Cascade Cytometry Users Group
are pleased to announce the 2007 NW Regional Cytometry Meeting,
which ... Tree Star, Union Biometrica, and Verity Software House. ...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0333.htm - 7.0KB
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30 Jan 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... DIVA Software on MAC
Intel Computers Pamela Shaw (Wed Dec 13 2006 - 13:25:52 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: RE: Diva 4.0 files
... Purdue Cytometry Mailing List: RE: Diva 4.0 files ... Mark E.
Munson Sales Manager Verity Software House, Inc. 45A Augusta Road PO
Box 247 Topsham, ME 04086 Phone: 207-729-6767 x191 Fax:
207-729-5443 ...
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20 Aug 04
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Purdue Cytometry Mailing List: Free WinList Update Available
... Purdue Cytometry Mailing List: Free WinList Update Available ...
Mark E. Munson Sales Manager Verity Software House, Inc. 45A
Augusta ...
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02 Apr 03
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Purdue Cytometry Mailing List: Extracting data from FACS measurements
... Purdue Cytometry Mailing List: Extracting data from FACS
measurements ... Mark E. Munson Sales Manager Verity Software House,
Inc. 45A Augusta ...
http://www.cyto.purdue.edu/hmarchiv/2003/0491.htm - 6.1KB
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18 Mar 03
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Purdue Cytometry Mailing List: Course Announcement - 25th ANNUAL
COURSE IN FLOW CYTOMETRY
... Purdue Cytometry Mailing List: Course Announcement - 25th ANNUAL
COURSE IN FLOW CYTOMETRY ... Mark E Munson Verity Software House,
Inc.
PO Box 247 ...
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23 Oct 01
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Purdue Cytometry Mailing List: New Purdue DVD - Cytometry Volume 10
... Purdue Cytometry Mailing List: New Purdue DVD - Cytometry
Volume ... Optical, Macs Miltenyi Biotec, SouthernBiotech, Verity
Software Accuri, Chroma, Coherent, Cyopeia, Duke ...
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17 Nov 07
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Purdue Cytometry Mailing List: New England Cytometry Meeting
Registration
... Purdue Cytometry Mailing List: New England Cytometry Meeting
Registration ... speakers this year: ... C. Bruce Bagwell, MD, Ph.D.
-
Verity Software House "Probability State Models: A new paradigm for
cytometry analysis ...
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18 Sep 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... PML protein Jan
Nelson (Wed Dec 16 1998 - 16:56:58 EST) ... Permeabilization and
Anti-
Coagulants Vincent Falco (Wed Dec 16 1998 - 09:07:16 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... Sales position in
Germany Brian Hall (Thu Dec 18 1997 - 12:23:18 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... Summarize "Free
software" Dorte Christiansen (Fri Dec 12 2003 - 07:45:44 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... staining
DARZYNKIEWICZ ZBIGNIEW (Wed Dec 20 2000 - 18:42:40 EST) ... CD45
expression on ADP-activated murine platelets Gregor Rothe (Thu Dec 21
2000 - 07:29:44 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Subject
... Purdue Cytometry Mailing List: By Subject ... 2444 messages
sorted
by: [ author ] [ date ] [ thread ] [ attachment ] Other mail
archives ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... is good enough?
Uriel
TK (Tue Dec 14 2004 - 16:04:58 EST) ... RE: How close compensation is
good enough? Gerstein, Rachel (Thu Dec 16 2004 - 07:07:48 EST) ...
http://www.cyto.purdue.edu/hmarchiv/2004/thread.htm - 363.4KB
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30 Jan 07
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Purdue Cytometry Mailing List: Applications Specialist - iCyt -
... Northwest Cytometry Users Group and Cascade Cytometry Users Group
are pleased to announce the 2007 NW Regional Cytometry Meeting,
which ... Tree Star, Union Biometrica, and Verity Software House. ...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0234.htm - 6.7KB
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30 Jan 07
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Purdue Cytometry Mailing List: By Date
... Purdue Cytometry Mailing List: By Date ... Re: Cell-Dyn 4000
Howard Shapiro (Wed Dec 18 2002 - 21:51:24 EST) ... pluronic acid
g...@biocfarm.unibo.it (Thu Dec 19 2002 - 07:07:54 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... free FACS analysis
software Wolfraim, Lawrence (NCI) (Wed Dec 19 2001 - 10:28:23
EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Thread
... Purdue Cytometry Mailing List: By Thread ... WinMDI software -
long filename problem WAS Doubts About WinMDI software Alan Bishop
(Thu Dec 01 2005 - 19:07:54 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Author
... Purdue Cytometry Mailing List: By Author ... 2 flow cytometry job
openings at Biogen (Thu May 23 2002 - 07:09:37 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: Re: DIVA Software on MAC Intel Co
... Purdue Cytometry Mailing List: Re: DIVA Software on MAC Intel
Co ... screen display issue, that made it difficult to read the text.
Verity provided us with a patch for this in remarkably little
time ...
http://www.cyto.purdue.edu/hmarchiv/2006/1979.htm - 6.9KB
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15 Dec 06
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Purdue Cytometry Mailing List: Re: Log-like transforms
... Purdue Cytometry Mailing List: Re: Log-like transforms ...
purposes. > > > > Bruce > > > > C. Bruce Bagwell MD, Ph.D. > >
President > > Verity Software House > > 45A Augusta Road > > PO Box
247 > > Topsham, ME 04086 ...
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22 Mar 06
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Purdue Cytometry Mailing List: RE: Software for merging FSC 3 fi
... Purdue Cytometry Mailing List: RE: Software for merging FSC ...
J.
Herbert Technical Support Manager Verity Software House, Inc. PO Box
247 ...
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03 Feb 05
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Purdue Cytometry Mailing List: RE: Software recommendations for
... Purdue Cytometry Mailing List: RE: Software recommendations
for ... Mark E. Munson Sales Manager Verity Software House, Inc. 45A
Augusta ...
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25 Oct 04
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Purdue Cytometry Mailing List: Analysis Software
... Purdue Cytometry Mailing List: Analysis Software ... Donald J.
Herbert Technical Support Manager Verity Software House, Inc. PO Box
247 45A Augusta Road Topsham, ME, USA 04086 ...
http://www.cyto.purdue.edu/hmarchiv/2004/1196.htm - 7.1KB
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30 Jun 04
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Purdue Cytometry Mailing List: Re: Software to overlay dot plots for
analysis
... Purdue Cytometry Mailing List: Re: Software to overlay dot plots
for analysis ... Quest for OSX - a new release from BD 4. WinList -
Verity Software House 5. FCS Express - from www.denovosoftware.com
...
http://www.cyto.purdue.edu/hmarchiv/2003/0979.htm - 5.6KB
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28 May 03
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Purdue Cytometry Mailing List: RE: Kolmogorov-Smirnov (Is there a
better solution?)
... Purdue Cytometry Mailing List: RE: Kolmogorov-Smirnov (Is
there ... Bruce Bagwell, MD, Ph.D. Verity Software House, Inc.
Published: Clinical Immunology ...
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18 Apr 03
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Purdue Cytometry Mailing List: Re: non-radioactive LPA and responses
to query on LPAs
... PKH Proliferation assays by flow cytometry Organization: Verity
Software House ... dartmouth.edu (Alice L. Givan) ModFit software
from
Verity has a "Proliferation Wizard" that ...
http://www.cyto.purdue.edu/hmarchiv/2002/1701.htm - 17.3KB
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20 Aug 02
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Purdue Cytometry Mailing List: RE: query on LPAs: replacing tritiated
thymidine with flow
... Purdue Cytometry Mailing List: RE: query on LPAs: replacing ...
J.
Herbert Technical Support Manager Verity Software House, Inc. PO Box
247 ...
http://www.cyto.purdue.edu/hmarchiv/2002/1649.htm - 9.5KB
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13 Aug 02
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Purdue Cytometry Mailing List: Re: Last Message on Purdue Cytometry
CD-
ROM Vol 6
... Cytometry Mailing List <cytome...@flowcyt.cyto.purdue.edu> ...
Associates, Inc; Spherotech, Tree Star, Verity Software, Spherotech,
Tree Star, Verity Software. ...
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03 Apr 02
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Purdue Cytometry Mailing List: UV excitable dyes for surface
phenotyping - ELF-97?
... Purdue Cytometry Mailing List: UV excitable dyes for surface
phenotyping - ELF-97? ... RE: Bacteria sorting?" ... Previous
message:
VSH - Tech Support: "Announcing User Forum at Verity Software House,
Inc." ...
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12 Mar 02
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Purdue Cytometry Mailing List: 25th ANNUAL COURSE IN FLOW CYTOMETRY:
BOWDOIN COLLEGE, ...
... Purdue Cytometry Mailing List: 25th ANNUAL COURSE IN FLOW
CYTOMETRY: BOWDOIN COLLEGE, BRUNSWICK MAINE - JUNE 2002 ... Mark E
Munson Verity Software House, Inc. PO Box 247 Topsham, ME 04086 Tel:
(207) 729-6767 x105 ...
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22 Jan 02
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Purdue Cytometry Mailing List: Re: G4's will run OS8.6 (ours sur
... Purdue Cytometry Mailing List: Re: G4's will run OS8.6 (ours
sur ... evidenced by the hundreds of labs running their XL software
under > DOS (yuk!). Maybe Verity or TreeStar will make some inroads
if
we demand ...
http://www.cyto.purdue.edu/hmarchiv/2000/0156.htm - 8.0KB
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13 Jan 00
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Purdue Cytometry Mailing List: G4's will run OS8.6
... Purdue Cytometry Mailing List: G4's will run OS8.6 ... edge
software, evidenced by the hundreds of labs running their XL software
under DOS (yuk!). Maybe Verity or TreeStar will make some inroads if
we demand state of ...
http://www.cyto.purdue.edu/hmarchiv/2000/0140.htm - 7.4KB
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13 Jan 00
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Purdue Cytometry Mailing List: RE: flow cytometry course in June
... Purdue Cytometry Mailing List: RE: flow cytometry course in
June ... Brunswick Maine. Course organizer is C. Bruce Bagwell. I
think that Verity Software may be sponsoring it, as their information
is on some of ...
http://www.cyto.purdue.edu/hmarchiv/1998/0905.htm - 5.1KB
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10 Apr 98
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Purdue Cytometry Mailing List: RE: utility software to convert fcs1.0
to fcs2.0
... Purdue Cytometry Mailing List: RE: utility software to
convert ...
PC, I suggest you contact Verity Software (207-729-6767) . I
quickly ...
http://www.cyto.purdue.edu/hmarchiv/1998/0707.htm - 5.9KB
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27 Mar 98
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Purdue Cytometry Mailing List: RE: utility software to convert fcs1.0
to fcs2.0
... Purdue Cytometry Mailing List: RE: utility software to convert
fcs1.0 to fcs2.0 ... Since you are using the PC, I suggest you
contact
Verity Software (207-729-6767) .  I quickly tried this function this
AM ...
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27 Mar 98
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Purdue Cytometry Mailing List: FW: FCS file transfer between BD Diva
(PC) and CellQuest ( ...
... Purdue Cytometry Mailing List: FW: FCS file transfer between ...
morphosys.com> Date: Thu Nov 08 2007 - 07:14:16 EST ...
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10 Nov 07
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Purdue Cytometry Mailing List: RE: 2008 NW Regional Cytometry Meeting
announcement
... Purdue Cytometry Mailing List: RE: 2008 NW Regional Cytometry
Meeting announcement ... Bioscience, Miltenyi Biotec, MDA Analytical
Technologies, Partec, Tree Star, Union Biometrica, and Verity
Software
House. ...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1644.htm - 6.5KB
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03 Nov 07
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Purdue Cytometry Mailing List: New England Cytometry Meeting
Registration Reminder
... Purdue Cytometry Mailing List: New England Cytometry Meeting
Registration Reminder ... speakers this year: ... C. Bruce Bagwell,
MD, Ph.D. - Verity Software House "Probability State Models: A new
paradigm for cytometry analysis ...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1458.htm - 8.6KB
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04 Oct 07
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Purdue Cytometry Mailing List: New England Cytometry Annual Meeting
Registration and Hotel ...
... Purdue Cytometry Mailing List: New England Cytometry Annual
Meeting Registration and Hotel Information ... year: ... C. Bruce
Bagwell, MD, Ph.D. - Verity Software House "Probability State Models:
A new paradigm for cytometry ...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1411.htm - 8.8KB
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23 Sep 07
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Purdue Cytometry Mailing List: SUMMARY of Responses: Biexponential
Plots and CSFE
... Purdue Cytometry Mailing List: SUMMARY of Responses:
Biexponential
Plots and CSFE ... FCS3.0 digital data was presented by Mark Munson
of
Verity Software House (makers of Modfit). Thanks Mark, it worked
great ...
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22 Sep 07
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Purdue Cytometry Mailing List: Invitation for Vendor Sponsorship for
the New England ...
... to announce the New England Cytometry Users Group Fall meeting;
Current Concepts in Flow and Image Cytometry which will be held
October ... Bruce Bagwell, MD, Ph.D. - Verity Software House http://www.vsh.com
...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1175.htm - 8.6KB
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11 Aug 07
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Purdue Cytometry Mailing List: RE: CFSE graphs (UNCLASSIFIED)
... Verity's MODFIT software has a very nice tool for
proliferation ... Stelekati [mailto:e...@fz-borstel.de] >>>Sent:
Monday, March 26, 2007 6:58 AM >>>To: Cytometry Mailing List

>>>Subject: CFSE graphs >>> >>>Dear all, >>>I want to ...

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30 Mar 07
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Purdue Cytometry Mailing List: Applications Specialist - iCyt -
... Purdue Cytometry Mailing List: Applications Specialist - iCyt ...
Sponsored by: The National Flow Cytometry Resource (NFCR) and Verity
Software House ...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0214.htm - 8.4KB
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30 Jan 07
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Purdue Cytometry Mailing List: By Date
... Purdue Cytometry Mailing List: By Date ... RE: DIVA SOFTWARE ON
INTEL CORE 2 DUO PROCESSOR Guy Hermans ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Author
... Re: Free Flow Cytometry Analysis software? (Fri Apr 14 2006 -
02:56:18 EDT) ... CORRECTION- Chesapeake Cytometry Consortium (Thu
Sep
07 2006 - 12:20:05 EDT) ...
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30 Jan 07
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Purdue Cytometry Mailing List: RE: Partec CyFlow ML? (was Re:
Analyzers)
... Purdue Cytometry Mailing List: RE: Partec CyFlow ML? (was Re:
Analyzers) ... Received on Fri Nov 30 18:07:07 2007 ...
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01 Dec 07
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Purdue Cytometry Mailing List: RE: Cytometry software for linux
... Purdue Cytometry Mailing List: RE: Cytometry software for
linux ... ugr.es] > Sent: Monday, September 10, 2007 12:28 PM > To:
Cytometry Mailing List > Subject: Cytometry software ...
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15 Sep 07
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Purdue Cytometry Mailing List: Re: Summary and replies on PCH101
... Purdue Cytometry Mailing List: Re: Summary and replies on
PCH101 ... From: clare Rogers <rog...@med.umich.edu> Date: Fri Sep 07
2007 - 17:04:21 EDT ...
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11 Sep 07
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Purdue Cytometry Mailing List: For Sale BD FACSVantage with DiVa
option
... Purdue Cytometry Mailing List: For Sale BD FACSVantage with DiVa
option ... ml tubes -- PC and Mac computers with all original BD
software (DiVa [PC] and CELLQuest [Mac.]) NOTE: I will only
guarantee ...
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01 Sep 07
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Purdue Cytometry Mailing List: BD bead array software and FC500s
... Purdue Cytometry Mailing List: BD bead array software and
FC500s ... From: Stephen Taylor - Porton Down
<Stephen.Tay...@hpa.org.uk> Date: Thu Aug 16 2007 - 07:01:09 EDT ...
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18 Aug 07
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Purdue Cytometry Mailing List: RE: Upgrading Computers and BD
Software
... Purdue Cytometry Mailing List: RE: Upgrading Computers and BD
Software ... utoronto.ca> > To: Cytometry Mailing List
<cytome...@flowcyt.cyto.purdue.edu> > Date: 8/13/2007 ...
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17 Aug 07
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Purdue Cytometry Mailing List: FACSort for sale.
... Purdue Cytometry Mailing List: FACSort for sale. ... Blue laser
and sorting option (bought in Oct. 1997) with Cellquest software
installed in Power Macintosh computer. The laser current is around
5.70Amps ...
http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0616.htm - 5.6KB
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02 May 07
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Purdue Cytometry Mailing List: By Date
... Purdue Cytometry Mailing List: By Date ... Summarize "Free
software" Dorte Christiansen (Fri Dec 12 2003 - 07:45:44 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Author
... Purdue Cytometry Mailing List: By Author ... Flow facility, again
(Fri Dec 04 1998 - 03:50:07 EST) ... Flow facility (Mon Nov 23 1998 -
07:07:29 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Date
... Purdue Cytometry Mailing List: By Date ... PML protein Jan Nelson
(Wed Dec 16 1998 - 16:56:58 EST) ... Permeabilization and Anti-
Coagulants Vincent Falco (Wed Dec 16 1998 - 09:07:16 EST) ...
http://www.cyto.purdue.edu/hmarchiv/1998/index.htm - 491.8KB
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30 Jan 07
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Purdue Cytometry Mailing List: By Subject
... Purdue Cytometry Mailing List: By Subject ... owner-cytometry
(Wed
Jun 07 2006 - 10:19:50 EDT) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Subject
... Purdue Cytometry Mailing List: By Subject ... Rosie Clarke (Fri
Feb 07 2003 - 07:14:11 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Author
... Re: Réf. : Free software? (Fri Dec 19 2003 - 22:39:46 EST) ... UV
vs Krypton UV (Thu Feb 20 2003 - 19:09:39 EST) ... RE: malignant
plasma cell detection by flow cytometry (Fri Feb 07 2003 - 19:48:43
EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Date
... Purdue Cytometry Mailing List: By Date ... Thu Dec 16 2004 -
07:07:48 EST ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Author
... Purdue Cytometry Mailing List: By Author ... Re: OS9+Cellquest
(Tue Mar 07 2000 - 08:07:34 EST) ...
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30 Jan 07
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Purdue Cytometry Mailing List: By Date
... Purdue Cytometry Mailing List: By Date ... Thu Dec 21 2000 -
07:29:44 EST ...
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Purdue Cytometry Mailing List: By Subject
... Purdue Cytometry Mailing List: By Subject ... JSC-SD) (Wed Sep 06
2000 - 08:37:10 EST) ... Walker, Don (SEA) (Thu Aug 31 2000 -
14:09:16
EST) ... Palkowetz, Kimberly H. (Tue Aug 29 2000 - 07:49:22 EST) ...
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30 Jan 07
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LIST+SOFTWARE&charset=iso-8859-1&si=0


PURDUE CONTROLS THE CYTOMETRY SOFTWARE WITH ONE PROTAL.

VERITY AND THE PURDUE CYTOMETRY MAIL LIST.

WHY DOES PURDUE HAVE THE DIRECT LINK TO ISAC?

On Thursday, December 12, 2002, at 05:43 AM, J.Paul Robinson wrote:
> Colleagues: I am sending out a copy of a message I have just sent to
> RNWAY laboratories of South Korea and all 20 worldwide distributors of
> RNWAY products most of whom are highly reputable companies. I am only
> sending it to you because I am going to propose to create a small
> "SCIENTISTS against EMAIL ABUSE"  type of revolutionary action.........

Paul,

Sounds like you're advocating fighting disease by eradicating the
antigen instead of boosting the immune response.  You can organize
all
you want on eliminating the pest, but until they put a stamp tax on
email, a better approach is to let the
messages be out there, but have them filtered to oblivion before you
ever see them.

In your case, the postmaster at Purdue is probably already filtering
millions of messages a day that come to the thousands of email users
on
campus. They are probably capable of shutting down any RNWAY mail,
and
spreading the word to other postmasters that they also should filter
those messages.

So if you can get the IT people at the university to tighten their
sieve, that's best. Otherwise you have to switch to an email program
that has good junk filters.  I think I get 500+ messages a day, and
only 10 to 20 make it past the junk filter.
Until last summer I was using Outlook Express and spam was a huge
problem. Since then I switched to the free Mail program in OS X,
which
just added special features for spam detection and removal.  Its
probably 97% effective, and I haven't found any false positives.
So, of course, the best answer is to get a Mac  :)

I'm sure the PC mail clients are addressing this issue as well.  I
believe there are central databases of offenders so programs can
learn
from others which messages to delete.   I would imagine this is the
most important feature in any email program sold these days, so I bet
Eudora or other third party mail programs have this solved.

There's a lot of information on the subject at:

http://spam.abuse.net/

Whether you fight the problem on the server or the client, it
definitely is worth getting it cleaned up.   I found it screwed up my
whole communications process because every time I wanted check email,
I
had to wade through dozens or hundreds of useless ads.

Adam

---------------------------------------------------
Adam Treister
a...@treestar.com
www.flowjo.com  800-366-6045

HERE IS WHAT YOU DO NOT SEE....HOW THE MARKET IS ON THE PURDUE
CYTOMETRY MAIL LIST.
Verity House software
RE: gate-specific data cropping
*    This message: [ Message body ] [ More options ]
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From: VSH Tech Support <Tech@vsh.com>
Date: Fri Feb 16 2007 - 09:01:56 EST
Stevan

At the risk of sounding like a commercial, WinList can do exactly what
you
want.  The problem of "sucking up air" or perhaps having a clogged
nozzle at
the end of a run has gotten all of us at one time or another, and then
the
data (most of which is probably fine) appears to be unusable.  WinList
addresses this issue with the FTIM parameter, which is basically a
"chronology" parameter defined over 1024 channels.  Each event is
assigned
an FTIM channel based on its order in the listmode file, channel zero
having
the first n/1024 events, and channel 1023 having the last n/1024
events.

Displaying a 2P dot plot of FTIM vs. side scatter, for example, will
clearly
show the aberrant events.  You may then gate on the "good" events, or
gate
out the "bad" events.  Either way, you can salvage an otherwise bad
run.

You can also save the gated listmode using WinList's Save Data Source
option, and it will contain only
the "good" events.  Another feature of the Save Data Source option is
the
ability to set the number of events to save in the listmode file,
which at
least partially addresses the desire to save a larger file into
smaller
segments that will each have the same number of events within given
regions,
as you are requesting.

Best regards,
Don
Donald J. Herbert
Technical Support Manager
Verity Software House

-----Original Message-----
From: Stevan Lauriault [mailto:stevan@lauriault.com]
Sent: Friday, February 09, 2007 6:24 PM
To: cyto-inbox
Subject: Re: gate-specific data cropping

Thanks for your very helpful comments.    I guess what I am trying to get
at
is this: is
there any analysis software available that can reduce list mode data
in a
reverse order-specific matter (in reverse sequence)?  Correct me if
I'm
wrong, but I believe this function would also help in the event that a
user
lets a sample run dry and sucks up air bubbles, or over collects their
intended gating target (for example, in acquisition and storage, 5000
of
R1).

Thanks,

Stevan
---------- Original Message ----------------------------------
From: "Byron Ellis" <bcellis@stanford.edu>
Date:  Wed, 7 Feb 2007 16:21:28 -0800

>On 2/7/07, Stevan Lauriault <stevan@lauriault.com> wrote:
>> Hi and thanks,
>>
>> Since we want to directly compare MFIs (in FL2) between any two
>> subsets (R1 vs. R3)
>that are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in
>separate sample tubes would introduce the extra probability of
>experimental
error between sample tubes.
>Directly comparing the subsets from the same sample tube, and even
>better, the same data set, would eliminate this extra unknown.
>
>It doesn't necessarily eliminate the unknown, it may just keep you from
>finding out about it. If you were to prepare one sample on Monday, see
>significant differences, celebrate, etc and then on Wednesday prepare
>another sample where you didn't you'd probably want to know that (and
>figure out why). Simply taking the FACS tube off the cytometer and
>putting it back on won't give you that information. Now, would I be
>surprised if that actually happened in your case? Yes.
>Would I do replicates anyway? Yes.
>
>> Let us say we have acquired 100,000 total events (stained with 3
>> fluorochromes,
>measured in FL1, FL2, and FL4 respectively).  We are using a bivariate
>dot plot of FL1 vs. FL4 in which we are isolating 3 subsets (R1, R2,
>and R3) based on their relative expressions of FL1 vs. FL4.  We then
>want to compare the MFIs, as measured in FL2, among these subsets.
>Within those 100,000 total events, there are 500 of R1, 700 of R2 and
>1200
of R3.

>> If we crop the 100,000 total events to 75,000 total events (from the
>> top in
>stack-collected data), there will become exactly 500 events in the R2
region. If we
crop
>the 100,000 total events to 40,000 total events, there will become 500
events in R3.

>> Now the three populations; R1, R2, and R3 each have exactly 500 total
>> events, and we
>can directly compare MFIs among the subsets that have identical sample
sizes.    We could
>also then say that, when comparing means between these subsets under
>identical experimental conditions, Rx gives a consistently higher
fluorescent signal than Ry.

>Well, depending on what you're doing (you've never said how you intend
>to compare means), equal sample sizes is not particularly required so
>there's no particular reason to cut the data to obtain equal sample
>sizes. For example, one-way ANOVA (or one-way ANOVA with repeated
>measure in the event that you chose to do _real_ replicates), which
>simply says "they're different" (there are other tests, variants of
>one-sided t-tests essentially, that give you directionality statements
>such as mu_{R_1} > mu_{R_2} ). In this case your assumptions are:
>
>1. Each group is independent
>2. Normality of group populations (or at least "close enough" to
>Normal) 3. The _population_ variances of the dependent variable for
>each group are equal (or pretty close). (Actually check this. It would
>be unsurprising to encounter large differences in the population
>variances among your different groups).
>
>Like I say, it depends a bit on what you intend to do for your
>analysis. For example, _two_-way ANOVA actually expects equal sample
>sizes.
>
>> Is this a reasonable strategy?  Is there any software available that
>> can perform this
>function?
>
>On an FCS file directly? Probably not (neither the manipulation of the
>flow data nor the testing). Once you've got the data out of FCS form
>and appropriately labeled with group membership or split into separate
>files or something similar, then any reasonable statistics package
>(Excel is not included in the list of reasonable statistics packages)
>can perform the statistical tests.
>
>Personally, I use R (http://www.r-project.org) for analyzing all the
>flow data I have, but it can be intimidating for new users (though
>extremely powerful once you learn to use it). There are two packages in
>R for manipulating flow data at the moment (prada and rflowcyt),
>available through the Bioconductor Project
>(http://www.bioconductor.org) that can actually read in and manipulate
>FCS data directly or slightly manipulated data from say FlowJo (so you
>can do your gating there for example). I'm also part of a group made up
>of the people who did rflowcyt and prada that are making a combined
>package of the best bits of both (and some other new bits) that we
>expect to be available in the next Bioconductor release (probably
>sometime in April).
>
>Hope that helps,
>
>Byron
>
>> Kind Regards,
>>
>> Stevan Lauriault
>>
>> ---------- Original Message ----------------------------------
>> From: "Byron Ellis" <bcellis@stanford.edu>
>> Date:  Tue, 6 Feb 2007 12:17:35 -0800
>>
>> >Speaking as a statistician, I would not count running the same tube
>> >3 times or simply cutting the FCS file (the two are equivalent) as
>> >three replicates so I wouldn't do either to achieve what you want
>> >(though I can imagine situations where you would resample to
>> >calculate statistics). To get three replicates you would have to
>> >prepare three separate samples---you're interested in the
>> >variability of the mean due to experimental error as well as the
>> >biological variability of the cells and a single sample preparation
>> >only
captures the latter.

>> >On 2/5/07, Stevan Lauriault <stevan@lauriault.com> wrote:
>> >> Dear All,
>> >>
>> >> Question:
>> >>
>> >> We are isolating leukocyte subsets to measure and compare relative
>> >> levels of
>expression
>> >> of certain antigens.  For example, there are three subsets within
>> >> a bivariate dot
>plot;
>> >> gated on R1, R2 and R3 respectively, and we would like to
>> >> statistically analyze the relative mean fluorescence intensities
>> >> of a
biomarker, among the subsets.

>> >> To get statistically comparable sample sizes among these subsets,
>> >> we are running
the
>same
>> >> tube three times and changing the storage criteria to 500 events
>> >> for each subset (example, the first run is 500 events of R1, the
>> >> second 500 of R2, and the third is
>500
>> >> of R3).  Instead of repeating the same tube three times, and
>> >> wasting valuable
>sample, it
>> >> seems like a good idea to "crop" a preexisting data file of, for
>> >> example, 100,000
>total
>> >> events, three times to get an identical sample size for all three
>> >> gated subsets
(R1,
>R2,
>> >> and R3).
>> >>
>> >> Scientifically, this shouldn't be a problem, since flow cytometry
>> >> data is collected randomly within the same sample tube.  Not only
>> >> could we run one acquisition to get different monocyte subset
>> >> populations, but also to statistically compare constant
>numbers
>> >> of monocytes, PMNs, lymphocytes, lymphocyte subsets, etc. However,
>> >> I can see why
>some
>> >> scientists might be uneasy with the idea of manipulating raw
>> >> list-mode
data.

>> >> However, Since the data is collected randomly from the same
>> >> sample, doing this
>should
>> >> give exactly the same readings as if we just collected less
>> >> events, since we would
>only
>> >> be cropping (from stack-collected data) the most recent events
collected.

>> >> Currently, we are acquiring 3 different data files for each tube,
>> >> and adjusting the acquisition and storage settings for each
>> >> acquisition.  Is there a way to perform a gate-specific data
>> >> cropping function with any current flow cytometry data analysis
software?

>> >> Kind Regards,
>> >>
>> >> Stevan Lauriault
>> >>
>> >> ________________________________________________________________
>> >> Sent via the WebMail system at lauriault.com
>> >
>> >--
>> >Byron Ellis (byron.ellis@gmail.com)
>> >"Oook" -- The Librarian
>>
>> ________________________________________________________________
>> Sent via the WebMail system at lauriault.com
>
>--
>Byron Ellis (byron.ellis@gmail.com)
>"Oook" -- The Librarian

________________________________________________________________
Sent via the WebMail system at lauriault.com
Received on Fri Feb 16 16:38:00 2007
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This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 -
03:12:00 E
RE: DNA analysis software
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to ]
From: VSH Tech Support <Tech@vsh.com>
Date: Wed Feb 21 2007 - 11:29:45 EST
Hello Ibtissam,

ModFit LT, for PC or Mac, has advanced modeling capability for
research
applications in DNA cell cycle analysis.  You may use any of the model
templates the program offers, or create your own models for non-
traditional
analysis, including non-mammalian DNA cell cycle studies. ModFit LT
can be
linked to our WinList program to provide a complete cell cycle
analysis on
any number of sub-populations with a single click of a button.

For an overview, visit  <http://www.vsh.com/products>
http://www.vsh.com/products .

Best regards,

Don

Donald J. Herbert
Technical Support Manager
Verity Software House

________________________________

From: Ibtissam Abdul-Jabbar [mailto:iajabbar@cicr.uq.edu.au]
Sent: Wednesday, February 14, 2007 11:41 PM
To: cyto-inbox
Subject: DNA analysis software

Dear All, before buying software to analyse DNA on PC, I would like to
get
your opinion. I already have ModFit for Macintosh.

What are you using and what do you recommend for research purposes.

Is MultiCycle Av the one of choice?

I appreciate your comments.

Ibtissam A Jabbar (PhD)

Manager of the FACS facilities

Diamantina Institute for Cancer, Immunology and Metabolic Medicine
(DI)

The University of Queensland

Level 4 R Wing

Princess Alexandra Hospital

Ipswich Rd Buranda QLD 4102

Australia

Ph: 07 3240 5945

Fax: 07 3240 5946

Mob: 0401154744
Received on Thu Feb 22 15:18:00 2007
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Re: gate-specific data cropping
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From: WEHICytometry <facs_copy@wehi.EDU.AU>
Date: Mon Feb 12 2007 - 18:25:38 EST
Stevan,

For what it's worth, we have a utility we call Hackit that can crop
cells from the front or back of a FCS file ( see http://
www.wehi.edu.au/cytometry/freesoftware/index.html).  We use it for
the tasks you suggest in cleaning up violated data.  I don't know
how
useful that would be for your current purpose because it can't do
gating; numbers clipped are total cell numbers.  I guess if you knew
the proportions of your gated cells you could eventually clip out
the
file segments you need.

Frank Battye.

On 10/02/2007, at 10:24 AM, Stevan Lauriault wrote:

> Thanks for your very helpful comments.    I guess what I am trying to
> get at is this: is
> there any analysis software available that can reduce list mode
> data in a reverse
> order-specific matter (in reverse sequence)?    Correct me if I'm
> wrong, but I believe this
> function would also help in the event that a user lets a sample run
> dry and sucks up air
> bubbles, or over collects their intended gating target (for
> example, in acquisition and
> storage, 5000 of R1).

    |     |  << The Cytometry Laboratory
     \__/ <<<< The Walter & Eliza Hall Institute
------!!<<<<<< 1G Royal Parade, Parkville
     /!!\ <<<< Victoria 3050, Australia
    o !! \  << ph: 61_3_9345 2540, fax: 61_3_9347 0852
Received on Tue Feb 13 15:18:00 2007
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Re: gate-specific data cropping
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From: Stevan Lauriault <stevan@lauriault.com>
Date: Fri Feb 09 2007 - 18:24:07 EST
Thanks for your very helpful comments.    I guess what I am trying to get
at is this: is
there any analysis software available that can reduce list mode data
in a reverse
order-specific matter (in reverse sequence)?  Correct me if I'm wrong,
but I believe this
function would also help in the event that a user lets a sample run
dry and sucks up air
bubbles, or over collects their intended gating target (for example,
in acquisition and
storage, 5000 of R1).

Thanks,

Stevan
---------- Original Message ----------------------------------
From: "Byron Ellis" <bcellis@stanford.edu>
Date:  Wed, 7 Feb 2007 16:21:28 -0800

>On 2/7/07, Stevan Lauriault <stevan@lauriault.com> wrote:
>> Hi and thanks,
>>
>> Since we want to directly compare MFIs (in FL2) between any two subsets (R1 vs. R3)
>that are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in separate sample
>tubes would introduce the extra probability of experimental error between sample tubes.
>Directly comparing the subsets from the same sample tube, and even better, the same data
>set, would eliminate this extra unknown.
>
>It doesn't necessarily eliminate the unknown, it may just keep you
>from finding out about it. If you were to prepare one sample on
>Monday, see significant differences, celebrate, etc and then on
>Wednesday prepare another sample where you didn't you'd probably want
>to know that (and figure out why). Simply taking the FACS tube off the
>cytometer and putting it back on won't give you that information. Now,
>would I be surprised if that actually happened in your case? Yes.
>Would I do replicates anyway? Yes.
>
>> Let us say we have acquired 100,000 total events (stained with 3 fluorochromes,
>measured in FL1, FL2, and FL4 respectively).  We are using a bivariate dot plot of FL1
>vs. FL4 in which we are isolating 3 subsets (R1, R2, and R3) based on their relative
>expressions of FL1 vs. FL4.  We then want to compare the MFIs, as measured in FL2, among
>these subsets.  Within those 100,000 total events, there are 500 of R1, 700 of R2 and
>1200 of R3.
>>
>> If we crop the 100,000 total events to 75,000 total events (from the top in
>stack-collected data), there will become exactly 500 events in the R2 region.    If we
crop
>the 100,000 total events to 40,000 total events, there will become 500 events in R3.
>>
>> Now the three populations; R1, R2, and R3 each have exactly 500 total events, and we
>can directly compare MFIs among the subsets that have identical sample sizes.    We could
>also then say that, when comparing means between these subsets under identical
>experimental conditions, Rx gives a consistently higher fluorescent signal than Ry.
>
>Well, depending on what you're doing (you've never said how you intend
>to compare means), equal sample sizes is not particularly required so
>there's no particular reason to cut the data to obtain equal sample
>sizes. For example, one-way ANOVA (or one-way ANOVA with repeated
>measure in the event that you chose to do _real_ replicates), which
>simply says "they're different" (there are other tests, variants of
>one-sided t-tests essentially, that give you directionality statements
>such as mu_{R_1} > mu_{R_2} ). In this case your assumptions are:
>
>1. Each group is independent
>2. Normality of group populations (or at least "close enough" to Normal)
>3. The _population_ variances of the dependent variable for each group
>are equal (or pretty close). (Actually check this. It would be
>unsurprising to encounter large differences in the population
>variances among your different groups).
>
>Like I say, it depends a bit on what you intend to do for your
>analysis. For example, _two_-way ANOVA actually expects equal sample
>sizes.
>
>> Is this a reasonable strategy?  Is there any software available that can perform this
>function?
>
>On an FCS file directly? Probably not (neither the manipulation of the
>flow data nor the testing). Once you've got the data out of FCS form
>and appropriately labeled with group membership or split into separate
>files or something similar, then any reasonable statistics package
>(Excel is not included in the list of reasonable statistics packages)
>can perform the statistical tests.
>
>Personally, I use R (http://www.r-project.org) for analyzing all the
>flow data I have, but it can be intimidating for new users (though
>extremely powerful once you learn to use it). There are two packages
>in R for manipulating flow data at the moment (prada and rflowcyt),
>available through the Bioconductor Project
>(http://www.bioconductor.org) that can actually read in and manipulate
>FCS data directly or slightly manipulated data from say FlowJo (so you
>can do your gating there for example). I'm also part of a group made
>up of the people who did rflowcyt and prada that are making a combined
>package of the best bits of both (and some other new bits) that we
>expect to be available in the next Bioconductor release (probably
>sometime in April).
>
>Hope that helps,
>
>Byron
>
>> Kind Regards,
>>
>> Stevan Lauriault
>>
>> ---------- Original Message ----------------------------------
>> From: "Byron Ellis" <bcellis@stanford.edu>
>> Date:  Tue, 6 Feb 2007 12:17:35 -0800
>>
>> >Speaking as a statistician, I would not count running the same tube 3
>> >times or simply cutting the FCS file (the two are equivalent) as three
>> >replicates so I wouldn't do either to achieve what you want (though I
>> >can imagine situations where you would resample to calculate
>> >statistics). To get three replicates you would have to prepare three
>> >separate samples---you're interested in the variability of the mean
>> >due to experimental error as well as the biological variability of the
>> >cells and a single sample preparation only captures the latter.
>> >
>> >On 2/5/07, Stevan Lauriault <stevan@lauriault.com> wrote:
>> >> Dear All,
>> >>
>> >> Question:
>> >>
>> >> We are isolating leukocyte subsets to measure and compare relative levels of
>expression
>> >> of certain antigens.  For example, there are three subsets within a bivariate dot
>plot;
>> >> gated on R1, R2 and R3 respectively, and we would like to statistically analyze the
>> >> relative mean fluorescence intensities of a biomarker, among the subsets.
>> >>
>> >> To get statistically comparable sample sizes among these subsets, we are running
the
>same
>> >> tube three times and changing the storage criteria to 500 events for each subset
>> >> (example, the first run is 500 events of R1, the second 500 of R2, and the third is
>500
>> >> of R3).  Instead of repeating the same tube three times, and wasting valuable
>sample, it
>> >> seems like a good idea to "crop" a preexisting data file of, for example, 100,000
>total
>> >> events, three times to get an identical sample size for all three gated subsets
(R1,
>R2,
>> >> and R3).
>> >>
>> >> Scientifically, this shouldn't be a problem, since flow cytometry data is collected
>> >> randomly within the same sample tube.  Not only could we run one acquisition to get
>> >> different monocyte subset populations, but also to statistically compare constant
>numbers
>> >> of monocytes, PMNs, lymphocytes, lymphocyte subsets, etc. However, I can see why
>some
>> >> scientists might be uneasy with the idea of manipulating raw list-mode data.
>> >>
>> >> However, Since the data is collected randomly from the same sample, doing this
>should
>> >> give exactly the same readings as if we just collected less events, since we would
>only
>> >> be cropping (from stack-collected data) the most recent events collected.
>> >>
>> >> Currently, we are acquiring 3 different data files for each tube, and adjusting the
>> >> acquisition and storage settings for each acquisition.  Is there a way to perform a
>> >> gate-specific data cropping function with any current flow cytometry data analysis
>> >> software?
>> >>
>> >> Kind Regards,
>> >>
>> >> Stevan Lauriault
>> >>
>> >> ________________________________________________________________
>> >> Sent via the WebMail system at lauriault.com
>> >
>> >--
>> >Byron Ellis (byron.ellis@gmail.com)
>> >"Oook" -- The Librarian
>>
>> ________________________________________________________________
>> Sent via the WebMail system at lauriault.com
>
>--
>Byron Ellis (byron.ellis@gmail.com)
>"Oook" -- The Librarian

________________________________________________________________
Sent via the WebMail system at lauriault.com
Received on Mon Feb 12 12:18:00 2007
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03:12:00 EST
Mitch Haynes - 18 Jan 2008 19:41 GMT
> THE PROOF IS BEING DYSTROYED AS THE ARCHIVES ARE REMOVED!
>
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> This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 -
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PURDUE CYTOMETRY WHAT THEY DID NOT WANT YOU TO KNOW

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flowcytometry - 23 May 2008 23:22 GMT
>> THE PROOF IS BEING DYSTROYED AS THE ARCHIVES ARE REMOVED!
>>
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>
>DNA SOFTWARE MESSAGES WERE TO BE DELETED

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