FlowJo and CellQuest (was RE: OS9+Cellquest)
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From: Adrian Smith <A.Smith@centenary.usyd.edu.AU>
Date: Wed Mar 08 2000 - 20:33:48 EST

I'm not really sure that is the point here. Haven't we been talking
about ANALYSIS?

Most, if not all, the people who have been having problems have
bought new G4 machines for post-acqusition analysis (and other uses).
Those who simply upgraded to OS 9.0 could easily downgrade to OS8.6
when it didn't work - it was those people with machines that only run
OS9.0 that were stuffed (by Apple and by BD)

If you bought one for acquisition then I agree wholeheartedly that
you should consider it an object lesson (esp given *BDs* record (AND
their recommendations) as well as Apple's)

Excuse me?

That is entirely subjective (and I'm not even sure what you mean by
"graphical" analysis!). As I have said before I find that complete
novices pick up FlowJo MUCH more quickly than CellQuest.

Not true either. I touch the flow cytometer while it collects all my
data AND I always use FlowJo for my analysis. No, FlowJo is not a
solution for acquisiton but again I don't think that is what we have
been talking about.  FlowJo has been an excellent solution for us and
we do all our own acqusition (using CellQuest on an older machine
with an older OS - as you said, if it ain't broke...).

Our data is of such a nature that ANY increase in machine speed
directly translates to increased analysis throughput - FlowJo has
allowed us to take advantage of those increases in speed. Analysis
takes MUCH longer the acqusition in our experiments  and acqusition
doesn't require any where near the same computing power.

We were even using FlowJo while the cytometer was still running from
an HP - CellQuest nowhere in the loop!

I think acquisition and analysis are two separate tasks and it makes
sense to use the best tools for each one.

Most people need two computers, and hence two software licenses,
anyway...

I don't think I was being "simplistic" in advocating dropping
CellQuest :)
( but I should have made it clearer I was talking about ANALYSIS only)

Neither is CellQuest last time I looked!
Received on Thu Mar 9 11:25:22 2000
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RE: G4 for FACSCalibur - and a plug for Mario!! and one more comment..
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From: J.Paul Robinson <jpr@flowcyt.cyto.purdue.edu>
Date: Wed Oct 04 2000 - 12:27:16 EST
The issue of platforms actually does become important and more
so than if you just like one more than the other. I don't want to
bash this issue, but last week the New York Times reported Apple
stock fell 58% and things are not so rosy it seems, and today in
the Wall Street Journal Apple looks like its going to take another
hit..with lost sales and production goals... worlwide sales dropped
to 3.2% .

The issue really is important - Coulter once invested heavily in the
Terak system becuase it had fantastic graphics (and it did..) it was
very expensive and many people invested .. (like us) but I suspect
there is not a single one operating today.

B-D appears to be walking a fine line - they went from HP I think  to
MACs and from what I could gather at the ISAC meeting in May
they appear to be pushing a hybrid PC data collection system and
a MAC analysis system. It is unclear to me if they are going to PC
or not. I suspect that you don't just jump from one platform to the
other --- anyway, this is an issue of sorts since in looking to
purchase a new system for our lab, I need to appreciate the
complicating factors of how to deal with a lab that has 40 odd PCs
and a MAC......and the real question for me is not how good the
MAC is, but how long it will be around....is the cube another
NEXT...???

I like FloJo by the way - think its great software !!!

Paul Robinson
On 30 Sep 2000, at 11:06, Adrian Smith wrote:

And even if you are using the "other" platform for acqusition, you
can always buy a Mac just to run FlowJo. Some of us think it is that
good...

Adrian

J.Paul Robinson, PhD        PH:(765)4940757
Professor of Immunopharmacology
Professor of Biomedical Engineering
Purdue University      FAX:(765)4940517
EMAIL:jpr@flowcyt.cyto.purdue.edu
WEB: http://www.cyto.purdue.edu
Received on Fri Oct 6 13:36:23 2000

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Re: G4 for FACSCalibur - and a dig at Mario!!
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From: J. Paul Robinson <jpr@flowcyt.cyto.purdue.edu>
Date: Wed Sep 27 2000 - 20:23:51 EST
So Mario, when are you going to talk about software that runs on
computers that
the other 90% plus that people have.......in terms of world computer
sales, Apple is right up there at .....4%!!
Paul

Date sent:        Tue, 26 Sep 2000 16:16:30 -0400
To: cyto-inbox
From:            Mario Roederer <Roederer@drmr.com>
Subject:        Re: G4 for FACSCalibur

J.Paul Robinson, Ph.D.,
Professor of Immunopharmacology
Professor of Biomedical Engineering
Director, Purdue University Cytometry Laboratories
Hansen Hall, Roon B050
Purdue University, West Lafayette, IN 47907-1515
(Ph) (765) 494-0757  Fax (765) 494-0517
jpr@flowcyt.cyto.purdue.edu

http://www.cyto.purdue.edu

http://www.bioscope.org
Received on Thu Sep 28 13:55:27 2000
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RE: OS9+Cellquest
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From: Ray Hicks <rh208@cus.cam.ac.uk>
Date: Fri Mar 10 2000 - 11:59:21 EST
But if it IS just analysis you're after, you can get three copies of
FCSPress for the price of the (~$450) B-D upgrade quoted here (and
you're
well on the way to affording a copy of FlowJo), and run on any mac
with
system 7.1 to 9.0 bought from a third party at street price.

You can try FCSPress for free before you buy it from
http://www.fcspress.com, or fax +44 870 7408595 for an information
sheet.

Ray

(FCSPress is a program written by me and I do profit from it if you
buy it!
Users of G4/OS9 should run the bundled USB Floppy Enabler Installer
before
launching FCSPress for the first time)

At 8:08 pm +0000 8/3/00, CJett wrote:

                             Ray Hicks
_________________________________________________________________________

_________________________________________________________________________

For Low Cost Text Books Try:
    http://click.linksynergy.com/fs-bin/stat?id=e9BnhDua0r8&offerid=11737&type=3&su
bid=0
Received on Fri Mar 10 18:25:29 2000
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    Re: Paint-a-Gate
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From: Adam Treister <adam@treestar.com>
Date: Mon Feb 21 2000 - 18:41:41 EST
Helen,

I would presume that Paint-a-Gate will not read Summit's files
because BD's software expects 8 or10 bits per data value, and
Summit writes 12 bits.

FlowJo has a hidden feature in the Export function that would let
you write the files in a format Paint-a-Gate could read (I think).
This is not visible in the "consumer" version of the program but I'd
can issue you a special serial number to do it.  As Larry pointed
out, Summit can create these graphs, (as can FlowJo) so doing this
translation step may not be worth the trouble.

For more on FlowJo's color gating and overlays, see:
<http://www.treestar.com/flowjo/v3/html/leoverlays.html>

Adam

----->>> On 21-Feb-2000, Larry Arnold wrote:

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

----------------------------------
Adam Treister
Tree Star, Inc.
ph:  650-508-9349
fax:  650-508-9186
www.treestar.com/flowjo
----------------------------------
Received on Tue Feb 22 12:14:04 2000
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Re: Applescript and Flowjo?
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From: Adam Treister <adam@treestar.com>
Date: Thu Apr 06 2000 - 19:19:50 EST
----->>> On  6-Apr-2000, Jan Hendrikx wrote:

--------------
I know I haven't.

As Adrian noted, FlowJo does support some minimal level of
AppleScript, but
doesn't have the object model implementation which is what you'd need
to do
anything meaningful.  I did this in an earlier application
(FlexiTrace) and
it turned into a huge amount of work to enable obtuse functionality to
a
small number of users.  My personal experience with AppleScripts is
that
they're really brittle.  If you move something, or want to something
different from the script writers intention, the script gets
annoyingly
confused and its much easier to start over than to fix it.   Publish
and
Subscribe is an easier addition feature we've considered, but there
just
aren't many people who'd take advantage of this if it were included.
(Let
me know if you think otherwise.)

If properly constructed, a workspace in FlowJo is the script of all
analyses and reports in that experiment.  Dropping your new data
folder
onto the workspace should perform all the analyses that one might
automate
with AppleScript.  We have considered automating it further, but the
logical next step is auto-printing.  In deference to trees, we chose
to
stop short of automating the output without making you look at the
data.

Someday soon, FlowJo will store its workspace in an XML syntax, which
means
that we can utililze generic scripting tools, or you can even hack the
files yourself.  I think this is a better approach than addiing
AppleScript.

Adam

----------------------------------
Adam Treister
Tree Star, Inc.
ph:  650-508-9349
fax:  650-508-9186
www.treestar.com
----------------------------------
Received on Fri Apr 7 12:51:48 2000
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FlowJo/G4/OS X update [was: Cellquest/G4/OS9 update]
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From: Adam <adam@treestar.com>
Date: Thu Apr 27 2000 - 23:53:34 EST
bunny wrote:

FlowJo does histogram overlays.  See
<http://www.treestar.com/flowjo/v3/html/leoverlays.html>

I called Bunny, and she was referring to the Kolmogorov-Smirnoff
statisitic to perform histogram comparison.  FlowJo will create and
export the Cumulative Distribution Functions (the integral of the
histogram) which is the basis of the K/S statistic, so you can easily
perform this test with the help of a spreadsheet.  But we still don't
have that function built in.  I have a prototype built, and you'll
likely see this feature included one day soon.

We'll probably get it into the OS X compatible release, due when Apple
releases the new operating system in the summer. But the tools we need
don't get released until next month, so its hard to predict the
schedule.  Nevertheless, FlowJo worked with OS9 and the G4 the day
they
shipped, and we'll endeavor to support OS X on that same timeframe.

Of course, that's relative to CellQuest on a G3.  On the same
equipment
with the same data, FlowJo outperforms CellQuest hands down.

Adam

-----------------------------------
Adam Treister
Tree Star, Inc.
www.flowjo.com
800-366-6045
-----------------------------------
Received on Fri Apr 28 14:17:53 2000
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FloJo clarification
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From: bunny <bunny@cotleur.com>
Date: Thu Apr 27 2000 - 23:46:45 EST
Fellow Flowers-

My comment about FloJo not capable of histogram overlays was a wee bit
off kilter.
Yes, FloJo DOES do fabulous overlays. (In fact, it's pretty cool that
it
can overlay DOT PLOTS!)
What I failed to mention was my interestreally is in having K-S stats
on
those overlays: I was looking for numbers, not the visual.
BUT! I've been told that K-S stats are just around the corner; so stay
tuned......

Bunny

*******************************************************
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Cleveland Clinic Foundation      *+*       2001 Lester RD
Neurosciences  NC30              +*+       Valley City, OH  44280
9500 Euclid Avenue               *+*       330-483-4800
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Received on Fri Apr 28 13:47:54 2000
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Interest in a FlowJo Users Meeting at ISAC?
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From: Adam Treister <adam@treestar.com>
Date: Wed May 10 2000 - 18:44:43 EST
Dear ISAC Attendees:

I've received a few requests to hold a FlowJo Users Group meeting at
the
ISAC conference.  If this is something you'd be interested in, please
drop
me a note.  If I get sufficient response then I'll arrange a time and
place
to meet.  Of course, you're also welcome to bring your questions (and
bring
some data!) to our booth (#105) for one-on-one assistance.

Tree Star is sponsoring an "Internet Lounge" at the conference,
providing
access to email and the web so that you can keep in touch.  We will
provide
several computers, as well as hookups for your laptops.  If you have
special software or computing needs, please let me know and we'll try
to
accommodate you.

I look forward to seeing you all in Montpellier,

Adam

----------------------------------
Adam Treister
Tree Star, Inc.
ph:  650-508-9349
fax:  650-508-9186
www.treestar.com
----------------------------------
Received on Thu May 11 11:30:51 2000
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FlowJo Training in Boston Sept 26
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From: Adam Treister <adam@treestar.com>
Date: Wed Sep 20 2000 - 14:02:17 EST
It is gratifying to see a growing demand we're getting for training in
how
to use FlowJo.   There are more and more people hearing about the
program,
realizing that it can help them in their analysis, and wanting to
learn its
novel approach to experiment based analysis.

I will be giving two training sessions in using FlowJo software in the
Longwood area of Boston on Tuesday, Sept 26.  There is a morning
session
from 11:30 am - 1:00pm at Dana Farber Cancer Institute, in Dana 5
Conference Room (Rm D521) and an afternoon session from 2:00 to 3:30
in the
Level 6 Conference Room at the Harvard Institute of Medicine Building.

Both sessions are open to the general flow community.

------------------------------------------------------------
Adam Treister      Tree Star, Inc.
ph: 1-650-508-9349  fax: 1-650-508-9186
adam@treestar.com   <http://www.treestar.com>
------------------------------------------------------------
Received on Thu Sep 21 11:43:34 2000
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FlowJo v3.2 adds new Histogram Comparisons
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From: Adam Treister <adam@treestar.com>
Date: Sun Jul 23 2000 - 01:15:45 EST
Dear Flow-ers,

We have released a new version of FlowJo, available for immediate
download.
Along with sundry bug fixes and refinements, this version contains a
powerful new algorithm for comparing histograms.

Version 3.2 of this popular off-line analysis program provides a
unique
integrated platform for comparing univariate distributions.  FlowJo
provides the standard K-S statistic, with its inherent limitations,
but we
also provide a new metric to compare histograms.  This "Chi-Squared T
Value"  provides an indication of the statistical significance with
which
two histograms are different, and its value scales with the degree of
difference.  This means that, for the first time, histograms can be
ranked
by a value that conveys how different they are!

We would like to invite everyone to explore the power of this new
algorithm.  For more information, see
<http://www.flowjo.com/v3/html/comparison.html>.

We are maintaining our policy that allows you to download and try
FlowJo
for 60 days at no charge.  See <http://www.flowjo.com> for more
information
and download instructions.

Adam

----------------------------------
Tree Star, Inc.
New Phone Number:  1-650-591-2854
Or Toll Free (in US): 1-800-366-6045
fax:  1-650-508-9186
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----------------------------------
Received on Mon Jul 24 11:41:31 2000
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Re: Applescript and Flowjo?
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From: Adrian Smith <A.Smith@centenary.usyd.edu.AU>
Date: Thu Apr 06 2000 - 18:04:46 EST

There appears to be a small AppleScript dictionary for FlowJo 3.1 but
it looks to be just the standard commands, ie nothing specific to
FlowJo. Not knowing anything about programming in Apple Script I have
no idea if this is of any use but you might be able to do something
with them...

What sort of things did you want to do with AppleScript? Personally I
can't really thing anything that I do that AppleScript would make
easier/quicker, but that may be just because I don't know much about
AppleScript.

Depending on what you want to do you might be able to do it with one
of the macro programs like OneClick, Quickeys or Key Quencer. A while
ago I made a simple OneClick palette to make some FlowJo features
more accessible. It saved me a bit of time for a while but I
eventually gave up using it because OneClick seemed to decrease
FlowJo's stability.

Adrian
Received on Fri Apr 7 12:06:47 2000
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Re: Apple grumble...
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From: Adrian Smith <A.Smith@centenary.usyd.edu.AU>
Date: Mon Aug 07 2000 - 15:32:51 EST
At 4:41 PM -0700 4/8/2000, David Chambers wrote:

I'm pretty sure we have it running for analysis only on our G4/400
with OS9.0.4. We have a Griffin iMate for the dongle (USB to ADB
convertor) and I think we just copied it from our old G3 (along with
the EVE INIT for the dongle).

I'll confirm when I get into the lab...(I don't actually use it
myself)

What exactly have you tried David?

Adrian Smith
Received on Tue Aug 8 12:43:32 2000
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Re: G4 for FACSCalibur
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From: Mario Roederer <Roederer@drmr.com>
Date: Tue Sep 26 2000 - 15:16:30 EST
I tested FlowJo for a number of different tasks (e.g.,generating
complex graphical layouts; generating large tabular outputs; even
analyzing 13-parameter, million-event data files) on G4's vs. G3.
The G4 was significantly faster (taking into account the clock
speed), even when the program was not G4-optimized.  I also tested a
G4-optimized version of FlowJo that takes advantage of the AltiVec
instructions (no, not yet commercially available!), and it's another
large step up.

As more and more applications come out to be AltiVec-aware (and they
are!), everyone will realize the enormous speed benefit from this
technology.

Note that the multi-processing nature of Altivec should not be
confused with the multi-processing capability of dual-processor
machines (like the new G4 cube).  There's a completely different set
of optimizations that programs need to fully take advantage of
multi-processor machines (and I'm sure that will be forthcoming in
the next year or two as well).

Bottom line--G4's are faster, but G3's are a lot cheaper (right now).
But as more and more applications are Altivec-aware, then there won't
be a comparison.

mr

(PS--Intel-based machines, even the gigaherz processors, don't come
close to the G4 capabilities.)
Received on Wed Sep 27 12:44:13 2000
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RE: G4 for FACSCalibur - and a plug for Mario!!
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From: Fischer, Randy (NIAMS) <fischer1@mail.nih.gov>
Date: Thu Sep 28 2000 - 16:59:18 EST
Paul,

Like you and many others in this world, I have one of the other 90% of
the
computers at home.  I do not like it, but the other major occupant of
the
household (my wife) required it for her job.  However, like 90% of the
Folw
Cytometry users out there, I have a BD instrument that uses a MAC to
acquire
and analyze my data.  So, I subscribe to the "do work at work" theory
and
use the MAC, which by the way I do prefer.  Mario's (and Adam's)
FlowJo
software is a very nice alternative, and any software that is an
alternative
to paying big bucks to certain Flow companies should be most heartily
encouraged.

So, let Mario plug away and let the users of the minority instruments
tout
their advantages if they wish as well.  That is, if there are any???

Randy Fischer
NIAMS/NIH

Received on Fri Sep 29 14:39:45 2000
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