Friday, May 23, 2008

ISAC Wrap-up Part 1

Planning to submit a paper to J. Exp. Med. anytime soon? Well then you'll want to pay attention to the new guidelines generated by the Data Presentation Standards Committee and adopted by J. Exp. Med. What the cytometry field has been noticing for quite a while is the amount of publications in high-end journals with really poor flow cytometry figures. It's not that the data is bad, or doesn't support the authors conclusions, it's just that the figure is annotated so poorly, and the methods written so vaguely that it's nearly impossible for anyone to try and repeat complicated analyses. Being the premier flow cytometry authority, ISAC has taken it upon itself to lay down some guidelines to assist authors in properly presenting the necessary information to describe their flow cytometric data. A member of the Data Standards Committee, Dr. Mario Roederer, shared the conclusions of the committee this week at the ISAC Congress. Here are a few examples from the guidelines. Once a comprehensive list is created, I'll post them for the group to see.

Author must list the instrument(s) used, the laser(s) used for excitation, and the filter(s) used for emission. This will be done in an excel template that will be available from ISAC or J. Exp. Med.

Axis on plots must have the reagent and fluorescence labelled (ex. CD3-FITC).

The number of events in a plot must be displayed in the plot or figure legend.

The frequency of populations must be displayed on the plot or in a table

Graph-types should be used consistently throughout.

You MUST show the entire gating tree for your figure as an example. Back-gating analysis is the best way to show this. This can (and probably should) be in the supplemental data portion of the manuscript.

You must also state how you drew your gates. For example, did you draw them based on unstained cells, or an isotype control, or and FMO control, or did you just subjectively draw it around a population.

These are a few of the guidelines that will be implemented soon. J. Exp. Med. has decided to adopt them sooner rather than later, but we anticipate more and more journals will begin to require this information. If you have any questions, or need help filling in the appropriate information, the flow can certainly help. We will try to provide filled out examples for each of the instruments so that you can simply modify them for your use. We'll provide more info as it becomes available.

27 comments:

  1. From: Ray Hicks
    Sent: Wednesday, October 17, 2001 8:42 PM
    To: Cytometry Mailing List

    Subject: Re: Bad Flow Data & reviewing -- What can we do?


    Many good points Mario,
    but

    I'm going to take you back a few years to our
    discussion on dot plot versus contour, and how misleading contours are.
    I'd
    reverse your logic in " remember that contour plots are also
    histograms (2D histograms),

    and

    they have no numbers on the "Z" axis
    corresponding to event frequency. Why should univariate histograms have
    them?", and suggest that contour plots need even more annotation.

    I'm sorely tempted to attach a few figures to this e-mail,

    but

    I've restrained myself, and made them available at:
    www.fcspress.(Who's computer is this?)

    and
    fcspress.com/512AlongTheAxis.gif (Who's computer is this?)

    The first
    fcspress.gif (Who's computer is this?) > shows how strikingly different contour plots of the same data can be

    (the data is from the FlowJo tutorial set, the figures are made in FlowJo 3.2 and FCSPress 1.3).

    The top left dotplot is from FlowJo,

    and

    shows the crowding you object to, the upper central plot is FlowJo's default contour plot of SSCvFSC with ten thousand
    cells, the upper right plot is a plot of 1600 cells gated from the same
    file
    - doesn't look like fewer cells does it?
    The lower left plot is a log 50% contour plot of the data in the top left
    and top centre plots, what is one to make of those contours based on four
    cells that jump out in the lower left?

    The lower central plot is a dot plot from FCSPress, plotting data at 512 points along the axis

    (the data has a range of 512 "channels"),

    FCSPress has dithered the plot to represent how it would

    (and does) print on a printer which isn't limited to screen resolution

    (using the "clarify option),

    you'll notice that using higher resolution avoids much of the coalescing to a black blob that you object to in dot plots

    (the second figure, TheAxis. (Who's computer is this?) >,
    .
    shows this graph at full size with no dithering)
    The lower right plot shows a density plot from FlowJo,
    the smoothing belies the sparsity of the data.

    What's an expert to do when presented with this kind of thing?

    Would labelling the upper left and lower left plots as having the same number of cells be enough to make you see them as representing the exact same data
    set?

    The dot plot of 1600 cells (not shown for brevity) clearly has fewer
    cells than that of 10000, and does a better job of warning the viewer,
    expert or not, of how confident they should be in making conclusions based
    on the plot than numbering the events on the two contour plots (upper left
    and upper right).
    Oh, alright then, I've put a further figure up with two dot plots and two
    contour plots with paired numbers of events at:

    .fcspress.com/nowDoYouSee.gif (Who's computer is this?)

    The other issue I take is;

    how is the collective going to select the
    experts?Surely the people who are publishing this stuff ARE people

    "with a modicum of experience in flow".

    Putting the responsibility on editorial
    boards is probably going to end up in a status quo.

    How about pressuring your lab-fellows

    to sling the FACS aspect of papers, that

    they're reviewing anyway,

    in your direction?


    Ray

    ps

    as an aside,

    there's something freaky happening on the axes of these graphs -

    they're 512 channel data,

    but

    the linear FSC axis runs out
    just past 200,

    and one of the events exceeds the maximum for side scatter
    (ie the one that juumps above the red line in the left hand plots -

    has this beenfixed in later versions of

    FlowJo?

    Would this be

    something an expert could

    criticise/reject

    a paper for?

    ReplyDelete
  2. From: Randy T. Fischer
    Date: Thu Jul 17 1997 - 03:25:15 EST
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    ________________________________________
    I agree with both Marty and Gunter in the very important issue
    of
    standardizing data formatting. I would point out that lobbying ISAC is
    only, however, part of the answer. Regardless of what ISAC may choose
    to
    recommend, it is still up to the manufacturers to implement what they
    want
    to do, and if they do not agree with ISAC, then too bad for ISAC and
    the
    flow community. A potentially more powerful force for change might be
    the
    FDA, which regulates machines used in CLINICAL settings. If the FDA
    could
    be persuaded to require all CLINICAL data be universally both
    accessible
    and readable, then the manufacurers would be forced to upgrade
    machines and
    software or lose theLUCRATIVE CLINICAL market. This would make
    analyzing
    data from different sources easier, and could facilitate the exchange
    of
    crucial clinical results from various trials where multiple sites and
    machines are in use.
    So how does this get done? Gunter (and Paul's agreeing
    response)
    are correct this needs to be revisited at Asilomar, with perhaps an
    additional idea. Any concrete standardization protocol, FCS3.0 or
    whatever
    it ends up being designated, should be then presented to any and all
    regulatory agencies by ISAC to ensure no individual manufacturer
    decides
    FCS3.0 in their format is acceptable, even if it is not universally
    readable.

    Randy T. Fischer
    NIA/NIH
    GRC
    Baltimore, MD 21224

    ReplyDelete
  3. At 01:00 PM 10/16/01 -0400, Roederer, Mario (VRC) wrote:

    >This topic strikes a nerve with many of us. Indeed, ISAC did at one point
    >have the decent notion to have a committee on "data presentation standards"
    >or something like that. I remember seeing something at Montpellier--a
    >pamphlet on presentation, I think. Since then, I haven't heard about the
    >progress of this committee. I made a number of suggestions on the
    >committee's effort, as it was a reasonable start, but don't know if that had
    >any affect. Indeed, even this pamphlet had a number of mistaken notions,
    >showing how ingrained things can get even within the community.
    >
    >For example, there was the suggestion that we should always put numbers on
    >the Y axis of a univariate histogram ("# of cells"). In reality, these
    >numbers are meaningless--they depend on the resolution with which the data
    >is binned, which can vary from program to program and instrument to
    >instrument. The reasoning was that the only way to compare histograms was
    >to have these numbers to ensure that the data was interpreted properly.
    >However, this is a misconception--in reality, the peak height in a histogram
    >is rarely meaningful; it is the peak area which carries meaning. What is
    >necessary in a histogram presentation is to identify how many cells were
    >collected (and displayed in the histogram), and, if any peak in the
    >histogram is cut off, to identify what fraction of the vertical scale is
    >shown. I.e., the only thing worth putting on the Y axis label is "% max",
    >where "max" is the maximum peak height. Admittedly, many of my papers have
    >the meaningless numbers on the axis... but I'm still learning...
    >
    >I am sure that even this little discussion may set off a minor
    >firestorm--and that's probably good: it will be educational, which is the
    >main point of this list! (By the way, remember that contour plots are also
    >histograms (2D histograms), and they have no numbers on the "Z" axis
    >corresponding to event frequency. Why should univariate histograms have
    >them?)
    >
    >Jim Houston asks about the needed information for histograms or dot
    >plots--always, the minimum information is the number of events displayed.
    >(And yes, I am guilty of not always putting that information in my own
    >publications.) I still strongly advocate against dot plots; there are much
    >more informative displays available.
    >
    >But the point of this email is not to address the specific defects in data
    >presentation, nor even to start to lay them out. That, in fact, would be
    >better done in a book.
    >
    >Both Jim and Robert Zucker bring up the lack of the Community's involvement
    >in peer review. It is worth noting that JAMA requires every paper to be
    >reviewed by a statistician, outside of the normal review. Why not have the
    >same thing for every flow paper? It seems that the major publications
    >should require an expert to review papers containing FACS
    >presentations/analyses for appropriateness. But it won't happen: if we
    >can't even police our own Journals to ensure appropriate data presentation,
    >then what makes anyone think we have the competence to do so for other
    >Journals?
    >
    >Some years ago, a few of us bantied around an idea of "post-publication"
    >review of articles that would be placed online. The concept was as follows:
    >each major journal would be assigned to one or two expert reviewers. Each
    >issue would be examined for articles that had flow cytometry in them, and
    >then the reviewer would go over the paper with a predefined list of
    >criteria. The review would explicitly avoid any judgment about the paper's
    >conclusions; it would only address whether the flow cytometric analyses were
    >properly presented, interpreted, and then to note what additional
    >information is required, what possible artifacts need to be eliminated, etc.
    >The review process would be fundamentally based on a checklist (e.g., "was
    >cell viability assessed?", "what staining controls were performed?", "is the
    >data properly compensated?", "did the authors note how many events were
    >displayed?", "are the statistical intreprations of low event counts
    >appropriate?" etc. etc.... I could envision a 100-item list). There would
    >be "sub-lists" for different types of flow, like "cell cycle",
    >"immunophenotyping", "intracellular detection", and "it's obvious I dropped
    >my samples off at my local core facility, didn't tell them what was in each
    >tube, forgot my controls anway, had them generate a few graphs for me, and
    >then xeroxed them until the dots I didn't like went away, so don't blame me
    >because I can't understand the difference between a contour plot and a
    >photomultiplier tube." The reviews would be posted on-line.
    >
    >The idea of the online post-publication review is that the general
    >scientific community, when reviewing an article, could turn to the web site
    >and quickly see if there are major problems with the technology that they
    >might not appreciate because of the subtleties. Since the criteria would
    >all be published online as well, the goal would be that authors would start
    >turning to this site before publication in order to better present data,
    >rather than seeing criticisms of their papers show up afterwards. Authors
    >might be allowed to appeal aspects of a review that they feel are
    >inappropriate, thereby providing an ongoing evolution of the evaluation
    >process. There might even be a manuscript pre-review service where authors
    >could ensure appropriateness before submitting for review.
    >
    >What would this require? No more than a one or two dozen FACS-savvy people
    >to volunteer for this public service. Anyone with a modicum of experience in
    >flow would be excellent for this; in fact, it's probably better to recruit
    >younger (less jaundiced) people for the process. In reality, the review
    >process would be very rapid, since these are not detailed reviews aimed at
    >the science of the paper, but only at the data presentation. I was so hot
    >on this idea (now 2 years old) that I even registered a domain for its use
    >(http://www.sciwatch.org)--a registration I renew in the hopes that
    >something might actually come of it.
    >
    >In my idealistic vision, eventually journals would turn to the Flow
    >community to do this as a standard of practice rather than have it go on
    >post-publication. Journals might even adopt the standard data presentation
    >requirements. People might actually publish FACS data that we can believe.
    >
    >But maybe we need to start at home first. I'd like to suggest that
    >Cytometry and Clinical Communications in Cytometry both make an editorial
    >decision to require all published papers to come up to some minimum
    >acceptable standard. If these journals make the commitment, then perhaps
    >there will be enough motivation for a document outlining these procedures to
    >be put together. However much it makes sense, I do not suggest that this be
    >done by a committee under the auspices of ISAC, since that effort has
    >essentially failed, principally through inaction. Rather, I think the
    >Editorial Boards should empower a group to put such a document together. If
    >such an effort works, it can serve as a model for other journals to adopt.
    >
    >mr

    ReplyDelete
  4. On Thu, 18 Oct 2001, Ray Hicks wrote:
    some interesting points, as did Mario, and although I have not checked
    for typos or glaring grammatical errors, I have snipped them all except this bit
    The other issue I take is; how is the collective going to select the
    experts? Surely the people who are publishing this stuff ARE people "with a
    > modicum of experience in flow". Putting the responsibility on editorial
    > boards is probably going to end up in a status quo. How about pressuring
    > your lab-fellows to sling the FACS aspect of papers, that they're reviewing
    > anyway, in your direction?

    ReplyDelete
  5. Re: Re digital data
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    From: WEHICytometry
    Date: Tue Mar 14 2006 - 23:28:16 EST

    On 14/03/2006, at 9:03 AM, Mario Roederer wrote:

    > Actually, there aren't several transforms -- basically there are
    > only two ("Logicle", from Dave Parks and Wayne Moore at Stanford,
    > used by DiVa and FlowJo; and the "HyperLog" from Bruce Bagwell at
    > Verity used by WinList). And, in fact, these two are
    > mathematically nearly identical; the Logicle function is a slightly
    > more complex, and slightly smoother version, but probably without
    > noticeable visual difference when the same parameters to the
    > function are used. The primary difference between the two is that
    > the Logicle algorithm provides for a mechanism to automatically
    > select parameters to the function that are optimized to the actual
    > distribution of the data--hence, the transformation can, if
    > desired, be stronger or weaker for one fluorescence channel than
    > for another (which is reasonable, as the magnitude of the error in
    > the measurement is very different in these channels, and the error
    > in the measurement is the primary reason we need the transforms!).
    >

    I feel obliged to correct Mario there; there are indeed more than
    two. Another is the "split scale" form that is used in the WEASEL
    fcm analysis and display program (see http://www.wehi.edu.au/ (Who's computer is this?)
    cytometry/WEASELv2.html). This transform is mathematically simpler
    but, I assert, no less valid. It has been used in WEASEL for a year
    or so and was described to the Australasian Flow Cytometry Group
    last
    year (see the abstract at http://www.wehi.edu.au/cytometry/Abstracts/ (Who's computer is this?)
    AFCG05B.html).

    Frank.

    | | << The Cytometry Laboratory
    \__/ <<<< The Walter & Eliza Hall Institute
    ------!!<<<<<< 1G Royal Parade, Parkville
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    o !! \ << ph: 61_3_9345 2540, fax: 61_3_9347 0852
    Received on Wed Mar 15 16:18:00 2006
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  6. For all of the mr groupies out there in cytometry cyberspace. Don't wet your pocket protectors over this.

    http://www.apple.com/science/profiles/ro... On Aug 20, 2004, at 2:25 PM,
    J. Paul Robinson wrote:

    ummm....Mario says.. "In life sciences -- particularly in research life sciences -- probably 50 to 70% of research..

    ReplyDelete
  7. Re: FCS file headers
    MUR...@A.CFR.CMU.EDU
    Tue, 15 Jun 1993 15:57:43 -0400 (EDT)

    Messages sorted by: [ date ][ thread ][ subject ][ author ]
    Next message: MUR...@A.CFR.CMU.EDU: "Re: FCS file headers"
    Previous message: Steve Kelley: "FCS file headers"
    Maybe in reply to: Steve Kelley: "FCS file headers"
    Next in thread: MUR...@A.CFR.CMU.EDU: "Re: FCS file headers"
    In response to a question from Alice Givan, there are three ways to
    get
    listings of keyword values for FCS files on VAX systems.

    1. Use the DR command in DISP4 or DISP2D. This will give values for
    some of the common FCS keywords.

    2. Use the FCSDMP program to get a listing of all of the keywords
    in one or more FCS files. If more than one file is specified
    (wildcards and ranges allowed), only the DIFFERENCES between the
    first file and the later files will be listed.

    3. Use the FCSTAB program to generate a table or listing of specific
    keyword values for each file in an input list, one line per file.
    FCSTAB calculates a number of additional keywords, such as means
    and s.d.'s for each parameter.

    VMS versions of FCSDMP and FCSTAB can be obtained by anonymous FTP
    from
    a.cfr.cmu.edu. They are in subdirectories [.VMS.FCSDMP] and
    [.VMS.FCSTAB]. Help files suitable for insertion in VMS help libraries
    are included. Source files are in [.SOURCE] subdirectories (note that
    only .OBJ files are included for some utility routines).

    For users generating files on systems other than Consort/VAX, these
    files may be analyzed using FCSDMP or FCSTAB as long as they adhere
    to the FCS 1.0 or 2.0 standards and the FCS file identifier contains
    the string "FCS1.0". FCS files created on other systems often have
    different strings (such as "FCS 1.0") as the FCS file identifier.
    The program FCSFIX (in [.VMS.FCSFIX]) can be used to modify these
    files so that they can be read by FCSDMP and FCSTAB, as well as
    Consort/VAX programs. We have successfully analyzed many ELITE
    files with FCSTAB after running them through FCSFIX.

    Comments welcome.

    Bob Murphy

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  8. On Thursday, March 16, 2006, at 02:06 AM, A.J. Rossini wrote:
    > On 3/13/06, Mario Roederer roede..drmr wrote:
    >> I am a firm believer in the use of these transformations--in the
    >> multicolor> world,
    > they have revolutionized our ability to look at the data. (Note that>
    > the transforms in
    > no way affect statistics or gating--they ONLY affect the> visual
    > representation of the
    > data). The point of these transforms is to> make the data more easily
    > conveyed to
    > readers--something that a simple log> scale (which is itself a
    > transformation!) no longer
    > does adequately.
    > I'm going to nitpick a bit -- while the general overall
    > conclusionsMario draws are
    > correct, there are a few subtle points. If you don'tget what I'm
    > saying, believe Mario,
    > it's simpler that way. Read onfor the fine details:
    > Transformations actually do affect the statistical
    > analysis/conclusions.
    > data != transformed data.
    > Conclusions drawn on transformed data do not have to be the same as
    > onraw data (a
    > difference on a log scale using a particular statisticisn't
    > necessarily different using
    > the raw data with the samestatistic).
    > Why transform?
    > To pull the data back to a state of nature where we feel
    > comfortablewith decision making.
    > To pull the data back to a state of nature where certain
    > probabilisticassumptions are
    > met, allowing for "believable" statistical estimationand testing (and
    > opposed to
    > unbelieveable statistical muck)
    > To focus on particular ranges or features of the data.
    > All are valid.
    > The detail is just "comparison on the transformed scale isn't the
    > sameas comparison on
    > the original scale". The point is that it's ratherimportant to do,
    > both to match up
    > with historical scientificapproaches as well as to match up with
    > common practices
    > forcomparability within the cytometric field.
    >>> The Data Presentation Standards Committee, formed by ISAC, will take
    >>> the>
    > responsibility to contact the editors of the Journal with which there
    > are> problems. Our
    > goal is to educate not only the reviewers, but importantly> the
    > Editors--so that they can
    > be made aware that any complaints that> reviewers might have regarding
    > this visualization
    > are baseless.
    > This is important! Visualizations, done well, are critical
    > formultidimensional data.
    > best,-tony
    > (Novartis Pharma AG / University of Washington)
    > blindgl...@gmail.comMuttenz, Switzerland."Commit early,commit often,
    > and commit in a
    > repository from which we can easilyroll-back your mistakes" (AJR,
    > 4Jan05).


    Julia Whynot
    Rockefeller University
    Investigative Dermatology
    212-327-7581
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  9. 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

    ReplyDelete
  10. ISAC Homepage - ISAC E-News -- March 2008
    Mar 13, 2008 ... Since the Society’s inception, we have developed a
    mailing list which .... Mark Munson, Verity Software House, Inc., E-
    mail: sa...@vsh.com. ...
    www.isac-net.org/content/view/732/44/ - 53k - Cached - Similar pages
    -
    Note this

    The Daily Dongle
    Cytometry Developers Workshop is attended by the industry and academia
    alike. ... J Paul Robinson delivered an effective summary of the
    problem, ...
    flowjo.typepad.com/ - 40k - Cached - Similar pages - Note this ...



    Joseph Robinson: ZoomInfo Business People Information
    ... Paul Robinson, chair of the Optics East Life Sciences symposium **********
    (see sidebar) and director of Purdue University Cytometry Laboratories
    (West Lafayette, ...
    www.zoominfo.com/people/Robinson_J._-82453.aspx - 24k -



    International Congress Montpellier 2004
    File Format: PDF/Adobe Acrobat - View as HTML
    Co-Chairs: Bartek Rajwa and J Paul Robinson. The Cytometry of
    Plants .... analytical cytometry publishing and software companies,
    pharmaceuti- ...
    www.afc.asso.fr/actu/congres/isac04.pdf - Similar pages - Note this



    Africa Business Conference 2007
    J. Paul Robinson Director, Purdue University Cytometry Laboratories
    and Deputy ... in bioengineering with hardware and software groups
    developing innovative ...
    www.hbsafricaconference.org/2007/panels_healthcare.html - 27k - Cached
    - Similar pages - Note this



    Review Members and Corporations on the Purdue Cytometry Mial list

    Photonics: Principles and Practices - Google Books Resultby Abdul Al-

    Azzawi - 2006 - Science - 968 pages
    Newport Corporation. Optics and mechanics. Newport 1999/2000
    catalog, ... Robinson. Paul, Laboratory Manual to Accompany
    Conceptual
    Phvsics. ...
    books.google.com/books?isbn=0849382904...

    Purdue Cytometry Mailing List: RE: EPICS C data
    From: J.Paul Robinson
    (j...@flowcyt.cyto.purdue.edu) ..

    . From: Suzanne Leif President of ********
    Newport Instruments Via Robert C. Leif, Ph.D. Vice President ...
    www.cyto.purdue.edu/hmarchiv/1998/1995.htm - 7k - Cached - Similar
    pages - Note this
    Dayong JinJingli Yuan’s group),
    Newport Instruments **************
    (Dr. Robert Leif’s group) and
    Purdue University Cytometry Labs
    (Prof. J.Paul Robinson’s group). ... ******

    www.ics.mq.edu.au/gen/person/jin.html - 13k - Cached - Similar pages
    -
    Note this
    Data and Image Analysis Special Interest Group Meeting 2007J. Paul
    Robinson, SVM Professor of Cytomics, Purdue University and
    President, ... (*) Robert C. Leif, Newport Instruments. "Cytometry
    Standards Continuum" ...
    www.ravkin.net/SBS/D&IA_SIG2007.htm - 14k - Cached - Similar pages -
    Note this

    [PPT] DIA SIG 2007: What are the Issues?File Format: Microsoft
    Powerpoint - View as HTML
    ... J. Paul Robinson, President, International Society for Analytical
    Cytology, ... (*) Robert C. Leif, Newport Instruments "Cytometry
    Standards Continuum" ...
    www.ravkin.net/SBS/DIA%20SIG%202007%20Intro.ppt - Similar pages -
    Note
    this

    Wiley Cytometry - ISAC 2000 International Congress POSTER
    ABSTRACTS
    Stephanie Ann Sincock,
    Purdue University; J.Paul Robinson,
    Purdue University ...... Robert Leif, Newport Instruments; John
    Quagliano, Los Alamos National ...
    www.wiley.com/legacy/products/subject/life/cytometry/isac2000/posters...
    - 223k - Cached - Similar pages - Note this

    Verity Software House, Inc.
    10 New Lewiston Road
    Topsham, Maine 04086
    207 729 6767 voice
    207 729 5443 fax

    Phoenix Flow Systems
    11575 Sorrento Valley Road, Suite 208
    San Diego, CA 92121
    619 453 5095 voice
    619 259 5268 fax

    Cytomation, Inc.
    400 E. Horsetooth Rd., Suite 100
    Fort Collins, CO 80525
    800 822 9902 voice
    303 226 2322 fax NEW ADDRESS FORT COLLINS DRIVE

    DOES THE FEDERAL GOVERNMENT REGULATE ISAC CONGRESS ...



    A numerical recipe for accurate image reconstruction from discrete ...
    - 2 visits - Nov 28
    J. Paul Robinson, Bindley Bioscience Center, Purdue University, 1203
    West State St., West Lafayette, IN 47907, USA and Cytometry
    Laboratories, ...
    portal.acm.org/citation.cfm?id=1221224 - Similar pages - Note this

    Ø [PDF]
    > GREAT LAKES INTERNATIONAL IMAGING AND FLOW CYTOMETRY
    > ASSOCIATION
    > File Format: PDF/Adobe Acr
    > obat - View as HTML
    > J. Paul Robinson, Philip Marder. Iowa. Bruce Pesch. Michigan .... flow
    > cytometry software. Clearly, traditional cytometers can not handle the
    > demands of HTS ...
    > gliifca.org/pdf/GLIIFCA-2001.pdf - Similar pages - Note this
    > International Congress Montpellier 2004
    > File Format: PDF/Adobe Acrobat - View as HTML
    > Co-Chairs: Bartek Rajwa and J Paul Robinson. The Cytometry of
    > Plants .... analytical cytometry publishing and software companies,
    > pharmaceuti- ...www.afc.asso.fr/actu/congres/isac04.pdf- Similar pages - Note this



    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 ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0490.htm - 9.0KB
    72%
    ||||||||||||||||||||
    30 Mar 07



    Purdue Cytometry Mailing List: 31st Annual Flow Cytometry Course ...
    From : Mark - Verity Software House m...@vsh.com ... and lectures
    you'll learn about pertinent topics in the art and science of flow
    cytometry. ...
    www.cyto.purdue.edu/hmarchiv/Current/0455.htm - 8k - Cached - Similar
    pages - Note this

    Purdue Cytometry Mailing List: ModFit LT 3.1 Service Pack 1 now ...
    For more information, contact Verity at sa...@vsh.com. Best regards,
    Mark Mark E. Munson Sales Manager Verity Software House, Inc. 45A
    Augusta Road PO Box ...
    www.cyto.purdue.edu/hmarchiv/2003/1134.htm - 6k - Cached - Similar



    From: J. Paul Robinson j...@flowcyt.cyto.purdue.edu

    Date: Mon Mar 31 2008 - 01:18:05 EDT



    From J. Paul Robinson - Moderator

    Robert is right - there is too much politics and not enough
    science...

    What is happening here, is that there are too many cooks.

    Let me make it very clear that we work hard to keep this list clean.
    It
    does not always work. When we identify a failure, we usually respond
    to
    the person concerned and don't waste all your time.

    We frequently note in our posts, that advertising is not allowed.
    This
    list was developed from 2 or 3 individuals who actually had email in
    1990, to 3000 over the past 19 years. It did not happen by chance,
    nor
    was it overnight. It was developed with a lot of cost ($$$), a lot of
    time, and what was a pretty darned good idea when it started. We
    don't
    tolerate people who try to damage the list.

    Now that it's highly successful, there are a number of individuals
    that
    are trying to either circumvent the list, use it for their own
    purposes,
    or simply sideline it. There are even some proposing that they should
    be
    able to manipulate the list and its contents in any forum for any
    purpose. I am really shocked at this rather callous approach to a
    scientific discussion board. I am not making public those individuals
    or
    their companies, but if I am pushed, I will identify them publicly.
    If
    I
    do so, and they create havoc, it could shut the list down - or end up
    in
    a nasty legal battle. I don't suppose that would be popular?

    So, it seems to me, that we need to get back to basics and focus on
    the
    reason this list has been so successful (and why you all want to use
    it
    for advertising - or even why those who what to hijack it...) - it
    does
    a good if not great job overall.

    thanks for your support - all 3000 of you ...well most of you!

    Clearly we will provide a mechanism for companies to provide a means
    for
    communication....it's on our list...

    Maybe I am getting too old for all this abuse....!

    regards

    Paul Robinson
    Purdue University

    ReplyDelete
  11. Collusion is an agreement, usually secretive, which occurs between
    two
    or more persons to deceive, mislead, or defraud others of their legal
    rights, or to obtain an objective forbidden by law typically
    involving
    fraud or gaining an unfair advantage. It can involve "wage fixing,
    kickbacks, or misrepresenting the independence of the relationship
    between the colluding parties."[1] All acts affected by collusion are
    considered void.[2]

    In the study of economics and market competition, collusion takes
    place within an industry when rival companies cooperate for their
    mutual benefit. Collusion most often takes place within the market
    form of oligopoly, where the decision of a few firms to collude can
    significantly impact the market as a whole. Cartels are a special
    case
    of explicit collusion. Collusion which is not overt, on the other
    hand, is known as tacit collusion.

    According to neoclassical price-determination theory and game theory,
    the independence of suppliers forces prices to their minimum,
    increasing efficiency and decreasing the price determining ability of
    each individual firm. However, if firms collude to increase prices
    loss of sales is minimized as consumers lack alternative choices at
    lower prices. This benefits the colluding firms at the cost of
    efficiency to society.

    One variation of this traditional theory is the theory of kinked
    demand. Firms face a kinked demand curve if, when one firm decreases
    its price, other firms will follow suit in order to maintain sales,
    and when one firm increases its price, its rivals are unlikely to
    follow, as they would lose the sales' gains that they would otherwise
    get by holding prices at the previous level. Kinked demand
    potentially
    fosters supra-competitive prices because any one firm would receive a
    reduced benefit from cutting price, as opposed to the benefits
    accruing under neoclassical theory and certain game theoretic models
    such as Bertrand competition.

    Practices that facilitate tacit collusion include:

    Uniform prices

    A penalty for price discounts

    Advance notice of price changes **************************

    Information exchange ******************

    From: Adam Treister (a...@treestar.com)
    Date: Mon Apr 22 2002 - 00:15:07 EST
    * Reply: Mario Roederer: "Job Opening -- Immediate -- Vaccine

    ______________________________________...
    Only two more weeks until ISAC, that biennial bacchanalia of flower
    power
    and fun! So I hope you'll excuse a bunch of blatantly commercial
    announcements to the list, but endulge me this one time and read on.

    At the show we'll be releasing FlowJo Version 4. We've got new
    platforms
    for overlaying and clustering, we've made it work better across the
    Internet, added all sorts of new

    For those who haven't found it yet, we've unveiled a spanking new
    FlowJo
    website. Flowjo.com is chuck full of new content, functionality and
    spunk.
    Automated price quotes, online ordering, a FAQ that will guide you to
    new
    depths of understanding, and none of that awful yellow on black text.
    The
    search engine even works. No ads & cookie-free. Check it out.
    *************
    Specifically, you should check our pricing. Prices are going up on
    *******
    May 10. ************
    It has been a number of years since we've changed our prices and with
    the
    development of the OSX and PC versions, it¹s time for a leap. I
    guess
    there's no such thing as a free launch. Anyway, this may be a great
    time to
    buy that FlowJo ten pack you've been thinking about. Licenses
    purchased
    before May 10 are entitled to a year of free upgrades, including the
    4.0
    release.
    Unleash the flower power!
    Adam
    --
    Adam Treister
    Tree Star,

    Recent FlowJo announcement

    From: Steve Kelley
    (SKEL...@flowcyt.cyto.purdue.edu)
    Date: Wed Dec 30 1998 - 06:13:04 EST

    Next message: Steve Kelley: "Possible minor disruption"
    Previous message: Mark A. Corio: "Chemdex no help..."
    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]
    I know that many people on the mailing list are adamantly opposed to
    anything that even looks a little commercial, and to try to forestall
    any possible

    complaints about the FlowJo announcement
    , I'll explain what

    I'd like to see. In my opinion, announcements about new products, and
    product updates are completely appropriate as long as they aren't
    abused.
    I've never wanted to specifically encourage that, because I really
    don't want to be put into a position of having to decide whether a
    message is an

    "announcement"
    or an

    "advertisement"
    . The companies involved in our cytometry community have always been
    extremely good 'citizens' as far as I can tell.

    We have representatives of many companies on the list, and they have
    always had the power to make my life miserable, and the list no more
    than junk mail. Instead, they have helped build this mailing list
    into one of the most useful around, through their contributions and
    responses. I'm not going to try to set specific rules about what
    people can say about their own products, and when they can say it.
    I'll just ask that everyone continue to show restraint; that the
    commercial representatives ask themselves before they submit an
    announcement whether they'd mind seeing every other company in the
    business sending the same message they are about to, and that the
    non-
    commercial (and anti-commercial) people accept discreet announcements
    as simple information, and continue the sometimes brisk discussions
    about problems and benefits of particular products, alongside the
    purely scientific (and occasionally purely entertaining)
    conversation.
    Steve Steve Kelley

    ReplyDelete
  12. Re: EMAIL ABUSE - how to
    stop**************************************************************************
    From: Adam Treister (a...@treestar.com)
    Date: Mon Dec 16 2002 - 16:00:07 EST
    Next message: PAUL HALLBERG: "Summary: Sorting CHO cells"
    Previous message: Mojgan Shaiegan: "RBC phenotyping by flow"
    In reply to: J.Paul Robinson: "EMAIL ABUSE - how to stop"
    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]
    ---------------------------------------------------------------------------
    ¬-----
    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

    ReplyDelete
  13. From: Bushnell, Timothy Timothy_Bushn...@URMC.Rochester.edu
    Date: Fri Mar 21 2008 - 07:21:57 EDT

    Colleagues:

    As you probably know, ISAC is holding elections this year. The
    deadline
    for voting is next Wednesday, March 26th. This was announced via
    email
    and on the ISAC homepage at:
    http://www.isac-net.org/content/view/730/2/ .

    I am a candidate for Biological Councilor, and would like to share
    with
    you my thoughts on my goals and plans should I be elected. I would
    welcome anyone's comments on these goals because, as Bob pointed out,
    with discussion we can refine our positions and be responsive to you,
    the members of ISAC.

    What I hope to bring to ISAC is an expansion of the existing programs
    which serve to unite and coordinate existing affiliated societies in
    North America and abroad. ISAC is uniquely positioned to support the
    growth and development of regional meetings and other events to
    facilitate professional networking and contacts directly related to
    cytometry. Networking at such meetings is a very effective way of
    communicating and sharing pertinent information about cytometry -
    often
    to those not affiliated with ISAC - which will increase membership as
    the benefits of ISAC association are presented to an untapped market.

    These meetings can also serve as a clearinghouse to discuss and
    promulgate the ISAC initiatives including: education, data
    presentation,
    data file standardization, and biosafety. Getting this information in
    the hands of the casual user will greatly enhance ISAC's efforts to
    affect wholesale change in the scientific community.

    I'm very enthusiastic about adding my efforts to the ISAC - most
    specifically areas I have expertise in:

    * Expanding the membership base in
    North
    America and abroad by developing ISAC initiated outreach programs, at
    the local and regional level. These programs will seek to identify
    the
    casual user of cytometry, and provide them with the methods,
    protocols
    and standards that ISAC has and will continue to develop.

    *

    * Finding, recognizing and recruiting
    cytometry facility core directors as a group vital to our membership
    and
    supporting them by offering ISAC models, standards, information, as
    well
    as an international resource to which they can come with problems,
    questions and issues.

    *

    * Supporting and building more
    regional
    meetings with a greater ISAC presence via an information kiosk,
    financial support for speakers, and a level of professional
    camaraderie
    that has been the hallmark of cytometry users around the world.

    *

    * Building stronger, mutually
    beneficial
    alliances with corporate sponsors at a regional level to facilitate a
    growing base of new and existing regional groups.

    My experience in developing and growing the WNYFUG from nothing, as
    well
    as my training as a member and program chair of the long-running
    GLIIFCA
    meeting provides me the perspective and skill-set necessary to
    achieve
    these goals.

    I am an avid supporter of technology, specifically cytometry based
    instrumentation, for the greater understanding of biology across the
    board - however, with such change and development as we've seen in
    just
    20 years, that needs to be tempered with sound practices, strength of
    information, networking on a global scale so that we are keenly aware
    of
    both developments in cytometry as well as potential pitfalls. The key
    to
    this level of awareness on a global scale is by seeing and serving
    the
    regional areas, where those 'in the trenches' can find guidance and
    direction from those around the world.

    I would urge all ISAC members to take a few minutes to review the
    candidates and cast a vote. Your selection helps shape the future of
    the Society.

    Thank you in advance for your support,

    Tim Bushnell

    Timothy Bushnell, Ph.D.

    Research Assistant Professor, Pediatrics and Oncology

    Co-Director, URMC Flow Cytometry Facility

    Office: 585-273-5535

    Lab: 585-273-1361

    Cell: 585-690-5157

    Fax: 585-276-0233

    http://www.urmc.rochester.edu/Aab/geneped/flow/

    http://www.urmc.rochester.edu/wnyfug/

    Received on Fri Mar 21 15:58:00 2008

    ReplyDelete
  14. This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -
    17:35:29 EST

    Purdue Cytometry Mailing List: Re: Thanks for the suggestions -

    [Disclaimer: Yes, I live off FlowJo sales, and that's a blatantly
    commercial statement,

    but it gets technical from here on.] We've
    played with spatial 3D ...
    www.cyto.purdue.edu/hmarchiv/2006/0939.htm

    Tim Bushnell & Ryan Duggan ..... Purdue
    University Cytometry Laboratories, West Lafayette, IN ...
    www.gliifca.org/pdf/GLIIFCA-2004.pdf - Similar pages - Note this

    MyCyte

    Thanks Tim Timothy Bushnell, Ph.D. Research Assistant
    Professor, ... Justin, We're working hard to finalize FlowJo
    Collectors' Edition, ...
    mycyte.org/index.php?

    option=com_newsfeeds&task=view&feedid=11&Itemid=70 - 133k - Cached -
    Similar pages - Note this

    From: Adrian Smith A.Sm...@centenary.usyd.edu.AU



    (Disclaimer: - I provided a some input into the way the platform
    works and I have been beta testing FlowJo for a while now)



    ISAC Congress Bilologiacl Councilor, UR, Webmaster and Great lakes
    Imaging

    Sales Rep?

    Subject: Final Call for Flowjo order
    From: "Bushnell, Timothy" tim_bushn...@URMC.ROCHESTER.EDU
    Reply-To: Bushnell, Timothy
    Date: Wed, 13 Aug 2008 16:59:51 -0400
    Content-Type: multipart/alternative
    Parts/Attachments: text/plain (39 lines) , text/html (40 lines)

    Content-Type: text/html
    This is the final call for the bulk Flowjo order. I need all orders
    in by Monday afternoon (8/18). The original message is below:
    ------------

    Hello all:

    In case you missed our spring order, I am putting together another
    order for Flowjo software. I will be placing it in the month of
    August, to try to take advantage of the

    “Buy 2- get 1 free” sale.

    Currently a single dongle costs $1495.


    However, if there are three
    investigators interested in getting a dongle during this promotion,


    each dongle would cost $997



    (2x1495 = 2990/3 = $997).


    This is a
    great
    price.

    There is also no limit to the number of free dongles
    available.

    So, if you are interested, please email me the following information:

    PI:
    Contact name and number:
    Account number to charge:

    Regards
    Tim Bushnell

    --
    Tim Bushnell, Ph.D.
    Co-Director, URMC Flow Cytometry Facility
    Office: 585-273-5535
    Cell: 585-690-5157
    http://www.urmc.rochester.edu/flow-core/
    http://www.urmc.rochester.edu/wnyfug/

    ____UR_Cytometry______Subscribers Corner_____ https://lists.rochester.edu
    LISTS.ROCHESTER.EDU ( UR_CYTOMETRY: 24 matches.. )

    Item # Date Time Lines Subject
    000139 2008-08-13 16:59 112 Final Call for Flowjo order
    000138 2008-08-06 14:54 75 Summer Flowjo special
    000131 2008-07-17 08:49 104 Re: Reminder: Flowjo lecture and support
    000129 2008-07-17 06:24 73 Reminder: Flowjo lecture and support
    000127 2008-07-14 14:05 87 Tree Star Flowjo Training/discussions,
    Thursday, July 17th
    000081 2008-03-14 12:21 228 Reminder: Spring Flowjo order
    000079 2008-03-03 13:03 221 Spring Flowjo order
    000070 2008-01-23 13:24 291 Feedback requested on Flowjo web seminars
    000069 2008-01-18 09:57 249 Reminder: TODAY 1 pm - Flowjo Seminar on
    DNA Analysis and Cell Proliferation
    000068 2008-01-16 11:31 378 Resend: Reminder: Friday 1 pm - Flowjo
    Seminar on DNA Analysis and Cell Proliferation
    000067 2008-01-16 09:59 220 Reminder: Friday 1 pm - Flowjo Seminar on
    DNA Analysis and Cell Proliferation
    000066 2008-01-11 10:31 221 Reminder: Today 1 pm - Flowjo Seminar on
    Compensation and Transformation
    000065 2008-01-09 11:20 214 Reminder: Friday 1 pm - Flowjo Seminar on
    Compensation and Transformation
    000063 2008-01-04 10:12 193 Reminder: 1 pm - Flowjo Seminar
    000061 2008-01-02 09:46 244 January is Flowjo month at URMC
    000057 2007-12-04 09:13 267 January is FlowJo Month at URMC
    000047 2007-10-19 10:11 209 Today is the last day to join the Flowjo
    bulk order
    000046 2007-10-17 10:55 284 Last call - Fall Flowjo order
    000042 2007-10-09 09:29 256 2nd call - Fall Flowjo order
    000040 2007-10-01 09:30 242 Fall Flowjo order
    000034 2007-07-12 06:35 198 Reminder: Flowjo seminar today 1-3 pm
    000032 2007-07-03 15:36 88 Post WNYFUG 2007 FlowJo Seminar
    000005 2007-04-12 09:41 218 Reminder - Flowjo order
    000002 2007-04-03 14:55 248 Flowjo purchase 2007

    In the study of economics and market competition, collusion takes
    place within an industry when rival companies cooperate for their
    mutual benefit. Collusion most often takes place within the market
    form of oligopoly, where the decision of a few firms to collude can
    significantly impact the market as a whole. Cartels are a special
    case
    of explicit collusion. Collusion which is not overt, on the other
    hand, is known as tacit collusion.

    *********************************************************************************************

    Answer: The Purdue Cytometry discussion group is strictly for
    discussion of scientific issues relating to the fields in which ISAC
    is generally involved. This includes flow cytomery and imaging and
    basic science areas of cellular function, cell cycling, immunology,
    microbiology and the many areas where single cells or tissues are
    analysed.

    To join you must send a request to: Subscr...@flowcyt.cyto.purdue.edu
    and you must include your name, your institution and your area of
    scientific interest. All subscriptions are reviewed - it is not
    automatic.

    **********************************************************************************************

    > From: J. Paul Robinson
    > Reply To: j...@flowcyt.cyto.purdue.edu
    > Sent: Friday, August 20, 2004 2:25 PM
    > To: Cytometry Mailing List
    > Subject: Re: mr on Apple web site

    > ummm....Mario says..
    > "In life sciences - particularly in research life sciences -
    > probably 50 to 70% of research laboratories used
    > Macs"....while I have a passionate dislike for Windows......is
    > this really true ??? or is the key word there "used"?? (Ok...I
    > have put on my helmet and armor....waiting...)
    > paul

    > > For all of the mr groupies out there in cytometry cyberspace. Don't wet
    > your
    > > pocket protectors over this.

    > > Honestly though, well deserved praise for Mario & the Tree Star group:
    > > http://www.apple.com/science/profiles/roederer
    **********************************************************************************************



    Re: mr on Apple web site

    ReplyDelete
  15. ISAC Congress Executive Joanne Lannigan



    joannelanni.._at_virginia.edu with questions

    University of Virginia's Site License for FlowJo

    http://www.healthsystem.virginia.edu/internet/cyto ...

    FlowJo Site License
    Registration Form

    Complete the form below to access the University of Virginia's Site
    License for FlowJo data analysis software. All fields with * must be
    completed or your registration will not be processed. Once your
    information has been received and verified you will receive a serial
    number which you must enter in FlowJo on the computer whose hardware
    address you provided. Cost per user license will be determined at the
    end of the year depending on the average number of registered users
    for the year. (See instructions for pricing structure) This amount
    will be billed to the PTAO provided below, so please make sure the
    PTAO you provide does not expire before that time. Completion of this
    registration form is a valid request for services and assumes the
    approval of the Principal Investigator of the PTAO account provided.
    Cont
    act
    Joanne Lannigan joannelanni..._at_virginia.edu with questions.

    *****************************************************************************************************





    GLIIFCA 2007-2008 Officers and Committees

    President and Scientific Program Chair Paul Wallace

    Program Committee Members Mike Sramkoski, Vera Donnenberg

    Executive Secretary
    Co-secretary

    Mary Paniagua
    Ryan Duggan*
    Treasurer Brian K. DuChateau
    Education and CMLE Chairs Jonni Moore***********
    Vendor Liasons: Karen Domenico, Tom Sawyer
    Website Manager Tim Bushnell* *******************

    STEERING COMMITTEE MEMBERS
    Canada David Hedley , Betty-Anne McBey,Nicole McFarlane
    Illinois Charles Goolsby , Maurice R. G. O'Gorman , Mary
    Paniagua,
    Ryan Duggan*
    Indiana Lisa Green ,** Bartek Rajwa********************
    Iowa Bruce Pesch , Kristi Harkins
    Massachusetts Betsy Ohlsson-Wilhelm, Brian K. DuChateau
    Michigan Alexander Nakeff , Louis King
    Minnesota Paul Champoux
    New York Paul Wallace , Timothy Bushnell************************
    Ohio Karen Domenico , Tom Sawyer , Mike Sramkoski
    Pennsylvania Jonni Moore *, Vera Donnenberg
    Virginia Joanne Lannigan**************************************
    Wisconsin Kathy Schell , Kathy A. Muirhead , Matt Hanson
    Emeritus Carleton C. Stewart, Sigrid Stewart

    Review the Executive Members on ISAC Congresss

    Re: clinical flow cytometry


    This message: [ Message body ] [ More options ]
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    to ] [ Next in thread ]
    From: Ryan Farmer far...@treestar.com *********** WEBMASTER


    Date: Mon Apr 14 2008 - 19:05:51 EDT

    There is another site of interest along these lines.

    Mycyte.org

    is well established and has a variety of online texts, articles and
    other links (protocols, standards, etc.). Users can expand the
    variety
    and
    amount of information as well.

    It is located at http://www.mycyte.org.

    Ryan F ********WebMaster Mycyte.org

    ReplyDelete
  16. ISAC Montpellier CyberCafe

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    From: Adam Treister adam@treestar.com

    Date: Tue May 11 2004 - 17:28:22 EST

    Dear ISAC Montpellier attendees:

    We once will again be putting on an Internet cafe for your

    gastronomical and connectivity pleasure at ISAC.

    This year, we'll be rechristening the establishment. Its has been

    renamed the Fluor-de-lis. See our logo, below. We've adopted the

    twelfth century crest of King Louis VII, but we've added more colors,

    and installed a two-way sort. We hope to provide an oasis for you to

    rest your feet and mind, check in with home, and enjoy an atmosphere of

    old world provincial charm, combined with blindingly fast packet

    throughput.

    Since every time we do this, it gets bigger and more elaborate (on a

    log scale), we've invited a couple of new companies in to bring you

    more space, more computers, more food and drink. We're pleased to

    share the sponsorship of the Fluor-de-lis with two young companies,

    Biotrue (www.biotrue.net) & Cytopeia (www.cytopeia.com).

    Both are introducing exciting new products for cytometry. We think

    you ought to know about them, and they've agreed to donate their

    boothspace to be your connection to the outside world. ISAC is

    generously supplying the bandwidth.

    We'll also be showing brand new versions of FlowJo, for both

    Mac and Windows. This will be our biggest release ever. If you've

    heard

    FlowJo is the flow cytometry software to beat, we're about to raise the

    bar once again.

    Au revoir,

    Adam

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

    Adam Treister

    Tree Star, Inc.

    340 A St.

    Ashland OR 97520

    1-800-366-6045

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

    Received on Wed May 12 16:38:00 2004

    This message: [ Message body ]

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    ReplyDelete
  17. histogram raw data

    This message: [ Message body ] [ More options ]

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    From: VSH - Tech Support tech@vsh.com

    Date: Tue Apr 27 2004 - 09:02:24 EST

    Hello, Flow-ers,

    WinList software, for PC or for Mac, can export FCS file data in a

    tab-delimited ASCII text format. You may choose any or all parameters for

    export, raw and/or compensated data, and gating may be applied as well. For

    more information, please see our web site at www.vsh.com or contact me

    directly.

    Best regards,

    Mark

    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

    Received on Tue Apr 27 13:18:00 2004

    This message: [ Message body ]

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    ReplyDelete
  18. Creating a database of FCS files

    This message: [ Message body ] [ More options ]

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    From: VSH - Tech Support tech@vsh.com

    Date: Tue Apr 27 2004 - 09:00:36 EST

    Hello, Flow-ers,

    With reference to databasing FCS file keywords, WinList from Verity Software

    has full databasing capability. The user may choose FCS file keywords and

    results keywords to database in a delimited ASCII text format. The database

    can be easily imported into Excel and similar programs. WinList supports

    batch processing, and is available for PC and Mac platforms. For more

    information and to download a trial version, visit our web site at

    www.vsh.com.

    Mark Munson

    Sales Manager, Verity Software House.

    Received on Tue Apr 27 12:58:00 2004

    This message: [ Message body ]

    Next message: VSH - Tech Support: "histogram raw data"

    Previous message: James Mittler: "Hoechst on Aria"

    Next in thread: Smoot, Doug: "RE: Creating a database of FCS files"

    Maybe reply: Smoot, Doug: "RE: Creating a database of FCS files"

    Maybe reply: Ryan Brinkman: "Re: Creating a database of FCS files"

    Maybe reply: Christopher J. Groves: "Re: Creating a database of FCS files"

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    October 5, 2008 6:28 AM

    ReplyDelete
  19. From: Adrian Smith A.Smith@centenary.usyd.edu.AU

    Date: Thu Apr 22 2004 - 20:56:40 EST

    Hi all,

    Some of the users here have raised the desirability of having a

    database of all the FCS headers from all their data files. They could

    then, for example, search for all the files/experiments in which they

    used a particular stain etc.

    Is anybody doing this? Would this be something that other people

    would find useful?

    I would love to set something up but I don't have the requisite

    skills or time at the moment.

    As a temporary measure I suggested they export the FCS header info

    from FlowJo using using a table and then compile them all in another

    program like excel. This works for a few experiments but it needs to

    be automated (and easy) if it is going to be generally applicable.

    Any comments or suggestions?

    Adrian Smith

    Centenary Institute of Cancer Medicine and Cell Biology

    Sydney, Australia

    Received on Fri Apr 23 15:38:00 2004

    This message: [ Message body ]

    Next message: Mario Roederer: "ISAC - MultiColor Flow Cytometry"

    Previous message: Dorothea Torous: "histogram raw data"

    Next in thread: David Novo: "Re: Creating a database of FCS files"

    Reply: David Novo: "Re: Creating a database of FCS files"

    Reply: Robert C. Leif: "RE: Creating a database of FCS files"

    Reply: Marty Bigos: "Re: Creating a database of FCS files"

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    ReplyDelete
  20. Re: Creating a database of FCS files

    This message: [ Message body ] [ More options ]

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    From: David Novo dave@denovosoftware.com

    Date: Fri Apr 23 2004 - 19:52:09 EST

    Hello Adrian,

    If you are willing to use a PC, then FCS Express (www.denovosoftware.com)

    can do what you need. You can choose which keywords you are interested in

    and then automatically export them to Excel. Each keyword will become a

    different column and each data file will have its own row. You can choose

    which files you are interested in processing, and FCS Express will

    automatically extract the keywords you are interested in and place them in

    the spreadsheet.

    -Dave

    At 06:56 PM 4/22/2004, Adrian Smith wrote:

    >Hi all,

    >

    >Some of the users here have raised the desirability of having a database

    >of all the FCS headers from all their data files. They could then, for

    >example, search for all the files/experiments in which they used a

    >particular stain etc.

    >

    >Is anybody doing this? Would this be something that other people would

    >find useful?

    >

    >I would love to set something up but I don't have the requisite skills or

    >time at the moment.

    >

    >As a temporary measure I suggested they export the FCS header info from

    >FlowJo using using a table and then compile them all in another program

    >like excel. This works for a few experiments but it needs to be automated

    >(and easy) if it is going to be generally applicable.

    >

    >Any comments or suggestions?

    >

    >Adrian Smith

    >Centenary Institute of Cancer Medicine and Cell Biology

    >Sydney, Australia

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

    David Novo

    President

    De Novo Software

    www.denovosoftware.com

    phone: (310) 558-4955

    fax: (310) 943-1489

    Received on Mon Apr 26 13:18:00 2004

    This message: [ Message body ]

    Next message: jschmitz@bidmc.harvard.edu: "RE: Antibody titrations (2004)"

    Previous message: facs_copy@wehi.EDU.AU: "Re: histogram raw data"

    In reply to: Adrian Smith: "Creating a database of FCS files"

    Next in thread: Robert C. Leif: "RE: Creating a database of FCS files"

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    ReplyDelete
  21. RE: Creating a database of FCS files

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    From: Robert C. Leif rleif@rleif.com

    Date: Sat Apr 24 2004 - 11:57:17 EST

    The FCS header files have already been parsed and stored in a database(1).

    The product was QCTracker from Phoenix Flow Systems.

    Experience with the development of that product was one of the reasons for

    the creation of CytometryML. Since the data in a CytometryML file is all

    validated XML, it can be imported without any changes into commercially

    available databases, spreadsheets and other applications. The list mode

    data and associated index files are stored as a simple array of

    records(structs), which can be read by commercially available common

    programming languages or manipulated by .Net object.

    1. R. C. Leif, R. Rios, M. C. Becker, C. K. Becker, J. T. Self, and S. B.

    Leif, "The Creation of a Laboratory Instrument Quality Monitoring System

    with AdaSAGE". Advanced Techniques in Analytical Cytology, Optical Diagnosis

    of Living Cells and Biofluids, Ed. T. Askura, D. L. Farkas, R. C. Leif, A.

    V. Priezzhev, , and B. J. Tromberg.. A. Katzir Progress in Biomedical Optics

    Series Editor SPIE Proceedings Series, Vol. 2678, 232-239 (1996).

    2. R. C. Leif, S. B. Leif, and S. H. Leif, "CytometryML, An XML Format based

    on DICOM for Analytical Cytology Data ", Cytometry 54A pp. 56-65 (2003).

    3. R.C. Leif, S.H. Leif, S.B. Leif, CytometryML, a markup language for

    analytical cytology, in Manipulation and Analysis of Biomolecules, Cells and

    Tissues, D. V. Nicolau, J. Enderlein, and R. C. Leif, Editors, SPIE

    Proceedings Vol. 4962 pp 288-297 (2003).

    -----Original Message-----

    From: Adrian Smith [mailto:A.Smith@centenary.usyd.edu.au]

    Sent: Thursday, April 22, 2004 6:57 PM

    To: cyto-inbox

    Subject: Creating a database of FCS files

    Hi all,

    Some of the users here have raised the desirability of having a

    database of all the FCS headers from all their data files. They could

    then, for example, search for all the files/experiments in which they

    used a particular stain etc.

    Is anybody doing this? Would this be something that other people

    would find useful?

    I would love to set something up but I don't have the requisite

    skills or time at the moment.

    As a temporary measure I suggested they export the FCS header info

    from FlowJo using using a table and then compile them all in another

    program like excel. This works for a few experiments but it needs to

    be automated (and easy) if it is going to be generally applicable.

    Any comments or suggestions?

    Adrian Smith

    Centenary Institute of Cancer Medicine and Cell Biology

    Sydney, Australia

    Received on Mon Apr 26 14:38:00 2004

    This message: [ Message body ]

    Next message: Stojan Dimitrov: "anti-IL-6 antibody against not-recombinant IL-6"

    Previous message: Kroeger, Jodi: "RE: ISAC - MultiColor Flow Cytometry"

    In reply to: Adrian Smith: "Creating a database of FCS files"

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    ReplyDelete
  22. From: Marty Bigos mbigos@gladstone.ucsf.edu

    Date: Tue Apr 27 2004 - 11:05:04 EST

    Hi Adrian -

    The need of a management system for flow cytometry (as well as

    microscope image) data has been apparent for quite some time. Not

    only would it help in the research aspects you mentioned, it could

    also provide many other functions, such as secured sharing of data,

    easy availability from any networked site, etc.

    For several years I have been fortunate to be involved with Bill Hyun

    of UCSF through an SBIR with a local software company in SF (Biotrue,

    Inc.) to develop such a system. We are in beta test now.

    The product, (which doesn't have a formal name yet, but is informally

    called RDMS - Research Data Management System), will be announced at

    the ISAC meeting at the end of May. Biotrue will have a booth there

    to give demos of the product, and I will be giving a workshop talk on

    some of the ideas behind its design.

    I do have a (small) financial interest in Biotrue, but even if I

    didn't I would recommend that you look at the product as a possible

    solution to your needs. You can contact Jenny Liu (JLiu@Biotrue.Net)

    for more information.

    Marty

    Marty Bigos

    Director, Flow Core

    Gladstone Institute of Virology and Immunology

    Building 3 SFGH Rm 509

    415-695-3832

    >Hi all,

    >

    >Some of the users here have raised the desirability of having a

    >database of all the FCS headers from all their data files. They

    >could then, for example, search for all the files/experiments in

    >which they used a particular stain etc.

    >

    >Is anybody doing this? Would this be something that other people

    >would find useful?

    >

    >I would love to set something up but I don't have the requisite

    >skills or time at the moment.

    >

    >As a temporary measure I suggested they export the FCS header info

    >from FlowJo using using a table and then compile them all in another

    >program like excel. This works for a few experiments but it needs to

    >be automated (and easy) if it is going to be generally applicable.

    >

    >Any comments or suggestions?

    >

    >Adrian Smith

    >Centenary Institute of Cancer Medicine and Cell Biology

    >Sydney, Australia

    --

    Received on Tue Apr 27 13:58:00 2004

    This message: [ Message body ]

    Next message: J. Paul Robinson: "RE: ISAC - MultiColor Flow Cytometry"

    Previous message: Szmania, Susann M: "[Reagent source?]"

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    ReplyDelete
  23. RE: ISAC - MultiColor Flow Cytometry

    This message: [ Message body ] [ More options ]

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    From: Marty Bigos mbigos@gladstone.ucsf.edu

    Date: Tue Apr 27 2004 - 19:21:42 EST

    Just to give credit where it is due:

    The presentations at this workshop were (in order of appearance):

    Marty Bigos - Gladstone Institutes - Basic Concepts for Compensation

    Mario Roederer - NIH - The Hard, the Bad, and the Ugly

    Nicole Baumgarth - UC Davis - The "How-to Guide" to Compensation for

    Multicolor Cytometry

    Panel - the above 3 joined by Bill Hyun (UCSF) and David Parks (Stanford)

    The workshop was organized by Treestar, Inc. and the Gladstone Flow

    Core. Many companies contributed to making it happen (in alphabetical

    order):

    Amnis, BD Biosciences, Beckman-Coulter, Caltag, DakoCytomation,

    DeNovo Software, FloCyte Associates, Miltenyi, and Southern BioTech.

    Paul Robinson and Bartek Rajwa did the video post-production.

    Marty

    >The question has been asked about videoing ISAC

    >workshops and tutorials. On CD8 which will be coming out

    >at ISAC, we have a bonus. CD8 is a 2 cd set and the

    >second CD is an outstanding tutorial that Mario and Marty

    >Bigos and others put on in San Francisco last year. Its really

    >good!

    >

    >We would like to do this for selected tutorials even at ISAC

    >and we are developing a proposal for ISAC as we speak. It

    >would help to know if this was something of interest.

    >

    >Regards

    >paul robinson

    >Purdue

    >

    >

    >

    >On 26 Apr 2004 at 11:03, Kroeger, Jodi wrote:

    >

    >> What are the chances that this tutorial, (and others of high

    >>interest) could be

    >> video taped and broadcasted over the internet for those

    >>unfortunate souls unable

    >> to attend? At least to those of us who are ISAC members?

    >>

    >> -----Original Message-----

    >> From: Mario Roederer [mailto:roederer@drmr.com]

    >> Sent: Thursday, April 22, 2004 11:48 PM

    >> To: cyto-inbox

    >> Subject: ISAC - MultiColor Flow Cytometry

    >>

    >>

    >> For the second straight ISAC (officially making this a tradition),

    >> I'll be running a Saturday tutorial on Multicolor Flow Cytometry.

    >> This time, instead of being at the unhappy hour of 8 in the morning,

    >> it will be at a much more civilized early afternoon time.

    >>

    >> This tutorial (aptly numbered: Tutorial "X") will be much more

    >> pragmatic in nature than previous. We will have three talks that

    >> will center on how to plan and implement a multicolor

    >> immunophenotyping experiment, including instrument setup and

    >> validation (Steve Perfetto), multicolor panel design and optimization

    >> (myself), and bridging the gap to the clinic (Brent Wood). Assuming

    >> that most of us are not in a full post-prandial siesta mode, this

    >> should be a highly interactive session: please come with your

    >> questions, data, artefacts, and complaints in hand!

    >>

    >> If you are jumping on the 7, 10, or 15-color bandwagon, then this

    >> tutorial is for you! If you've never done more than 2-color

    >> staining, then enjoy the wonderful city of Montpellier instead :)

    >>

    >> If you have any suggestions for specific topics, or any general

    >> questions, please send them to me in advance and we will try to

    >> address them.

    >>

    >> Regards,

    >>

    >> mr

    >> ######################################################################

    >> This transmission may be confidential or protected from disclosure and

    >> is only for review and use by the intended recipient. Access by

    >> anyone else is unauthorized. Any unauthorized reader is hereby

    >> notified that any review, use, dissemination, disclosure or copying of

    >> this information, or any act or omission taken in reliance on it, is

    >> prohibited and may be unlawful. If you received this transmission in

    >> error, please notify the sender immediately. Thank you.

    >>

    >> ######################################################################

    >>

    >

    >

    >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

    >

    >Have you seen our new HCS webpage?

    >http://www.cyto.purdue.edu/hcs

    Received on Wed Apr 28 16:56:53 2004

    This message: [ Message body ]

    Next message: Christopher J. Groves: "Re: Creating a database of FCS files"

    Previous message: Cris Bare: "Re: RFI's on longitudinal data (question restated)"

    In reply to: J. Paul Robinson: "RE: ISAC - MultiColor Flow Cytometry"

    Next in thread: Jennifer Wilshire: "More Credit for Comp Workshop Video"

    Reply: Jennifer Wilshire: "More Credit for Comp Workshop Video"

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    ReplyDelete
  24. Purdue University Cytometry Labatories & Mail List
    RE: Bad Flow Data & reviewing -- What can we do? From: Claudio Vallan
    (claudio.val...@dkf7.unibe.ch) Date: Thu Oct 25 2001 - 02:39:08 EST •
    Next message: Howard
    Shapiro: "Re:Virus Sorting" • Previous message: Maciej Simm: "Re: Bad
    Flow data thread" • In reply to: Gerhard Nebe-von-Caron: "RE: Bad
    Flow
    Data & reviewing -- What can we do?" • Next in thread: sterling
    stoudenmire: "RE: Bad Flow Data & reviewing -- What can we do?" •
    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ] ________________________________________

    Maybe


    it is not a bad idea to make post print reviews, white papers,
    instructions to authors etc. etc.
    But I think al of this will be mainly for


    our own use. "Normal" scientist will probably never know that such
    stuff even exists.


    I think that the only way to make scientist aware of the problems
    thay
    may encounter when generating cytometric
    datas


    is to infiltrate their meetings and conferences and have the guts to
    stand up


    and tell them that what they are showing on that slide is just
    bullshit.


    If that happens a few time they will certainly have a closer look at
    what they are doing.


    Though, I do not think they will take us very seriously if we just
    tell them that they have mislabelled the axes.


    Claudio Vallan ===================================================
    Claudio Vallan PhD Phone Lab: 031 / 632 88 76 FACS-LAB DKF Phone
    Office: 031 / 632 99 68 University of Bern E-Mail:
    val...@dkf7.unibe.ch c/o Institute of Pathology Murtenstrasse 31
    Insel
    hosptial area only: 3010
    Bern Beeper: 181 67 59
    \
    On Aug 20, 2004, at 2:25 PM, J. Paul Robinson wrote:

    ReplyDelete
  25. If anyone is interested in their software to function properly please
    contact Kanecki Associates Inc.

    In November of 2007 Kanecki Associates Inc developed the FCS Cytopro
    to resolve the Memory issues with the Diva Software after a request
    from one person at BD. 10 Million Events By 40 Parameters with all
    128
    Permeations.


    As of today’s posts on the Purdue Cytometry Mail List the issues
    still
    exist.


    Since are not allowed on the Purdue Cytometry Mail List and have ISAC
    Congress Executives blocking us from the market we would like to make
    BD and all other Corporations, Hospitals, Universities, etc. aware
    that we can LICENSE A PATCH that will resolve the issues in BD's DIVA
    software.


    We are willing to work with BD and are unaware if they knew of the
    one
    person’s prior request or even what was done with the software once
    the one person from BD received it. We will send a letter to BD's
    corporate office to notify them we are willing to work with the
    corporation if they wish. We did develop the code and are willing to
    work directly with BD if they wish to compile it to the troubled
    software to end all the issues.


    There is no need for Purdue University Cytometry Laboratories
    Executives to keep up with suspected exclusion of those who can help.
    They need to resolve the issues in the system with the ISAC Congress
    Executives in the Data Standards Committee and work with other
    corporations even if the won't benefit financially personally.


    If anyone is interested in their software to function properly please
    contact Kanecki Associates Inc.


    Http://www.kanecki.com
    C...@Kanecki2.com
    Mi...@kanecki.com


    Mitchell Haynes
    Vp.
    Kanecki Associates Inc
    281-444-1619


    Diva 6.1.1 user issues
    This message: [ Message body ] [ More options ]
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    thread ] [ Replies ]
    From: Wayne Turnbull wayne.turnb...@kcl.ac.uk
    Date: Tue Oct 14 2008 - 09:32:19 EDT


    Afternoon flowers,


    Having recently moved to Diva 6.1.1, we're experiencing some software
    lock-up problems, usually after closing down CS&T, that require a
    full re-install, which is becoming tiresome, and I wondered if any
    others had experienced similar problems?


    Wayne


    Wayne Turnbull
    Flow Cytometry Services
    Department of Immunobiology
    GKT Guy's Hospital
    London SE1 9RT
    Received on Tue Oct 14 11:58:00 2008
    This message: [ Message body ]
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    RE: Diva 6.1.1 user issues
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    From: Nilles, Tricia L.. tnil...@jhsph.edu
    Date: Wed Oct 15 2008 - 09:43:57 EDT


    Wayne,


    Yes, we also have experienced a similar issue. After running CS&T,
    we
    cannot make any
    changes (ie renaming specimens, experiments) we first have to exit
    and
    relaunch the
    software. Logging out does not work. I have discussed this with our
    local service rep
    and also one of the software specialists who came in for local
    training and demos, and no
    one has offered a 'fix'.


    Tricia L Nilles
    Research Specialist
    Flow Cytometry Laboratory
    Johns Hopkins Bloomberg School of Public Health
    Phone: 410-502-9290
    Fax: 410-614-2503
    -





    -----Original Message-----
    From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
    Sent: Tuesday, October 14, 2008 9:32 AM
    To: cyto-inbox
    Subject: Diva 6.1.1 user issues

    Afternoon flowers,


    Having recently moved to Diva 6.1.1, we're experiencing some software
    lock-up problems, usually after closing down CS&T, that require a
    full re-install, which is becoming tiresome, and I wondered if any
    others had experienced similar problems?


    Wayne


    Wayne Turnbull
    Flow Cytometry Services
    Department of Immunobiology
    GKT Guy's Hospital
    London SE1 9RT
    Received on Wed Oct 15 12:38:00 2008
    This message: [ Message body ]
    Next message: Julie Nelson: "MoFlo pressure issues"
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    Cytometer anyone? Circa 1991"
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    Re: Diva 6.1.1 user issues
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    From: Berend b.hooibr...@amc.uva.nl
    Date: Thu Oct 16 2008 - 03:58:54 EDT


    We have seen similar problems with 6.1.1 and CST module. I am not
    able to run the cst when I started the diva software in a Windows
    (normal)User account. It locks-up immediately. So, we first log in
    as
    administrator in windows xp, do the cst run, quit diva after this qc-
    check and log in as (limited) user. Thereafter we startup diva again
    and everything works fine, except the cst and configuration modules.
    Our service engineer (BD) couldn't fix it so far. Still I prefer the
    let everybody work as limited user with the LSR, to keep systems
    clean from al kind of ?%^&b 9b b " people want to install.
    Berend


    On Oct 15, 2008, at 3:43 PM, Nilles, Tricia L.. wrote:


    > Wayne,


    > Yes, we also have experienced a similar issue. After running CS&T,
    > we cannot make any
    > changes (ie renaming specimens, experiments) we first have to exit
    > and relaunch the
    > software. Logging out does not work. I have discussed this with
    > our local service rep
    > and also one of the software specialists who came in for local
    > training and demos, and no
    > one has offered a 'fix'.


    > Tricia L Nilles
    > Research Specialist
    > Flow Cytometry Laboratory
    > Johns Hopkins Bloomberg School of Public Health
    > Phone: 410-502-9290
    > Fax: 410-614-2503


    > -----Original Message-----
    > From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
    > Sent: Tuesday, October 14, 2008 9:32 AM
    > To: cyto-inbox
    > Subject: Diva 6.1.1 user issues


    > Afternoon flowers,


    > Having recently moved to Diva 6.1.1, we're experiencing some software
    > lock-up problems, usually after closing down CS&T, that require a
    > full re-install, which is becoming tiresome, and I wondered if any
    > others had experienced similar problems?


    > Wayne


    > Wayne Turnbull
    > Flow Cytometry Services
    > Department of Immunobiology
    > GKT Guy's Hospital
    > London SE1 9RT


    Berend Hooibrink
    Flow cytometry core facility
    Dept.. Cellbiology & Histology room L3-115
    AMC
    Meibergdreef 15
    1105AZ Amsterdam
    Netherlands
    Tel.: 31(0)20-5666804
    Fax: 31(0)20-6974156
    Received on Thu Oct 16 15:38:00 2008
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    Meeting Report published; 14th Leipziger Workshop announcenment"
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    RE: Diva 6.1.1 user issues
    This message: [ Message body ] [ More options ]
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    to ] [ Next in thread ]
    From: Ted Hibbs Ted_Hi...@bonfils.org
    Date: Thu Oct 16 2008 - 22:27:10 EDT


    Berend,


    We had a similar issue when we first got our BD CantoII with Diva
    6.1.1. It
    is related to the permissions on the folders on the C:\ drive, though
    I donb t
    remember exactly where. Once I changed the permissions on the
    folders, it is
    working well.


    Ted


    From: Berend [mailto:b.hooibr...@amc.uva.nl]
    Sent: Thursday, October 16, 2008 1:59 AM
    To: Cytometry Mailing List
    Subject: Re: Diva 6.1.1 user issues


    We have seen similar problems with 6.1.1 and CST module. I am not
    able
    to run
    the cst when I started the diva software in a Windows (normal)User
    account.
    It locks-up immediately. So, we first log in as administrator in
    windows xp,
    do the cst run, quit diva after this qc-check and log in as (limited)
    user.
    Thereafter we startup diva again and everything works fine, except
    the
    cst
    and configuration modules. Our service engineer (BD) couldn't fix it
    so far.
    Still I prefer the let everybody work as limited user with the LSR,
    to
    keep
    systems clean from al kind of ?%^&b 9b b " people want to install.


    Berend


    On Oct 15, 2008, at 3:43 PM, Nilles, Tricia L.. wrote:


    Wayne,


    Yes, we also have experienced a similar issue. After running CS&T, we
    cannot
    make any


    changes (ie renaming specimens, experiments) we first have to exit
    and
    relaunch the


    software. Logging out does not work. I have discussed this with our
    local
    service rep


    and also one of the software specialists who came in for local
    training and
    demos, and no


    one has offered a 'fix'.


    Tricia L Nilles


    Research Specialist


    Flow Cytometry Laboratory


    Johns Hopkins Bloomberg School of Public Health


    Phone: 410-502-9290


    Fax: 410-614-2503


    -----Original Message-----


    From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]


    Sent: Tuesday, October 14, 2008 9:32 AM


    To: cyto-inbox


    Subject: Diva 6.1.1 user issues


    Afternoon flowers,


    Having recently moved to Diva 6.1.1, we're experiencing some software


    lock-up problems, usually after closing down CS&T, that require a


    full re-install, which is becoming tiresome, and I wondered if any


    others had experienced similar problems?


    Wayne


    Wayne Turnbull


    Flow Cytometry Services


    Department of Immunobiology


    GKT Guy's Hospital


    London SE1 9RT


    Berend Hooibrink


    Flow cytometry core facility


    Dept.. Cellbiology & Histology room L3-115


    AMC


    Meibergdreef 15


    1105AZ Amsterdam


    Netherlands


    Tel.: 31(0)20-5666804


    Fax: 31(0)20-6974156


    Confidentiality Notice: This e-mail message, including any
    attachments, is for the sole use of the intended recipient(s) and may
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    in accordance with those provisions. Any unauthorized review, use,
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    recipient, please contact the sender by reply e-mail and destroy all
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    Received on Fri Oct 17 13:18:00 2008
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    RE: Diva 6.1.1 user issues
    This message: [ Message body ] [ More options ]
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    From: Linkes, Sean Patrick sean.lin...@utoledo.edu
    Date: Tue Oct 14 2008 - 16:11:56 EDT


    No problems here. Our CS&T works wonderfully. Sometimes the setup
    doesn't work right even with a freshly prepared tube of beads (with
    the BD Field Service guy leaving one day prior having aligned the
    lasers). Sean


    Sean Linkes MS
    Research Associate
    Flow Cytometry Core Manager
    The University of Toledo HSC
    (419) 383 3402 http://hsc.utoledo.edu/depts/micro/UT_Flow_Cytometry.html


    ________________________________


    From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
    Sent: Tue 10/14/2008 9:32 AM
    To: cyto-inbox
    Subject: Diva 6.1.1 user issues


    Afternoon flowers,


    Having recently moved to Diva 6.1.1, we're experiencing some software
    lock-up problems, usually after closing down CS&T, that require a
    full re-install, which is becoming tiresome, and I wondered if any
    others had experienced similar problems?


    Wayne


    Wayne Turnbull
    Flow Cytometry Services
    Department of Immunobiology
    GKT Guy's Hospital
    London SE1 9RT
    Received on Wed Oct 15 14:18:00 2008
    This message: [ Message body ]
    Next message: Cappella, Paolo Elia [Nervianoms]: "FCS generator"
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    Cytometer anyone? Circa 1991"
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    RE: Diva 6.1.1 user issues
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    to ]
    From: Roberts, Daniel Daniel.Robe...@covance.com
    Date: Wed Oct 15 2008 - 18:53:42 EDT


    I've been using 6.1.1 since May - no problems here. I'd question
    your
    Ram,
    but if you bought the computer as part of the package - you should be
    OK. I
    know that sometimes leaving the beads on there can cause issues - but
    If
    memory serves (as opposed to habit) the CST software prompts/makes
    you
    take
    the beads off. Other than that, I can't think of why it wouldn't
    reconnect
    to Diva.


    Dan
    Technical Resource Specialist
    Covance Labs, NA
    Vienna, VA 20850


    -----Original Message-----
    From: Linkes, Sean Patrick
    To: cyto-inbox
    Sent: 10/14/2008 3:11 PM
    Subject: RE: Diva 6.1.1 user issues


    No problems here. Our CS&T works wonderfully. Sometimes the setup
    doesn't work right even with a freshly prepared tube of beads (with
    the
    BD Field Service guy leaving one day prior having aligned the
    lasers).
    Sean
    Sean Linkes MS
    Research Associate
    Flow Cytometry Core Manager
    The University of Toledo HSC
    (419) 383 3402
    http://hsc.utoledo.edu/depts/micro/UT_Flow_Cytometry.html


    _____


    From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
    Sent: Tue 10/14/2008 9:32 AM
    To: cyto-inbox
    Subject: Diva 6.1.1 user issues


    Afternoon flowers,


    Having recently moved to Diva 6.1.1, we're experiencing some software
    lock-up problems, usually after closing down CS&T, that require a
    full re-install, which is becoming tiresome, and I wondered if any
    others had experienced similar problems?


    Wayne


    Wayne Turnbull
    Flow Cytometry Services
    Department of Immunobiology
    GKT Guy's Hospital
    London SE1 9RT


    -----------------------------------------------------
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    If anyone is interested in their software to function properly please
    contact Kanecki Associates Inc.


    Http://www.kanecki.com
    Ceo@kanecki.com
    Mitch@kanecki.com


    Mitchell Haynes
    Vp.
    Kanecki Associates Inc
    281-444-1619


    Thank you

    ReplyDelete
  26. Purdue Cytometry Mailing List: SV: Thanks for the suggestions -


    ... cytometry/WEASELv2.html

    http://www.wehi.edu.au/cytometry/WEASELv2.html


    Winlist 3d from Verity House Software (www.vsh.com) Regards Tim


    Timothy Bushnell, Ph.D. Director, CPBR ... Contemporary messages
    sorted:

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    Find Similar
    Highlight
    Re: Thanks for the suggestions - was rendering in 3D

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    From: Adam Treister <...@treestar.com>
    Date: Thu May 18 2006 - 20:20:18 EDT

    On May 12, 2006, at 10:02 AM, Bushnell, Timothy wrote:

    > Thanks to everyone who suggested possible software to view data in
    > 3D. I’ll be trying several different platforms to see which works
    > best for our applications.
    >


    > The suggested platforms include (in alphabetical order):
    >


    > Coulters CXP software for the FC500
    >
    > Rflowcyt
    >



    > Weasel: http://www.wehi.edu.au/cytometry/WEASELv2.html
    >


    > Winlist 3d from Verity House Software (www.vsh.com)
    >
    > Regards
    >
    > TimTim,



    With all due respect to these solutions, you shouldn't think that



    Mario could sleep at night



    if anyone could perform high dimensional
    analysis better than FlowJo.



    [Disclaimer: Yes, I live off FlowJo
    sales, and that's a blatantly commercial statement, but it gets
    technical from here on.]



    We've played with spatial 3D plots a lot, both our own prototypes
    and
    others, and they just don't do a very good job of discriminating
    populations. And its impossible to coherently describe the
    populations you can see.

    I like the slice-and-dice approach that
    you get by making a flipbook on X vs. Y in slices along the Z axis
    (it shows up as a Quicktime movie), but that too is very difficult
    to
    use in a way that's better than two 2D graphs connected by a gate.
    If you really want to increase your dimensionality,


    we're just adding a new "Polyvariate Plot" to the Mac version of FlowJo for next
    week's

    ISAC.

    The idea was taken from RFlowCyt. We've added interface
    refinements to make it more interactive, but like any good R tool,
    it'll astound and confuse you.
    http://www.flowjo.com/v8/html/polyvarplot.html

    The Polyvariate Plot can model transformations in any number of
    dimensions. So it will produce a 3D plot, or as many dimensions as
    you want (Shown below in 5D). And it projects these transformations
    onto a graph window, so you can gate on them.

    We're still trying to figure out the applications for this
    visualization, but if you're looking for another dimension as a way
    to differentiate populations, we think this is potentially much more
    powerful than conventional spatial projections. This is explained
    in the poster P178 at ISAC next week, or at the web page above.

    Be forewarned: This is the opposite end of the sizzle/steak
    spectrum. Most people use 3D graphs to make their PowerPoints look
    spiffy. These graphs are absolutely impossible to explain in a
    presentation.

    Adam

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

    A 3D plot:



    A 5D plot:


    Received on Fri May 19 17:58:00 2006
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    Timothy: "Thanks for the suggestions - was
    rendering in 3D"


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    in 3D"
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    ReplyDelete
  27. I know the request was for Mac software but sometimes we have to
    swallow

    From: David Novo (no...@fhs.csu.McMaster.CA)
    Date: Thu Feb 26 1998 - 17:00:40 EST
    • Next message: JoAnne Thomas: "FACSLoader Upgrade"
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    files"
    • In reply to: Ray Hicks: "Re: Wanted- FCS keyword read ut"
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    [ attachment ]
    ______________________________________...
    If I am not mistaken, WinMDI comes with a little utility called
    FCSread
    that extracts file header information.


    I know the request was for Mac software but sometimes we have to
    swallow
    our pride and admit we live in Bill's universe :-(


    -Dave
    ______________________________________...
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    Wanted- FCS keyword read ut
    From: Diether (diet...@amcell.com)
    Date: Tue Feb 24 1998 - 07:57:50 EST
    • Next message: Marty_Gied...@cc.chiron.com: "Annexin V
    expression"
    • Previous message: Colleen Hou-En Woo: "FDG and cell surface
    markers"
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    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]
    ______________________________________...
    Subject: Time:
    13:54
    OFFICE MEMO Wanted: FCS keyword read utility for Date:
    2/24/98
    I am looking for a utility program for the MacIntosh to read and
    print
    filenames
    and FCS keywords like $BTIM and $ETIM.


    Diether R.
    AmCell Corp.
    Ph.: USA-408-752-1200
    FAX: USA-408-752-1212
    Email: diet...@amcell.com or for binary attachments diethe...@usa.net
    ______________________________________...
    • Next message: Marty_Gied...@cc.chiron.com: "Annexin V
    expression"
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    markers"
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    Re: Wanted- FCS keyword read ut
    From: David Novo (no...@fhs.csu.McMaster.CA)
    Date: Thu Feb 26 1998 - 17:00:40 EST
    • Next message: JoAnne Thomas: "FACSLoader Upgrade"
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    files"
    • In reply to: Ray Hicks: "Re: Wanted- FCS keyword read ut"
    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]
    ______________________________________...
    If I am not mistaken, WinMDI comes with a little utility called
    FCSread
    that extracts file header information.


    I know the request was for Mac software but sometimes we have to
    swallow
    our pride and admit we live in Bill's universe :-(


    -Dave
    ______________________________________...
    • Next message: JoAnne Thomas: "FACSLoader Upgrade"
    • Previous message: David McFarland: "MO drives and CellQuest
    files"
    • In reply to: Ray Hicks: "Re: Wanted- FCS keyword read ut"
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    [ attachment ]
    ______________________________________...
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    Re: Wanted- FCS keyword read ut
    From: Ray Hicks (rh...@cus.cam.ac.uk)
    Date: Thu Feb 26 1998 - 05:10:28 EST
    • Next message: Steve G. Hilliard: "For Palm Pilot users"
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    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]
    ______________________________________...
    Hi Diether,


    If you can't find one, try opening the files in microsoft Word
    (you'll
    probably need to use the "All Files" option),copy the text part to a
    new
    window and then get it to replace the delimiter with a paragraph
    mark.
    This
    will give you a list that looks like this:


    $TOT
    5000
    $P1R
    1024
    $P1B
    16
    $P2R
    1024
    $P2B
    16
    $P3R
    1024
    $P3B
    16
    $P4R
    1024
    $P4B [snip]


    Rather than this:


    \$TOT\5000\$P1R\1024\$P1B\16\$P2R\1024...
    \1024\$P4B\

    ReplyDelete