The Daily Dongle

FlowJo 7.6 Prefs - deployment considerations

Some of our larger sites want to roll out FlowJo via a MSI installer, which we don't yet have (putting it off till FlowJo X.) As a workaround to this we recommend that one user installs the software and then distributes the contents of FlowJo's installed location to other users via a login script. There are registry modifications which associate the program's icons and double-click behavior, these would not be propagated in this mechanism.

The second part of FlowJo installation deals with licensing - First time opening of FlowJo brings up the license dialog asking for a serial number license. If you enter a serial number here, it will be saved to your disk to a file "flowjo75.prefs" in your "my documents" folder. If your institution is on a site license, the serial number will be identical for all regisrered users, therefore, the initial prefs file can also be distributed (with the serial number in place) via a login script. 

FlowJo supports multiple layers of Preferences files locations, some more global than others. Here's the algorithm for how that's currently handled. These alternate locations of prefs files may also be used to aid authentication on machines where multiple people have their own os-level accounts.

• First look in the user's 'My Documents' folder (or user's home folder on mac).  If found, use it for all prefs.
• If not found, look in the flowjo installation folder (if running out of eclipse, look in the project folder).  If found, use it for all prefs.
• If not found, create a new prefs file in the user's 'My Documents' folder (or user's home folder), and use it for all prefs.  Serial number will be blank.
• To get a serial number for authorization, get it from whatever prefs file was found or created beforehand.
• If the serial number is blank, look for the prefs file in the 'All Users' folder (which is not found on mac).  Use this serial number for authorization, or bring up license dialog if absent.

new trick for preferences files

Adam writes: 

I implemented changing prefs files on the fly in 7.6. Either do an Open Workspace... and select anything.prefs, or drag anything.prefs onto an open workspace window. 

This should be good news to anyone trying to juggle multiple preferences file. Available in next 7.6 build I post. 

Population Comparison tutorial

Download Population video tutorial, 15MB (quicktime) 

This is to present a slight twist on the interface as you may have seen it in the Mac version. 

data range adjustment video tutorial/rant

Dataranges (quicktime, 13MB) 

this is to introduce the new tool for adjusting range parameters in high-res FCS3 data (Accuri, XDP, etc.) 

This is the first implementation, we expect to improve it for flowjo x,  given your feedback. This has been in all of the betas from the past 2-3 months or so, but I'll probably be posting new candidate release builds this week.  

feedback - simm@treestar.com

new USB keys

Forbidden Dongle

The daily dongle is blocked in China. Looks like a good opportunity for a localized clone of the blog. (Culturally witty) title suggestions are welcome!

64 bit flowjo, XDP data

news on the 7.6 front: 

we successfully opened a 2.18GB file generated by DIVA in the 7.6 version of FJ, compiled in 64 bit already, since we made it available for the mac. I just never got a file big enough to test that it's really 64 bitty. :)

The real test of course would be to open 1TB of 2.18B files. And batch. :)

The latest 7.6 build also supports XDP data, which uses the full 32 bit (4 billion) channel range. 

DeNovo software publishes cytometry book online

Claudio Vallan of FlowJo-Europe sent us a tip about a new site DeNovo launched:

http://flowbook.denovosoftware.com/

similarly to Invitrogen's initiative on putting up Dr. Howard Shapiro's Hitchhiker's Guide To Flow Cytometery [tic], DeNovo software published a well rounded electronic reference for Students of Flow.

Where's flowjo's book? Well, at least we have the DDongle. ;)

interesting publication stats

ApSci Nicholas Ostrout has done some diggin' on pubmed, to yield the following publication factoids:

Immunity:
85 papers in 2007 used Flow Cytometry either for sorting or analysis, and out of those, only 47 explicitly stated their analysis package.  Of those 47:

10 - used Cell Quest
3 -  FACSDiva
34 - FlowJo

J Exp Med:
129 papers in 2007 used Flow Cytometry either for sorting or analysis, and out of those, only 109 explicitly stated their analysis package. Of those 109:

38 - used Cell Quest
7 - FACSDiva
64 - FlowJo

Nat. Imm.: 80 papers that used Flow, 50 published analysis package:

10  CellQuest
5  FACSDiva
34  FlowJo
1 of 50 FCSExpress

Nat. Med.: 59 papers used Flow, 19 published analysis package.

8 CellQuest
3 FACSDiva
8 FlowJo

I'm surprised we didn't look at cytometry (or perhaps the stats weren't as flattering there ;P )

*Friday 9/5 update*
changed "J Immunity" to "Immunity". My bad.

Added stats from Nat Imm and Nat Med.

Plant flow cytometry

For those of you not on Purdue, Joao Loureiro from Portugal wrote:

It is with great pleasure that I announce the first forum and blog on plant
flow cytometry. These two new platforms are at your disposal to discuss
general topics in plant flow cytometry, to post any doubts or questions
related to (the analysis of plant cells using flow cytometry) PLANT FLOW
CYTOMETRY, to announce upcoming congresses and courses, etc.

Such platforms are only valuable if you participate actively and if there is
a regular number of new posts and comments. Therefore, I invite you to
register in the forum and use it on your best interests. The blog can be a
very informal way of communicating and posting new and interesting
information on plant flow cytometry, and you are encouraged to comment on
the various topics that will be regularly posted.

You can access the forum at the following address:
http://flowerdatabase.20.forumer.com/index.php and the blog at:
http://flowerdatabase.blogspot.com/ .

These (two) new tools of communication appeared first as a companion to the
FLOWER database (the Plant DNA Flow Cytometry Database:
http://flower.web.ua.pt/), but are now directed to plant flow cytometry in
general. Please consider that the FLOWER database is still in its beginning
(beta version), and thus it still presents some flaws.