Aquileo | Recent changes to wiki

Aquileo | Home modified by Sven Mostböck

Wed, 05 Jul 2023 22:12:14 -0000

--- v22
+++ v23
@@ -35,9 +35,9 @@

 FCSalyzer uses only data provided directly by the user. These are the [FCS data files](FACS data) used in the analysis, additional data that is [attached to the FCS analysis](AttachParameters), and information typed by the user into the document, such as a [comment](Comment) or a [custom parameter name](Custom parameter descriptions). All analysis is done according to the user's computer system setup. This means, FCS data files are accessed directly from where the user selected them (could be a local hard drive, a network drive, or any such storage location as provided by the user), the data files are not copied or transferred anywhere else.

-FCSalyzer also generated new files. These are the [FCX document file](Document), if a user saves an analysis, a .FCXA data file for [attached data](AttachParameters), and temporary files for calculation of [statistics](Statistics).
+FCSalyzer also generated new files. These are the [FCX document file](Document), if a user saves an analysis, a FCXA data file for [attached data](AttachParameters), and temporary files for calculation of [statistics](Statistics).

-These files may contain sensitive information, depending on the analysis the user performed, the FCA data files that were used, the comments that were added, and so on. I would like to especially point out that the FCX document file contains all information in a human readable xml format. For example, it stores the location of the FCS data files (so that FCSalyzer can find them again), which could be something like "c:\users\secret_user_name\secret_project_name\secret_secret.fcs". Please make sure that all of these files only contain information as permitted by your organization.
+These files may contain sensitive information, depending on the analysis the user performed, the FCS data files that were used, the comments that were added, and so on. Especially, the FCX document file contains all information in a human readable xml format. For example, it stores the location of the FCS data files (so that FCSalyzer can find them again), which could be something like "c:\users\secret_user_name\secret_project_name\secret_secret.fcs". Please make sure that all of these files only contain information as permitted by your organization.

 ##MacOS - Linux - Windows?##

Aquileo | Home modified by Sven Mostböck

Wed, 05 Jul 2023 22:10:20 -0000

--- v21
+++ v22
@@ -53,6 +53,10 @@
 This is a hobby project of a single developer. When I started with FCSalyzer, I was routinely doing flow cytometry analysis in my day job. Since then, my position has changed and now I rarely analyse flow data myself, and then I use the software provided by the company. So I can't test FCSalyzer very well. I do use several test files and perform certain analysis tests that should capture most case scenarios. nonetheless, a couple of days working on specific test data files does not reflect intense analysis necessary in research.
 So there might be bugs around, some of which might actually impact the analysis results. Users are strongly advised to check that the analysis results match their expectations and their experiences in their particular analysis strategies. I keep the "alpha" badge as a symbolic reminder for this. This is also the reason why FCSalyzer will probably never reach Version 1.

+##License and Warranty##
+
+FCSalyzer is a freeware open source project distributed under GPLv3 license: <https: www.gnu.org="" licenses="" gpl-3.0="">
+Please note especially points "15. Disclaimer of Warranty", "16. Limitation of Liability", and "17. Interpretation of Sections 15 and 16"

 [[project_admins]]
 *sven_mostboeck@users.sf.net* 
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Aquileo | Home modified by Sven Mostböck

Wed, 05 Jul 2023 22:02:18 -0000

--- v20
+++ v21
@@ -42,7 +42,7 @@
 ##MacOS - Linux - Windows?##

 FCSalyzer is a JAVA program and distributes as JAR bytecode. In principle, it should run on any system that has JAVA installed (Version 6 or higher). That requirement should easily be met - the current Java version is 16, and the reference version Java 8 was released in 2014.
-If Java is not installed on your system, you can find the OpenJDK versions here: <https: adoptopenjdk.net="" releases.html="">
+If Java is not installed on your system, you can find the OpenJDK versions here: <https: adoptium.net="">; older releases are also here:  <https: adoptopenjdk.net="" releases.html="">

 So FCSalyzer should run on Windows, MacOS and Linux, as long as the Java platform is installed. However, I am getting reports that FCSalyzer may have problems on MacOS.
 One problem: the dialog to open files might not work properly. That is the reason for the two versions - FCSalyzer.JAR and FCSalyzer_alternative.JAR. They are identical except for using different file dialogs. Give both a try and see, which one works for you.
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Aquileo | Home modified by Sven Mostböck

Wed, 05 Jul 2023 22:00:50 -0000

--- v19
+++ v20
@@ -41,7 +41,7 @@

 ##MacOS - Linux - Windows?##

-FCSalyzer is a JAVA program and distributes as JAR bytecode. In principle, it should run on any system that has JAVA installes (Version 6 or higher). That requirement should easily be met - the current Java version is 16, and the reference version Java 8 was released in 2014.
+FCSalyzer is a JAVA program and distributes as JAR bytecode. In principle, it should run on any system that has JAVA installed (Version 6 or higher). That requirement should easily be met - the current Java version is 16, and the reference version Java 8 was released in 2014.
 If Java is not installed on your system, you can find the OpenJDK versions here: <https: adoptopenjdk.net="" releases.html="">

 So FCSalyzer should run on Windows, MacOS and Linux, as long as the Java platform is installed. However, I am getting reports that FCSalyzer may have problems on MacOS.
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Aquileo | Home modified by Sven Mostböck

Wed, 05 Jul 2023 21:59:09 -0000

--- v18
+++ v19
@@ -9,7 +9,7 @@

 FCSalyzer creates documents onto which analysis dot plots, statistics, comments, annotations, and so on can be placed. It is a very visual approach, with plots drawn onto the document page with the mouse.  So first, an empty document is generated (that happens the moment FCSalyzer is started). Then, the user can place analysis plots etc. onto that document. The document can be saved (as a .FCX file), printed, and exported as a graphics file.

-I often get questions or complaints that FCSalyzer can't open FCS data files. Most often, that is because the user misunderstands the concept. An FCS data file is not "loaded/opened" using the file menu, but placed onto an FCX document. This is similar to PowerPoint: an image file is placed onto a PowerPoint slide, but not opened/loaded using the PowerPoint file menu. Please watch the YouTube tutorial to see how it works (link further down).
+I often get questions or complains that FCSalyzer can't open FCS data files. Most often, that is because the user misunderstands the concept. An FCS data file is not "loaded/opened" using the file menu, but placed onto an FCX document. This is similar to PowerPoint: an image file is placed onto a PowerPoint slide, but not opened/loaded using the PowerPoint file menu. Please watch the YouTube tutorial to see how it works (link further down).

 ##How To Get Started##

Aquileo | Home modified by Sven Mostböck

Wed, 05 Jul 2023 21:58:41 -0000

--- v17
+++ v18
@@ -5,7 +5,13 @@

 FCSalyzer is a small application for analysing flow cytometry data. It is intended to be intuitive in its use for people used to flow cytometry and general computer programs. We will see if that holds true.

-##First Usage##
+##Basic Concepts##
+
+FCSalyzer creates documents onto which analysis dot plots, statistics, comments, annotations, and so on can be placed. It is a very visual approach, with plots drawn onto the document page with the mouse.  So first, an empty document is generated (that happens the moment FCSalyzer is started). Then, the user can place analysis plots etc. onto that document. The document can be saved (as a .FCX file), printed, and exported as a graphics file.
+
+I often get questions or complaints that FCSalyzer can't open FCS data files. Most often, that is because the user misunderstands the concept. An FCS data file is not "loaded/opened" using the file menu, but placed onto an FCX document. This is similar to PowerPoint: an image file is placed onto a PowerPoint slide, but not opened/loaded using the PowerPoint file menu. Please watch the YouTube tutorial to see how it works (link further down).
+
+##How To Get Started##

 1. Download the zip-file, unpack it and double-click on the JAR file. You will have to have Java installed (Version 6 or higher).
     * starting with version 0.9.21, there are two JAR files provided. The only difference between the two is the system dialog used when users open or save files:
@@ -16,10 +22,22 @@
 - Now draw the frame of the new plot on the canvas of the document by clicking on the document without releasing the mouse button and dragging the mouse. 
 - When you release the mouse button, a dialog will open that will ask you to select a data file for the plot. Select your FCS file and the data will be shown in the plot. 

+##More Info On How To Use FCSalyzer##
+
+More detailed information on how to use FCSalyzer is found on this wiki. You can either browse all pages (see navigation bar to the left), or start by taking a look at his page: [Usage].
+
+There are also a number of tutorial videos on YouTube:
 [The FCSalyzer tutorial on Youtube](https://www.youtube.com/playlist?list=PLDnK1XYSv8tvFuKcdPF9FScM4nr3P9wOJ)
 [[embed url=https://www.youtube.com/watch?v=h8LTHK26lHM]]

-For more about the usage, see [Usage].
+##How FCSalyzer uses and stores data##
+FCSalyzer runs locally on the user's machine. As a JAVA program , it requires a Java Runtime Environment (JRE) and will use the JRE installed on the local machine. All activities of FCSalyzer are performed by this JRE and rely on its correct function. That's how JAVA programs work.
+
+FCSalyzer uses only data provided directly by the user. These are the [FCS data files](FACS data) used in the analysis, additional data that is [attached to the FCS analysis](AttachParameters), and information typed by the user into the document, such as a [comment](Comment) or a [custom parameter name](Custom parameter descriptions). All analysis is done according to the user's computer system setup. This means, FCS data files are accessed directly from where the user selected them (could be a local hard drive, a network drive, or any such storage location as provided by the user), the data files are not copied or transferred anywhere else.
+
+FCSalyzer also generated new files. These are the [FCX document file](Document), if a user saves an analysis, a .FCXA data file for [attached data](AttachParameters), and temporary files for calculation of [statistics](Statistics).
+
+These files may contain sensitive information, depending on the analysis the user performed, the FCA data files that were used, the comments that were added, and so on. I would like to especially point out that the FCX document file contains all information in a human readable xml format. For example, it stores the location of the FCS data files (so that FCSalyzer can find them again), which could be something like "c:\users\secret_user_name\secret_project_name\secret_secret.fcs". Please make sure that all of these files only contain information as permitted by your organization.

 ##MacOS - Linux - Windows?##

Aquileo | AttachParameters modified by Sven Mostböck

Wed, 05 Jul 2023 21:55:39 -0000

--- v8
+++ v9
@@ -46,5 +46,5 @@

 Please note that this data file contains also the name of the parameter (see above), which can be easily extracted from the .FCXA file using common file readers. Also, as FCSalyzer is a freeware open source program, anyone can analyse how the data is stored in the .FCXA data file.

-Please make sure that the .FCXA file contains only information according to your organization's rules. 
+Please make sure that the .FCXA file contains only information as permitted by your organization.

Aquileo | Document modified by Sven Mostböck

Wed, 05 Jul 2023 21:55:01 -0000

--- v6
+++ v7
@@ -4,6 +4,7 @@

 The saved file does not contain the FCS data files used in the analysis, only links to them. The links are stored absolute (i. e. with the full path pointing to the FCS file). When loading a data file, FCSalyzer first looks for it in a relative location, then in the same directory as the document is stored in, and as a last resort in the absolute location stored in the document file. It tries to first find the data file in a relative location so that the document can be properly opened even if the folder containing document and data files is moved after the document was saved.

-Importantly: XML files are human readable text documents. This means that all information in the .FCX document are in clear text that can be read in any text editor. All file paths, file names, comments, custom parameter descriptions and so on can be extracted directly from the .FCX data file. Please make sure that there is no sensitive information present in the file, before transmitting or sharing it. An example would be the file path of a FCS data file, which could be "c:\users\secret_user_name\secret_project_name\secret_secret.fcs"
+Importantly: XML files are human readable text documents. This means that all information in the .FCX document are in clear text that can be read in any text editor. All file paths, file names, comments, custom parameter descriptions and so on can be extracted directly from the .FCX data file. An example would be the file path of a FCS data file, which could be "c:\users\secret_user_name\secret_project_name\secret_secret.fcs"
+Please make sure that the FCX document file only contains information as permitted by your organization.

 [[embed url=https://www.youtube.com/watch?v=h8LTHK26lHM]]

Aquileo | AttachParameters modified by Sven Mostböck

Wed, 05 Jul 2023 21:54:02 -0000

--- v7
+++ v8
@@ -46,5 +46,5 @@

 Please note that this data file contains also the name of the parameter (see above), which can be easily extracted from the .FCXA file using common file readers. Also, as FCSalyzer is a freeware open source program, anyone can analyse how the data is stored in the .FCXA data file.

-Please make sure that the .FCXA file does not contain any sensitive information before transmitting or sharing it. 
+Please make sure that the .FCXA file contains only information according to your organization's rules.

Aquileo | Statistics modified by Sven Mostböck

Wed, 05 Jul 2023 21:49:54 -0000

--- v6
+++ v7
@@ -1,4 +1,3 @@
-
 [[embed url=https://www.youtube.com/watch?v=apKtw7xJf2Y]]
 Drawing events in a plot is nice, but having numbers to back the results up is even better. FCSalyzer allows the usual type of statistics to be calculated for the plots.

@@ -10,4 +9,6 @@

 A word of advice: as far as I can say, the calculated statistics are exactly the same values as are calculated by BD CellQuest(tm). However, you should definitely cross-check the analysis with your regular analysis program to make sure that FCSalyzer didn't make a mistake in the calculations.

+Technical note: FCSalyzer creates temporary files for calculating statistics. These files are generated using standard Java procedures and the details for that rest with the Java Environment installed on the user's computer system. The temporary files should thus be generated inside the standard file location for temporary files (such as "temp") and should be deleted automatically when FCSalyzer closes. These files only contain numbers used for calculation, and no further data. If the statistics calculations fail, make sure that FCSalyzer is able to generate temporary files on your computer system. 
+
 *BD CellQuest is a trademark of BD Biosciences*