Help

Help can be found in the User's Guide which can be downloaded and is available in the OSIRIS program from the Help menu. Answers to questions and issues can also be found in the FAQ and Troubleshooting guide below, and in the User's Guide.

Optimize OSIRIS

For the best performance using the latest improvements, OSIRIS settings must be optimized. Suggested starting analysis settings for either single source or mixed samples are available in the lab settings [PowerPlex Fusion HID Sole Source] and [GlobalFiler HID Mixture] in the OSIRIS program under the Tools > Lab Settings menu.

Updates

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Adding new markers and marker sets to OSIRIS

Instructions for adding marker sets to OSIRIS.

Attention Mac users with OSIRIS version 2.12.1 and earlier - With newer versions of Mac OSX, sometimes the OSIRIS windows do not appear. This can be remedied by clicking on the OSIRIS icon in the dock (usually at the bottom of the screen) to activate the OSIRIS window. You may need to do this for each new window in OSIRIS. This issue should be resolved in OSIRIS versions 2.12.2 and later.

Topics

Installing and upgrading OSIRIS

OSIRIS Windows instructions

OSIRIS Macintosh instructions

Attention Mac users with OSIRIS version 2.12.1 and earlier - With newer versions of Mac OSX, sometimes the OSIRIS windows do not appear. This can be remedied by clicking on the OSIRIS icon in the dock (usually at the bottom of the screen) to activate the OSIRIS window. You may need to do this for each new window in OSIRIS. This issue should be resolved in OSIRIS versions 2.12.2 and later.

When upgrading OSIRIS it is generally least confusing to remove old versions. On Windows, run the uninstall.bat file to uninstall MSI file installations, which will maintain your custom lab settings. Windows EXE or ZIP file installations may simply be deleted. Macintosh installations may simply be deleted. Remember to back up any custom lab settings before uninstalling. When installing multiple versions of OSIRIS for evaluation of newer versions, use EXE file installation on Windows. Use care to ensure that analyses are done with the correct version, when multiple versions are installed.

Adding new markers and marker sets to OSIRIS

If a marker set (kit) or internal sizing marker definition is not included in OSIRIS already, OSIRIS version 2.16 includes software that allows users to create new marker sets and internal markers for use in OSIRIS analysis. New marker sets must have an allelic ladder. Marker sets without an allelic ladder can be analyzed with the fragment analysis operating procedures in OSIRIS. New internal sizing markers can be added to a new marker set or used in fragment analysis. Newly created markers must be used with OSIRIS version 2.16. Download the instructions for adding marker sets to OSIRIS.

Contact Us

Questions and suggestions are welcome at .

FAQ

1. Can I analyze .hid and .fsa file types? Yes. The Operating Procedure must be set for the appropriate file type. See General – .fsa and .hid files in Lab Settings.

2. Can I enter a new kit in OSIRIS? Yes. See Appendix G for instructions. Contact us for help or advice.

3. Can I use a different ILS? Several different ILS are defined for various kits. Note that some of those are actually one ILS, but use more or fewer of the peaks, in case not all peak data gets collected. If the ILS you use is not defined for the kit you use, see Appendix G for instructions on defining a new ILS. Contact us if you need help.

4. What do I do if my multiplex has no ladder available? You can either construct a ladder, or you can use a DNA sizing ladder to add a new kit. See Appendix G or contact us for help.

5. How fast is OSIRIS? OSIRIS should process 2 to 4 samples per second, depending on the number of artifacts in the samples and the speed of your computer/network. So a plate of 98 samples with controls should take 30-60 seconds to analyze. If it runs significantly slower than that on your system, contact us for advice.

6. How many samples can OSIRIS process at once? OSIRIS will process at least 800 samples in a single batch (single directory). OSIRIS will process an essentially unlimited number of batches in a single processing run. This has been tested with approximately 10,000 samples in 110 directories (plates) in a single analysis that took approximately 1 hour 20 minutes.

7. How many users can use OSIRIS at the same time? This is limited only by the number of client computers you have and the speed of your network and server. Generally, it should be “lots.” Additionally, each user is creating a separate instance of OSIRIS running on the local client, so multiple users will not affect the speed of operation except as limited by sample data flow across the network to and from the server if the sample data and OSIRIS output is being stored on the server. A single user can run separate instances of OSIRIS on the same computer at the same time (Windows only), allowing different analyses or tasks to be performed simultaneously. Multiple analyses can also be run from a single OSIRIS process (Windows and Macintosh).

8. Is there any fee for OSIRIS software or use? No. OSIRIS is free and open source. No license or fees are required.

9. Is OSIRIS source code available? Yes. OSIRIS source code is available at GitHub: https://github.com/ncbi/osiris.

10. Can I modify OSIRIS, build it into my front end or incorporate it into my own software? OSIRIS is open source and public domain software. You may do anything your heart desires. In any work or product derived from this material, proper attribution to the authors as the source of the software would be appreciated.

Troubleshooting

Problems and Solutions

My analysis failed

• OSIRIS must have at least one acceptable ladder for the analysis to succeed. If the expected ILS or ladder allele peaks are below the analysis threshold or not present (e.g., cut off in collection) the ladder will fail to analyze. By opening a failed analysis, it may be possible to examine the ladder peaks to determine if the ladder was the reason the batch failed.
• A common cause of analysis failure is selection of the wrong kit or ILS definition in the Operating Procedure. Ensure that the correct kit and ILS combination is selected in the Operating Procedure being used for the analysis.
• Any time your analysis fails you can select the “Details” button to find troubleshooting information. Selecting “View Selection” or double clicking the failed run will open the ladder, if it could be found and partially analyzed. Click the ladder sample name to view all the channels of the ladder in the Preview pane or double click the ladder sample name to view it in the Graph View to determine the presence of artifacts and peaks and whether the locus and ILS peaks are below the analytical threshold.
• No ladder sample was present, or the file name did not contain the ladder file search string. OSIRIS requires a ladder for analysis.
• Artifact peaks made it impossible to analyze the ladder ILS. Sometimes this can be alleviated by adjusting the ILS analysis thresholds. Otherwise re-prepare or re-inject the ladder.
• The ladder’s ILS peaks are below threshold. Adjust the ILS analysis thresholds. Otherwise re-prepare or re-inject the ladder.
• The ladder’s allele peaks have artifacts or are below threshold. Sometimes this can be alleviated by adjusting the Ladder analysis thresholds. Otherwise re-prepare or re-inject the ladder.

My .hid/.fsa analysis failed

• If the Operating Procedure is not set for the correct file type on the General tab of the Lab Settings, the analysis will fail because no files of the expected type are present. If you select the failed run and click the details button, at the bottom of the list there will be a “Project did not meet expectations…No satisfactory ladder found…Ending” error message. Make sure that the correct file type is selected and reanalyze. Analysis of a directory tree with multiple file types will succeed only in those subfolders containing the expected file type.

I can’t edit the Operating Procedure

• To edit an Operating Procedure, you must have write permission to the site settings folder and its subfolders. To view this folder, select “Show site settings folder...” from the “Tools” menu on the menu bar.
• You cannot edit default Operating Procedures (shown in brackets) such as [PowerPlex 16]. Make a new Operating Procedure that can be edited.
• You cannot edit Operating Procedures opened through the “Parameters” button. These are static copies associated with the analysis file you are viewing. This is designed to preserve the history of the conditions used for a specific analysis.
• The Operating Procedure is locked while being edited by any user and cannot be edited by a second user or used for an analysis. Ask the user editing the Operating Procedure to close it or select a different OP.

• In Version 2.9.1 and earlier, locking the OP was based on the time it was last edited or used in an analysis:
  Check to determine whether other users are editing or analyzing with that OP. If you try to edit the Operating Procedure immediately after your own analysis, it may still be locked. If you have just performed an analysis, wait 30 to 60 seconds and try again. Locking the OP prevents change in the middle of analysis, or corrupting the Operating Procedure if two users were to make changes at the same time. The "Lock" button at the lower left corner of the Lab Settings window will be active (not grayed out) if the Operating Procedure has been locked by another user or if you do not currently have access privileges to modify the Operating Procedure. If that changes, you will be able to lock the Operating Procedure with the Lock button and begin editing.

• If you are operating on a network or in a forensic or clinical laboratory, your OSIRIS administrator may have limited write permissions on the Operating Procedure directories to prevent unintended changes. Contact your OSIRIS administrator.

Text and notices do not display correctly on a Macintosh

• The OSIRIS display is not optimized for "Dark Mode" on the Macintosh. Some text and notices do not display correctly when using Dark mode. To solve this issue, search the internet for "disable dark mode for specific app macintosh" to find a solution for turning off Dark Mode for OSIRIS only. Alternatively, you can turn Dark mode off when using OSIRIS on the Macintosh.

Known issues

• "Help" error: Some configurations of Microsoft Windows 10 will not open the OSIRIS Help document from within the program when the Microsoft Edge browser is the default reader for PDF files. This is a known MS Edge browser issue. The simplest solution is to select an alternate PDF reader: In File Explorer, open the folder where OSIRIS is installed. Right click the OsirisHelp.pdf file and select “Open with >” then “Choose another app” from the pop up context menu. Select a different PDF reader or a different browser that can open PDF files, check the “Always use this app to open .pdf files” checkbox, and click "Ok".

• Mac window issue: Mac users with OSIRIS version 2.12.1 and earlier and have newer versions of Mac OSX may find that the OSIRIS windows do not appear. This can be remedied by clicking on the OSIRIS icon in the dock (usually at the bottom of the screen) to activate the OSIRIS window. You may need to do this for each new window in OSIRIS. This issue should be resolved in OSIRIS versions 2.12.2 and later.

Privacy Information

Privacy Statement

OSIRIS is a desktop tool working on your computer with your own data. Your sample profile data is processed on your computer and is not sent over the internet.

For quality monitoring, OSIRIS versions 2.12 and higher send some information about usage statistics back to NCBI. This information is limited to use of the tool, without any sample, profile or batch data that would reveal the context of your analysis.

Down load the Ping_Failure_Message_Glossary.xlsx file for a list of error codes.

Opt-out of Statistics Collection

You can opt-out of statistics collection by performing the following operations:

• Open OSIRIS.
• Open the Tools menu and uncheck Allow Usage Reporting.
• OSIRIS will immediately stop reporting statistics.

See the OSIRIS User's Guide for additional details regarding usage statistics and opting out.

OSIRIS web pages

See the NCBI Privacy Policy for the policy that applies to the OSIRIS web pages.