This topic provides answers to some commonly asked questions about LabKey Sample Manager.
Data Ownership and Audit
If I store my data in hosted LabKey Sample Manager do I still own the data? If I choose to end my subscription later, will I be able to get it back?
Absolutely. Whether hosted or on premise, you always own your own data. If you stop using Sample Manager, you will receive a full export of all your data.
Will privacy be maintained if I use a hosted Sample Manager application?
Absolutely, the LabKey security model guarantees privacy and security using our role based access model.
However, if you need to store PHI and/or are interested in HIPAA compliant protection of your data, contact us to discuss whether another LabKey product might better meet your compliance needs.
Do samples have an audit trail for chain of custody tracking?
Yes! Every action is tracked in a set of audit logs on a row by row level. In the future, an enhanced chain of custody tracking feature will also be added.
Is the sample ID assigned by the system unique to just one lab? Can they be shared?
Yes, right now because there is a single Sample Manager application serving each lab, if you ask the application to generate sample IDs for you, they will be unique within that single lab. However, letting the system assign sample IDs is not the only option.
If you wanted to share sample information across multiple labs, you could override the automatic assignment option by providing your own unique sample IDs, such as by using a sample manifest. The distinct Sample Manager applications at many lab sites could accept and use these sample IDs that are drawn from a master assignment list ensuring that they are both unique within a single application and unique across multiple locations.
Does Sample Manager handle replicates?
Yes, sample replicates can be identified using custom naming conventions, i.e. S101-1 and S101-2 are replicates of one original sample.
Data Structures for Assays and Samples
How do I get my existing sample data into the system?
LabKey Sample Manager is specifically designed to make data import easy. Design the structure of existing data and drag and drop to upload it simply and efficiently. Note that very large uploads may need to be split into batches to upload successfully.
Are the Assays customizable? Can I create my own assays?
Absolutely. Our demos and example project include some possible ways to structure typical assays, but when you define your own, you have complete control over the fields and types of data collected. The only requirement is that assay data needs to provide a column linking to the sample.
Are there predefined templates for data in Sample Manager?
There are no predefined templates. Users have full control of creating data templates for your own needs. During the definition of assays, users have the option to let the application infer
fields in the data structure from the columns in a spreadsheet.
What happens if you import assay data but it has a column name that doesn't match?
The assay data import process will read only the "expected" columns from your data. If you have additional columns, they will be ignored. If you have a difference in column naming, you may be able to make use of column aliases to import data from a column of a mismatched name.
When importing data, you will see a preview of the first few rows to aid you in correcting issues or adding aliases.
How does a user know what columns are expected?
The handy Download Template
feature gives the user a blank template for what columns are expected. The user can either add their data to this template or simply confirm that they have the correct columns prior to import.
Can I build in customized data integrity checks?
Absolutely. Every field can have data validation performed, such as ensuring correct formats, valid ranges, and other such measures. Coming soon will be a mechanism for controlled vocabularies
, i.e. presenting uploading users with pulldown menus of options instead of free text entry fields.
Do you have support for tracking study visits, where multiple samples of different types are collected from one subject at once?
We don't have a built in mechanism for tracking study visits at this time, but by defining additional custom columns for your sample types, you can track the individual and date of collection for matching. For example, using a required column for study visit, you would capture this information.
What export types are supported?
Currently you can export data as CSV, TSV, and Excel.
Jobs, Tasks, and Templates
Does each workflow job depend on the completion of the previous job? Or can you have multiple jobs underway simultaneously? Can you configure which job is dependent on which other job?
Currently, each workflow job can begin/proceed independently of all other jobs. You can have as many jobs underway simultaneously as you like. If you want to have actions that proceed in a sequence, consider whether these should be defined as tasks
within a single larger job, rather than separate jobs.
In the future, we hope to add an administrative option to make a job dependent upon completion of another job, but at present this is not supported. In the meantime, you could also consider having a 'check for previous job completion' task at the start of the job you want to happen 'next'.
Sample Manager and LabKey Server
Can assay results loaded via Sample Manager be copied to LabKey Studies?
Yes, if you are using Sample Manager as part of a Premium Edition of LabKey Server, your application will be running on the same server as your other LabKey projects. After loading assay data into Sample Manager, you can access it via traditional LabKey Server folder management tools and copy that data into your study on the same server.
Can Sample Manager make use of assays already defined in my LabKey Server?
Yes, if you have defined general purpose assays in the scope available to your integrated Sample Manager application, you will see them in the list of assay designs. You may need to map one of the columns to your sample information before you can use them.
We are very interested in hearing your feedback about what is important to you. Future development of new features for LabKey Sample Manager is already underway.
Does Sample Manager track the subject of study, i.e the source of the sample.
Not yet, but coming soon you will be able to identify sample Sources
within the application.
Does Sample Manager provide a freezer management solution?
Not yet, but development of our freezer management
solution is already well underway and will be launched in the near future.
Does Sample Manager support using a barcoding system?
Not yet, but in the future, Sample Manager will support using barcodes
for samples. Our goal is to ensure that barcodes are simple to use and understand. Your input toward this goal would be welcome. One possible implementation would be integration with BarTender.
If there is a BarTender integration, that would be an option for groups to use and not required.
Does Sample Manager provide inventory features or track system wide volume?
Not at this time, but by adding a custom field to your sample type definitions, you can track and aggregate volume information across all your samples.
Do you need other software to do data analysis and generate reports?
Yes, at this time, users of the hosted Sample Manager application will export the managed sample data for analysis and reporting. In the future, analysis and reporting will be added within the application.
Note that LabKey Server itself is a candidate for such analysis and reporting, and in fact, users of Premium Editions of LabKey Server can access data from Sample Manager directly from the traditional LabKey user interface.
Does Sample Manager track reagents, vendor batch number, etc.?
Not explicitly at this time. You can use custom columns to track this information yourself. In the future, using controlled vocabularies will give another way to track reagents and their batches.
Have more questions or need additional information? Please get in touch with us: