Assay DM/I - Ordering Analyses
+ [Trying Scifeon](#trying-scifeon)
Assay Data Management is one of the research informatics areas in need of great improvements, as discussed in this Effective Assay Data Management without Giving Up Excel & Prism blog entry. Two Assay Data Manament Application Examples (the first one described on this page) demonstate how Scifeon can help you handle different aspects of these challenges.
Trying Scifeon
You can try out Scifeon by going to http://demo.scifeon.cloud and registering. Note that the database on this demo website is frequently reset and that your entries are visible to other users. Please contact Scifeon at scifeon@scifeon.com to arrange for a dedicated Scifeon instance that you can try out.
Elements
In the "Assay DM I - Ordering Analyses" application example, a "customer" (e.g. someone from a research project or another department) submits an analysis request through a website. The requests contains a list of samples to be analysed. The example includes the data processing as well as communication between assay department and customer.
Ordering and Communication
Research project communication often rely heavily on emailing Excel files back-n-forth. Ordering support in Scifeon add context to some of that communication, providing an alternative that helps ensuring that the right information is provided, that handovers are not dropped or forgotten, and that colleagues can pitch in when necessary.
Status Management
The status of entities in the system change as the workflow progresses. The Status Management page provides and overview of the status flow.
Method Definition
In Scifeon, you can define methods with fields that appear in the Ordering and Analysis Setup pages. For this application example, two methods have been defined, as described here.
Result Processing
Scifeon provides result traceability: The result-hierarchy from raw data over several levels of intermediate results with cross references to laboratory steps, input samples and data files is available, helding to cope with the complexity of research results.
Workflow
The overall workflow consist of a customer submitting an order, processing of the order in the assay department and finally reporting of results back to the customer.
Handovers
In Scifeon, an Order is represented as a Handover entity. The Handover represents a request for an activity. It will have a sender (a person and a department) and it is sent to a Handover Inbox. It can also be sent to a specific person. The handover is as the reference entity for communication between sender and recipient, and it goes through a well-defined sequence of states. You can read more about handovers in the Scifeon Data Management Guide.
End User Steps
The individual steps in the workflow are:
- A customer makes an analysis request through a webpage, specifying the samples to analyze, assay type and the recipient order inbox.
- An analyst (from the assay department) marks the order as "received", and the customer gets a notification by email or SMS.
- The analyst creates an experiment setup with samples from one or more requests.
- Raw data are imported to the database from an Excel file.
- The raw data are exported to another Excel file for analysis.
- The processed results are imported to the database.
- The assay step is marked as completed and sent to the responsible scientist for approval.
- The approved results are released and are now available for the customer, who receives an email or SMS.
Detailed descriptions of how to execute the steps are found in the Step Description pages:
- Step 1: Request Analyses (Customer)
- Step 2: Receive Handover
- Step 3: Setup Experiment
- Step 4: Load Raw Data
- Step 5: Export Raw Data
- Step 6: Load Processed Results
- Step 7: Result Publication
- Step 8: Read Results (Customer)
Data Structure in the Database
A description of the data that ends up in the database can be found on the data page.