The Biocode LIMS plugin can generate a number of useful reports on progress and performance by comparing data across both your lab and field databases. The reporting service can be accessed by clicking the Reporting icon below the Biocode icon in the service tree. A number of pre-configured report types are available, as well as more general reports that can be customized to show any kind of information.
Copying FIMS data
In order to speed up large comparisons and calculations, the reporting module makes a cache of your field information database (FIMS) inside the LIMS. The space requirements for this are generally small (for example the Moorea Biocode field database with over 50,000 records is approximately 30MB in size when cached in the LIMS). At the top of the reporting screen, you will see a message either telling you that you need to copy the FIMS, or when the FIMS was last copied. To copy your FIMS data, press the Copy Now button. The process may take a few minutes, depending on the size and type of your FIMS database.
Tip: If you don't want to copy your FIMS database into the LIMS, most of the report types will still be available, but you won't be able to make comparisons using data from the FIMS.
Creating a new Report
To create a new report, click the Add button at the top of the main window. This will bring up the Create Report dialog. Choose the report type you want using the drop down at the top of the window, and then fill in the options for your report. Enter a name, and click OK to save your report. Your report will then be saved in the list of available reports so that it can be re-run at a later date with a single click.
Running and Exporting a report
Your saved reports appear in a drop down at the top of the main reporting screen. Select your report, and click Calculate to generate the report. To print your report or chart, select File->Print or File->Save as Image. If your report is exportable, you can click the Export button to save your report to a file.
Table (Field Comparison)
The Comparison report allows you to count the number of reactions that have a particular value in your database (for example a particular primer or cocktail, or a particular reaction state such as passed etc.). These values are counted across all values of a field in your database (for example, the number of passed PCR reactions, counted across all Phylum). You can add multiple fields to the Y Axis (count) section, which will appear as multiple columns in the table.
Bar Chart (Field Comparison)
The Comparison report allows you to count the number of reactions that have a particular value in your database (for example a particular primer or cocktail, or a particular reaction state such as passed etc.). These values are counted across all values of a field in your database (for example, the number of passed PCR reactions, counted across all Phylum). You can add multiple fields to the Y Axis (count) section, which will appear as multiple series in the bar graph.
An accumulation report measures the total number of reactions with a particular field value over time. You can set the beginning and end date to count to at the top of the options, or choose Today to have the report always measure up to the current day. You can choose one or more series for the graph, and optionally restrict the counts to only reactions that match a particular search in the FIMS database by selecting Restrict by FIMS field.
Accumulation Curve (Across Field Data)
An accumulation report measures the total number of reactions with a particular field value over time. You can set the beginning and end date to count to at the top of the options, or choose Today to have the report always measure up to the current day. You can choose a reaction type and field value for the graph (for example "All Passed PCR Reactions"), and a field from the FIMS database to compare against.
The pie chart report allows you to compare the relative amounts reactions for all values of a given field. For example, you could compare the reaction state of PCR reactions to see how many have passed or failed, or see the distribution of different cocktails across your sequencing reactions.
Choose your desired reaction type, and then the field you want to compare. You can optionally restrict your counting to a particular locus by choosing one from the dropdown on the right hand side of the report dialog. You can also further restrict the reactions counted by checking the Restrict by Reaction or FIMS field checkbox, and choosing match criteria.
The Plate Search report allows you to search for all plates containing reactions that match your search criteria. This can be useful in tracking down problems in the LIMS (for example finding all plates containing PCR reactions that have been run but not scored).
To add a search term, click the + button on the right hand side of the report options dialog, enter your reaction type, and desired field and value. You can choose to search for reactions matching all or any of your search terms by choosing the corresponding value from the dropdown at the top of the report options.
Plate Status Report
The Plate Status Report shows you the progress of reactions performed on tissue samples, stored in tissue plates in your field database. For each tissue plate, the report shows you the number of reactions performed (as well as those passed and failed) for PCR and sequencing reactions, as well as the number of raw traces and sequences uploaded. Potential problems are highlighted in red.
Please note that this report uses tissue plates, stored in your field database, rather than extraction PCR or sequencing plates stored in your LIMS. If your field database does not store plate information, then this report will not be available.
The Primer Performance report shows you the performance of primers across some field in your field database. For example, you could compare the performance of a particular primer pair across all phyla in your database. Choose your reaction type (PCR or Sequencing), your primer pair, and the field to compare across from the dropdowns in the option dialog.
The results are presented in a table, with one row for each value of your comparison field, and columns representing the number of passed, failed, run, and not run reactions, and the primer performance (the percentage of passed reactions vs failed)