====== Quick Guide ======

===== High Level View =====

==== Automatic mechanism ====
The following process is carried out every day:
  * The automatic process runs overnight.
  * The result of the automatic analysis is added to the database.
  * The reprocessing tool (GUI) retrieves information from the database.

==== Automatic processing ====
{{:fujitsu:alphacod:quick_guide:automatic_treatment.png?700}}

Automatic analysis works in stages to detect molecules.
  * Analysis of the screening file: extraction of molecules from the series
  * Pre-calibration: search for peaks on high concentration range points
  * Data extraction: analyses all the files in the series and extracts the chromatograms.
  * Calibration: creates interpolation curves from range points
  * Dosage: calculates the concentration from the interpolation curve
Between each stage, alerts are raised based on the data calculated.

==== Alert system ====
{{:fujitsu:alphacod:quick_guide:flags.png}}

The alerts raised by the automatic processing enable the molecule to be classified for a given sample.
  * Detected: all the alerts raised suggest that the molecule is present in the sample. The operator must check whether this is indeed a detection.
  * Suspected: alerts that have been lifted do not allow the molecule to be excluded or considered as detected. The operator must check whether it has been detected or not.
  * Excluded: an alert allows the molecule to be safely excluded. It is not present in the sample.



===== Main functionalities =====

==== Login view ====
{{:fujitsu:alphacod:quick_guide:login.png?300}}

Authentication form
  * Username
  * Password
Once authenticated, redirection to the Backlog view

==== Navigation ====
{{:fujitsu:alphacod:quick_guide:navigation_panel.png?231}}

Direct access to the Backlog view.

Direct access to the current Batch view (only from Analysis / Compound view).

List of analyses in the current batch:
  * Direct access to analyses opens the Analysis view
  * Search on the list
List of Compounds (molecules) in the current Batch:
  * Direct access to molecules opens the Compounds view
  * Filter on the list
  * Search on the list

:!: Navigation is not displayed from the Backlog.

==== Backlog view ====
{{:fujitsu:alphacod:quick_guide:backlog_view.png?500}}

  * Batch list
  * Batch work progress display
  * Clicking on a line opens the detailed view of the selected Batch


==== Batch view ====
{{:fujitsu:alphacod:quick_guide:batch_view.png?500}}

An overview of the entire batch and the progress of reprocessing.
  * Information: panel containing general information about the batch
  * Calibration
    * List of calibration molecules in the batch
    * Interpolation curve for the molecule selected in the list
  * Quality Control: list of all analyses that are classified into blank, martix bio, matrix bio dopped, calibration and end standard
  * Customer samples: list of all customer samples analyses with their respective progress
  * Others: list of all analyses that the system couldn't find a match for classification


==== Analysis view ====
{{:fujitsu:alphacod:quick_guide:analysis_view.png?500}}

Synthetic view of an analysis within a series.
  * Information: panel containing general information about the analysis
  * Table of molecules
    * List of molecules in the series
    * The table contains the values (concentration, area, RT, S/N, etc.) for each molecule for the analysis in question.
  * Chromatogram grid
    * Displays chromatograms for each molecule in the series
    * Panel synchronised with the molecules table (same filters, sorting and selection)
    * Displays the calibration curve for the selected molecule


==== Compound view ====
{{:fujitsu:alphacod:quick_guide:compound_view.png?500}}

Synthetic view of a molecule within a series.
It enables a comparison to be made between all the analyses for a specific molecule.
  * Information: panel containing general information about a molecule. This information is constant for a series.
  * Analysis table
    * List of analyses in the series
    * The table contains the values (concentration, area, RT, S/N, etc.) for the molecule for each analysis in the series.
  * Chromatogram grid
    * Displays chromatograms for each molecule in the series
    * Panel synchronised with the Molecules table (same filters, sorting and selection)
    * Displays the calibration curve for the selected molecule


==== Validation ====
{{:fujitsu:alphacod:quick_guide:validation.png?500}}

Validation process
  * Each item can be validated in 4 states
    * Detected
    * Not detected
    * Relaunch
    * Nothing
:!: Quick validation is possible using multi selection


==== Progression ====
{{:fujitsu:alphacod:quick_guide:progression_001.png?100}}
{{:fujitsu:alphacod:quick_guide:progression_002.png?200}}

Progression of validation
  * Validation enables the progression component to progress
  * The progression is calculated for each customer sample.
  * The progression of the series is calculated from the progression of each sample.


==== Peak reintegration ====
{{:fujitsu:alphacod:quick_guide:pic_integration.png?500}}

Ability to integrate a peak or re-integrate an existing peak into a chromatogram
  * Reintegration of the area under the curve
  * Move points manually
  * Create points manually if there is no existing peak


==== Work process ====

Standard work process can be the following:

  - Select the series you want to work on
  - Check the series
    * Checking calibrations
    * Checking blanks
    * Checking organic matrices
    * Verification of bio-doped matrices
  - Choose a sample
    * look at the detected first, then suspected by sorting on the area, for example
  - Select the customer sample to be checked
    * Verification and validation of detected molecules
    * Verification and validation of suspected molecules
    * Optional verification and validation of excluded molecules
  - Update the LIMS via the Batch view