Bika LIMS is configured in the Bika configuration panel, reached by clicking on the site setup link top right or preferences on the top menu bar

The Bika Configuration portlet appears in the left hand navigational column from where all set-up items can be reached

This function is only available to the lab manager

Bika configuration portlet

All the menu functions are presented, and remain in the left navigation area while on the set-up pages

All your laboratory analysis profiles, are listed in the table below and are editable by lab managers

Click on [add new lab analysis profile] to add a new profile, or click on the title of an existing profile to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

The lab analysis profile Title will be shown in the drop down while creating new analysis requests, and is a mandatory field

Sample Type, each lab analysis profile is linked to a sample type, to select one use the drop down menu.

Analyses, to select which analyses need to applied to this lab analysis profile, tick the box next to the required analysis.

Once you're done with editing an existing profile or creating a new new one, click on Save to save your changes.

Client specific Analysis profiles can be created on AR creation forms by saving the parameters selected for creating the AR as a template. Clients may use this facility to create and maintain their own profiles. These are available for edits in their own set-up area too

All the analytical services offered by your lab are added and listed here and editable to lab managers

Analysis services

Click on [add new analysis service] to add a new service, or click on the title of an existing service to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

The analysis service Description may be used to capture information visible to clients. Typically this is a description of the analysis method and its results interpretation, assisting clients in deciding which analyses to request. Analysis services throughout the system are hyperlinked to pop-ups for clients to look up this information

Instructions are similarly available to lab staff and should contain technical information to guide them through the analysis

Unit must be completed with the unit of measurement for the analysis as it will be reported

In earlier Bika versions, minimum and maximum value fields were populated here to determine whether a test result is out of range, and then highlighted in the analysis request and worksheet results. Since Bika 2, these are maintained per sample type in a separate set-up item, Analysis specifications

Two prices can be kept on record for the analysis service, typically  a cheaper price for bulk buyers, called 'corporate' in the example above. Prices may be overwritten by lab managers on individual ARs, or a 'membership' discount applied per individual clients

The VAT % defaults to the system default but may be edited

The Instrument Import Keyword is the name of the analysis in the .csv file of results imported from lab instruments and is used to match results with analyses. This name must be spelled exactly the same here and as column header in the .csv

Instrument and Method are no more than place holders at this stage. In future versions they will be used in instrument maintenance modules

Maximum Hours Allowed is the time limit specified for this test to be concluded. When an analysis request exceeds this time limit, it is displayed in the late analyses pop-up

The Calculation Type drop down menu is used to select the calculation type associated with the analysis. These are defined in the Calculation Types section of the system set-up and typically includes a range of weight and titration calculations

For analyses requiring titration, the Titration Volume Unit, typically ml, needs to be provided as it appears on the analysis request once the titration volume has been captured

Duplicate Variation is a quality control measure indicating the maximum percentage difference allowed between results for this particular analysis of duplicate samples on the same worksheet. If the difference is bigger than the percentage specified here, the results will be highlighted on the worksheet and the worksheet rejection workflow entered

Department managers responsible for results are included on results publications including their contact details - to provide a short cut for clients having queries. Therefore every analysis service needs to be assigned to a department. The departments are entered in the Lab departments section of the set-up and presented as selection options on a drop down menu here

As indicated by the red square next to it, Department is a compulsory field

The intercept table of Uncertainties is used to determine the measure of uncertainty for the analysis. These uncertainty values are shown throughout the system as +/- value, after the result

Using the example above, a result of 15 units will be reported as 15 +/- 2 units

Press [save] to submit your edits, [cancel] if you don't want to

All the analytical services offered by your lab are added and listed here and editable to lab managers. The same functionality is available to clients in their own set-up areas where they may maintain their own specifications

Users may then apply either their own specifications or that of the laboratory on several Analysis request or Worksheet views where results are displayed. Results outside of the chosen range are then highlighted

In the lab, staff may then take measures such as entering rejection or re-testing workflows

Click on [add new lab analysis specification] to add a new specification, or click on the title of an existing service to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

Adding a New Lab Analysis Specification

Click on the tick box next to sample type to select the sample type you want to set specifications for. More than one sample type may be selected but all selected sample types will then get the same specifications

Then enter the minimum, maximum and percentage error for that sample type

Note: You'll notice that some sample types, have 'specified' behind it. This means that an analysis specification for that sample has already been set-up and if it is selected again, the previous specification will be overwritten

Click on [Save] to apply your set-up

How are the minimum and maximum values, and percentage error applied?

When a results is submitted it is compared to the minimum and maximum values for its sample type specification, also depending whether the lab or client specifications are selected. If the limits are not exceeded it is reported normally as 'in range'

If the result exceeds the limits, the error percentage is applied to it and it is again measured against the valid range limits. If it then falls in range, it is reported as 'in error range'. If it is still over the limits, it is reported as 'out of range'

Editing an existing Lab Analysis Specification

NB The Sample Type drop down menu

The Sample Type drop down menu at the top of this screen is used to apply the specification to the selected Sample type. It offers the sample type initially selected, and all others for which no specifications exist

If a new sample type is selected here and the specification saved, the specification for the sample type for which the screen was initially opened is removed and 'switched' to the newly selected sample type

In future editions this should be changed into a copy instead of deletion, and if technically impossible, the drop down replaced with plain text of the sample type for which the specification may be edited

Click on [Save] to apply your set-up

The Bika Calendar functionality and set-up is available in a separate manual in the manual section of the Bikalabs.com HelpCenter, which you can find by clicking here

The complete URL:

http://www.bikalabs.com/helpcentre/manual/bika-calendar-manual

Bika settings define default values for the Bika LIMS installation. System wide preferences are set here by the lab manager or system administrator

Click on bika settings for the settings screen to open:

System defaults

Bika settings

Password lifetime defines the number of days before users’ passwords expire, requiring them to renew their passwords. A zero value implies passwords do not expire

Automatic log-off defines the number of minutes of inactivity before the system automatically logs the user off. A zero value implies automatic log-off is disabled

Member discount defines the discount percentage that is applied to members. In the client set-up, lab managers may set clients up as a member of the discount group

VAT % is the Value Added Tax percentage to be applied to services and products. The VAT may be changed per individual service, but this value sets the system default

Bika LIMS generates sequential serial numbers as new objects are created, e.g. analysis requests, worksheets and orders. The prefixes and formats for these serial numbers are defined in the Prefixes list

The prefix may include special characters, typically ‘XX-‘, and a certain length of the string to be used, A typical AR number, as shown in the screen shot above, would be AR-00001

NB It is important not to include any dashes 
in the actual prefix as these are programmatically used 
to separate Sample IDs from AR IDs.



AR08- is valid but AR-08- is not

Click on [Save] to save your changes.

The calculations are used in the actual programming and cannot be modified without the intervention of programmers. The calculation descriptions are displayed with the instructions for analyses to analysts, and are the only information that should be edited here by lab staff

Click on the title of an existing Calculation to edit it

Title describes the title of the calculation, this will be populated in the Calculation Type drop down from your Analysis Services set-up, which is explained here

Description describes the formula to be used for the calculation and is for information purposes only

code describes that is used in the programs for the calculation

All the lab instruments used by your lab are added and listed here and editable to lab managers. Analysis services can be assigned to instruments in their set-ups

The instrument data are currently not used for anything else and this repository mainly serves to keep instrument data in one central place. In future developments this will be expanded to a fully fledged instrument maintenance module

Click on [add new instruments] to add a new instrument, or click on the title of an existing instrument to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

Self explanatory: Title is for what the instrument is called in the lab, its Description and Type, Brand and Model, Serial No. Calibration Certificate is used to store the name of the calibration certificate that applies to the instrument and its Calibration Expiry Date

All the lab contacts available to your lab are added and listed here and editable to lab managers. Each department in the lab (set-up here), has a manager assigned to it, which can be selected from the list of Lab Contacts

In the Analysis Services set-up (covered here), each analysis is linked to a department. When an analysis request is published, the system looks up the responsible manager's contact details and publish it with the results to assist clients with queries

 The signature of the manager is used in printed results certificates

Click on [add new labcontact] to add a new laboratory contact, or click on the title of an existing service to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

Self explanantory: Title e.g. Mr, Mrs, Dr, Miss, etc, Firstname, Surname, Email address, Phone (business),  Fax (business), Phone (home),  and Phone (mobile) for the mobile phone number where the lab contact can be reached

Job title describes the job title of the lab contact
Signature allows a signature in image format (png, gif, jpeg) to be uploaded for use in published report. To select an image, click [Browse] and you can upload an image from your desktop.

Click [Save] to apply your changes

All lab departments existing in your lab are added and listed here and editable to lab managers. The Lab departments are used to identify the lab managers responsible for published analysis results as all analysis services are assigned to departments

The responsible lab managers' names and contact details are then provided on results to provide a short cut to clients having queries

Click on [add new department] to add a new department, or click on the title of an existing department to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

Title describes the title of the laboratory department

Manager is a selection of Lab Contact (which is discussed here)

Click on the laboratory information link

A series of tabs will be presented with the |default| tab open where the laboratory name and contact details can be maintained. Using the [next] button, the lab addresses, bank account details and accreditation information  can be maintained on the subsequent |Address|, |Bank Account| and |Accreditation| tabs

Laboratory Name

Laboratory details

Name describes the name of the laboratory
Registration number describes the laboratory registration number
Tax number describes the VAT/Tax number associated with your laboratory
Number of employees describes the number of employees working at your laboratory
Phone describes the phone number of your laboratory
Fax describes the fax number of your laboratory
Laboratory Confidence Level % describes the accuracy level of results across the laboratory. More details confidence lvels can be set-up in the Analysis Services section (see here)

Click on the [next] button to navigate to the address form

Laboratory Address

Laboratory address details

You'll notice that there are three address sections; Physical Address, Postal Address and Billing Address, as the fields are all the same they will only be explained once, below.

Email address describes the laboratories email address
Address describes the address of the laboratory
City describes the city the laboratory resides in
State describes the province or state the laboratory is in
Postal Code describes the postal code  the laboratory is in
Country describes the country the laboratory resides in, you can select it, by using the drop down menu

Click on the [next] button to navigate to the bank account details form

Bank Account

Laboratory bank details

Type of account describes the type of bank account that is used by the laboratory
Account name describes the bank account name used
Account number describes the bank account number used
Brancg code describes the branch number of the bank the laboratory uses
Bank name describes the name of the Bank

Click on the [next] button to navigate to the bank account details form

Accreditation

Check the Accredited checkbox if the laboratory has been accredited. This will cause the accreditation body logo to appear with its link to accreditation details, and indicate which analyses have been accredited. Accreditation body and certification texts can be edited in the i18n Translation files

To further enable accreditation, analysis services need to be identified as being accredited, this can be done here 

Accreditation Body Abbreviation describes the short name or abbreviation of the accreditation body and Accreditation Body its full name, Accreditation Body URL its  web address

Accreditation is the accreditation type for your lab, typically ISO 17025

Accreditation Reference holds the number or unique identifier that the accreditation body issued to your laboratory

Email templates

Click on the links to view and edit the email templates

Excerpt of email template

Click on the |edit| tab to edit the template

Email template edit

Click on [save] to commit the changes

All the methods offered by your lab are added and listed here and editable to lab managers. The methods can then be assigned to analysis services in their set-up

Currently methods are not used anywhere else in the system (yet) but serves mainly as a repository for information regarding the lab methods. In future customisations this information could be surfaced where most needed by analysts, in work sheets say

Click on [add new method] to add a new method, or click on the title of an existing method to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

Title describes the title of the method
Method Description described the description of the method to be used for that analysis. This method is selected from the analysis service set-up, further explained here

The products available for sale are defined here

Laboratory products

Click on a product title to edit or [add new product] for product details

Edit product details

The VAT % defaults to the system defined value, but may be overridden here for this product

These are available on drop down menus on analysis request screens

Click on [add new sample point] to add a new service, or click on the title of an existing service to edit it. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

Edit or enter the Sample point Title and Description. Press [save] to submit your edits, [cancel] if you don't want to

The type of samples which may be submitted. This list appears for selection when the Sample Type is entered into an analysis request

Click on an existing sample type to edit it or the [add new sample type] button to create a new sample type. If you want to delete one, check the box opposite its title and press [delete] at the bottom of the page

Edit or enter the Sample type Title and Description

The sample type can be checked as Hazardous if necessary. Samples of this type will then be labelled as such and the sample will be displayed with hazardous icon in the system

Press [save] to submit your edits, [cancel] if you don't want to

QC standards are described here in generic terms, as it would apply to bulk standard stocks or a batch of standard samples, or simply QC standard 'types' or 'templates'

When actual QC standard samples are added to the system, they are added for Standard suppliers and if the QC sample adhere to one of these Standard Stocks' definition, the record can be created from the stock, inheriting its properties

In some cases, the lab would literally make up its own Standard stock and then dilute parts of it at a regular basis to be used as QC control samples - from there then 'Standard Stocks'

To delete an existing stock, check the box next to it and click [delete]

Click on [add new standard] to add a new stock, or click on an existing one to edit it, the Standard stock details screen will open:

Complete the compulsory Title field and supply a Description if you want to

If the stock has a limited shelf life, provide and Expiry date. Expired stocks will not be available when entering QC samples into the system. Date created can be used to record the date the stock was made up or manufactured

If the stock is of a Hazardous sample type, check the Hazardous check box

Select which analyses the stock can be used a standard for by checking the corresponding boxes. Enter the expected results for the stock and the % error to be tolerated before 'out of range' alerts will be raised to analysts. Corresponding minimum and maximum values will be calculated by the system

Click [Save] to save the information

Users

From the site setup page, select Users and Groups Administration to register personnel and assign their roles. Note that client contacts are not registered here – they are accessed via the Clients option on the main menu

Create a new user by clicking [add new user] on the user overview page, or serach for an existing user

Find or add a user

[show all] Lists all users in the system

Users

From this page, user email addresses may be modified in the email field, or passwords reset or the user removed by checking the corresponding checkboxes at far right, and clicking [apply changes] at the bottom of the page

Create a new user

Click on the [add new user] button to add a user

Enter the details in the fields, return to User/Group management and assign the required roles for that user. Once the user details have been registered an email is sent by the server to the user, so that the user can set his/her own password.

Note: This email must be answered within 24 hours.

Editing a user

Click on the user name on the list to view or modify user details

User properties edit

Enter the user details, and optionally load a portrait of the user

Groups and Roles

Click on the |group membership| tab to assign this user to a group
Roles determine the authorisation and functionality the user has within the system
The following roles are defined:

• member – all members of the portal are in the member group. Client contacts are typically only members of this group, and may view only their own company’s data

• labmanager – Bika setup functionality and all other functionality except system setup functions reserved to the system administrator

• labtechnician – analysts able to manage test results and worksheets

• labclerk – able to receive samples, submit analysis requests and manage product orders
• verifier –  permitted to verify and retract analysis requests and worksheets. This role must be combined with another role (e.g. labtechnician) to provide functional access to the system

• publisher –  permitted to publish and retract analysis requests. This role must be combined with another role (e.g. labtechnician) to provide functional access to the system

• manager

• owner

Groups are logical collections of users, such as departments and business units. Groups are then given roles, and users are assigned to groups. The users within the group inherit the functionality of the roles assigned to the group

Click on the |groups| tab from the main Users and Groups Administration  area to manage groups

Groups overview

To assign roles to groups, select the appropriate checkboxes and click the [apply changes] button

Click on the [add new group] button to add a group, or click on the group name to view or modify group properties

Group properties

Adding Users to Groups

Users may be added to groups in two ways: Edit the user, and select multiple groups they should join, or edit the group and add multiple users

Click on the |group membership| tab of the user properties form:

Group membership for user

The available groups are shown above, while the current groups to which this user belongs are shown below. Select the appropriate checkboxes and click on [add user to selected groups] to add the user. To cancel the user’s membership to the group select the appropriate checkbox from the Current Group Memberships list, and click on [remove selected groups]

To add multiple users to a group, click on the |group members| tab of the group properties form

Group membership

The available users are shown above, while the current group members are shown below. Select the appropriate checkboxes and click on [add selected users to this group] to add the user. To cancel the user’s membership to the group select the appropriate checkbox from the Current Group Members list, and click on [delete selected users]. Deleting a user does not remove the user from the system, it is only removed from this group

To delete an Worksheet Template, check the box next to it and click [delete]

Complete the compulsory Title field and supply a Description if you want to

You may specify normal analyses, of the types selected at the bottom of the screen, or any of Blank, Control or Duplicate QC analyses in any of the positions on the worksheet from the drop down menu as shown above

Calibration samples will be added to these in the near future - these will be used to apply correction factors to the results in the worksheet

Once a Blank or Control sample has been selected for a position, which standard to be used can be selected from drop down menus in the 3rd column as shown below:

The expected values for the Controls and Blanks will be used in the validation of results in the worksheets created with the template

Where a Duplicate sample has been specified, a drop down is activated in the last column to specify which position's sample must be used. In the worksheet results for these 2 positions will be compared as further QC measure

Finally which analyses to be performed on the samples in the positions marked Analysis, can be selected from the list of analyses at the bottom of the screen. More than one analysis may be selected for instruments which are capable of doing multiple analyses on the same sample