Workflows are customised to the needs and requirements of the laboratory, optimising lab efficiency and features automated data-capturing and exports to financial software

Client/user management and authorisation profiles for analysts, data clerks, managers and clients enforce reliable security. Audit logging ensures integrity

Access to the system is via web browsers, resulting in a smooth integration with no disruptive desktop installation or network installation

The Bika web portal provides laboratories with a groupware tool to further enhance collaboration and document publishing

This manual describes Bika LIMS 2 use from the view of the lab personnel. A separate manual is made available to Lab clients

Client contacts have functionality restricted to information pertaining directly to their own companies, and do not see data for other clients or lab data, please see Logging on and general navigation

Users, groups and roles are discussed fully under Bika System Setup

Lingo · In the context of this manual:

• The plural for 1 analysis is many analyses. An analysis is a spesific test, say pH,  on a sample, or 'analysis service' offered by the lab
• A lab technician is the staff member doing the analyses, some labs call them analysts
• An Analysis Request is the collection tests/analyses requested by the client to be carried out on a Sample by the laboratory. See Samples = Analysis Requests
• Some labs call worksheets, jobcards
• Text in square brackets indicates push buttons, eg [Submit]
• Text between vertical lines indicates navigational tabs, eg | Home |
  

We appreciate your feedback
Please report all discrepancies
in this manual to the team at info@bikalabs.com
The manual will continually be upgraded with improvements

This is version 0.1 of the Bika LIMS 2 manual

Lemoene Smit · Anneline Sweetnam · Joris Goudriaan

For the Content Management manual, visit  Managing Content in Plone

Access to content may be authorised to specific groups or individuals. Marketing material such as promotions, news and price lists to the wider public and anonymous visitors, information on methods to clients, technical information and HR to lab staff and research data to specific project teams

No html knowledge is required as through-the-web word processor like editors are included

All standard web content types, pages, images, links, animations, sound, file download and folder structure apply. Events are indicated as shaded dates in the LIMS' calendar

Bika LIMS portals also hosts a Help centre that can be populated with site specific reference, manuals and e-training material

Explaining Bika LIMS workflow

The Contact works for an organisation that is a Client of the laboratory. He represents a Client Contact in the system and is registered as a user with password authentication

When he or she has a sample ready, the contact logs onto the system at the lab's web site on the world wide web. She completes an on-line Analysis Request form, checking all the analyses he wants done

Once submitted, the request is shown with status sample due, the system returns an ID and the contact writes this on the sample label. If he has a label printer, he may print a label from the system and stick that on. He ships the sample to the lab

By this time a sample due alert is shown to clerks at the lab

When the sample arrives at the lab, a lab clerk 'receives' it in the system. The Analysis Request's status changes to in the lab. If the client contact was watching, he'll know that his sample arrived safely and analysis is starting

New in Bika LIMS 2

Clients may now submit sample batches per spreadsheet produced manually
or by up stream systems. These are then imported by lab clerks on arrival
of the samples at the lab

Similarly, results can be published per emailed spreadsheet for 
importation in downstream systems

Workflow is set-up by lab staff with the help of worksheets, requested analyses for the same lab workstation, gets grouped together and assigned to analysts and lab technicians who capture results data onto the worksheets in the system. Manually or automated from interfaced lab instruments

Analysis requests on Worksheets are shown and listed with the status assigned

As soon as results become available, lab managers or appropriately authorised analysts, are alerted that results - with status to be verified - are ready for verification. Results out of range are highlighted and managers may decide to retract these results for retesting

Valid results are verified. All through this process the client contact may track his samples in the lab, but only when verified, does he get to see results itself

Finally the results get published to the contact using the publication preferences he set up for himself earlier, normally per email or fax

New in Bika 2

Client contacts may also receive results as emailed spreadsheets 
or signed certificates

They may nominate colleagues for cc'd results

At any given time, the client contact and lab staff may query analysis results from a query form. Never does the contact see any other data but his own organisation's

Apart from scientific analysis functionality, Bika also offers an
on-line Product ordering module for labs also selling laboratory products

Price lists can be generated and emailed off the database,
Invoices made up and Management reports and queries run
against orders and invoices too

Setting up Bika LIMS 2 is discussed in detail at the end of the manual, so as not to confuse readers at the outset

Please see the Bika LIMS 2 System Setup chapter

The static display part of the laboratory's intranet or world wide web site, e.g. www.yourlab.com, is the entry point to the Bika LIMS system. The LIMS system integrates seamlessly into the the site, maintaining the laboratory’s brand

Clients are led to log onto Bika LIMS via the client’s homepage, where they are informed of product and service updates, promotions, industry news and digital resources pertaining to the client's activities

Static display pages and dynamic pages in Bika LIMS are hyper linked where appropriate, e.g. Price lists, Analytical Services and Laboratory Products offered are listed from the system data

References to individual analyses in Bika LIMS can be hyper linked to content displaying the analytical method used to make it easier for client contacts when requesting analyses

System users may bookmark pages within the Bika LIMS part of the site – a logon prompt is issued before they are given access

A log-off link is provided on all pages for logging out of the Bika LIMS part of the site. The user is returned to the client’s homepage. Users must log off and close their browsers and not leave any open sessions unattended

As a security measure, the Bika LIMS system can be configured to log any user off after a predetermined period of inactivity

The registration of users and assignment of roles and groups is performed by the system administrator. See Bika LIMS System Setup

Once the user has been defined to the system, the login screen or portlet is used for logging on. If the login portlet is enabled it is displayed on all pages while the visitor is not logged in, the login form can be reached from the log in link at top right on the horizontal menu bar

The login portlet

The user name and password is case sensitive. The Remember my name checkbox may be used to have the system automatically fill in the user name in subsequent sessions but is not advised for security use

Login screen

Upon successful log on, the home screen is displayed

Home Screen for lab personnel

The home screen, and all subsequent screens, provide a number of functions and menu choices

At top right, the user may select text size from the three links provided

A search area and [search] button provide the ability to search for entries in the Bika LIMS database

Tabs accross the top of the screen, and a navigation area to the left, give access to the functional areas of the system

The status bar below the tabs shows

• the current location within the system, "breadcrumbs" a la Hans and Gretel
• the user currently logged on to the system
• a link to user preferences
• an undo link – lab managers only
• a link to the setup of the bika system – lab managers only
• a log out link
  

For lab managers, alerts on the right of the screen show analysis requests and worksheets awaiting verification and publication

For lab clerks, alerts on the right of the screen show analysis requests for which samples are due, and orders which are pending

For lab technicians, the home page shows the list of current worksheets

All lab staff see alerts for late analyses

Client contacts are able to view data pertaining only to their own company
The home screen for client contacts shows the list of analysis requests 
which are in sample due status

Client contacts may modify company and contact information,
submit analysis requests and view their progress through the system,
submit orders and change their personal preferences

Client contact's home screen (click to enlarge)

If the lab is accredited, the logo of the accreditation body appears in the left column. The logo is a link to the accreditation detail information

Accreditation seal for SANAS accredited lab

The accreditation text may be modified in the i18n translation files. Accredited analyses are indicated by an '*' in all subsequent  screens

Links everywhere

Analysis description links

Clicking on the analysis will bring up its description in a pop-up

Analysis description in a pop-up

If a user enters a wrong password, he/she will be presented with a screen offering advice on retrieving the password:

Sign-in failure

The user may also click the Forgot your password? link below the log in fields on the portal's front page:

Login portlet

In both cases the user will be led to a screen from where a password can be requested. Enter your user name and press [send me my password]

Lost password request form

If the system is set up to generate user passwords, a system generated password will be emailed to the user. The user will be instructed in the email how to go about changing her password

If the system is set up for the user to create her own password, the system will mail a link to be followed to a screen where the user may enter his or her password of choice:

Password email

Click on the link in the email

A page will open in your browser where you'll have the opportunity to select a new password. Complete the fields and press the [set my password] button

Set your password screen

If all went well, the next screen will confirm that you may continue using your new password

Password confirmation

If you made a mistake - your password is not long enough, or you 
misspelled it in the confirmation field -  you'll be requested to 
repeat the last steps. Corrective steps will be clearly spelled 
out, like in this screen:

The first time you log in, you are invited to setup your preferences. These preferences may also be reached via the link on the menu bar

First time login screen

The My Preferences area provides the ability to change password and set user preferences

User preferences

The Change Password hyperlink presents the form for changing the password. The current password must be entered to ensure security

Change password

The Personal Preferences hyperlink presents the form to change preferences for the logged on user

Personal preferences

The user name and email address are required. It is possible to add a portrait which will be stored in the Bika Wine system

LiveSearch increases the value of Bika's search engine by simplifying the search process. Results from a search are now instant

You'll find Bika's LiveSearch field top right on all Bika Wine pages

Bika's LiveSearch keyword entry field

As you type letters for a search, possible matches appear below the search box — without changing the current page. Here ilustrated is an attempt to find 'alcohol' in the system:

Typing the first few letters in LiveSearch brings up a list of matches

Every item in the list is a live link - click on them to navigate to them if it matches the item you were looking for

Found!

So, instead of entering a search term, waiting for results, and refining your search, this live feedback on searching makes finding things faster and more effective

If the LiveSearch results are unsatisfactory, click the [search] button, upon which a list of  hyperlinked results will be displayed to you

Hyperlinked search results

If the list is too long, or the results not immediately found, click on the Queries link. You'll then be led to a query menu from where you may specify search criteria as described in the Analysis Request Queries paragraph

Just click on the column header. Clicking the column header a second time will reverse the order. The sort order is indicated by an arrow next to the column header the table is sorted on

The same table sorted on client and on number of requests

The |clients| tab or clients folder on the navigation bar lists current laboratory clients. Clients may be deleted from the system by selecting the corresponding check box, and clicking on the [delete] button

To maintain database integrity, you will not be able to delete clients that have analysis or order data in the system already

Client contacts do not see the |clients| tab or clients folder on the
navigation bar. Any modifications to the client details are for their own
company only

Client list

Click on a client to navigate to their pages

Only lab managers and clerks are authorised to create new clients
Clients should however be encouraged to maintain their address information
and preferences once it has been created to reduce the lab's admin load
Client contacts are allowed to create more contacts at the same
Client organisation, handy for storing additional information

A new client is added by clicking on the [add new client] button on the clients list and enter its details in the following screens. The client default page first

Create new client

Enter the client name and information

If your lab provides discount to certain clients, like members of a co-operative lab, and the client is a member, check the Member discount applies check box

Member's discount are set-up in the Bika Settings management screen

Select whether the client is a Corporate or Non Corporate client - this is a further price differentiation set-up per analysis representing a use case where bulk buyers are given cheaper prices

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

Client address

An email address for the client company may be added. Please note that analysis results are faxed and emailed to the Client Contact requesting the analyses. Email addresses for Contacts are maintained in from the contacts page, as described in the Client Contacts section

An address may be added for each of Physical address, Mailing address, Billing address sections. These will be used on Bika invoices and where Client contact addresses are not available, also on printed results certificates

The added addresses are presented in the client address form, where they may be deleted or edited

Click [save] to save your work

In Bika LIMS 1.2 clients had one row of tabs available in the central work area. Due to expanded functionality in LIMS 2, the client tabs are now divided into two groups: |setup| and |actions|

When the tabs are displayed, the right most tab, either |setup| and |actions|, allows the user to switch to the alternative set of tabs. See the screen shots below. The |actions| tabs are the client's default view

The |setup| items consist of several set-up pages for configuring static client information, reached with the tabs:

• |edit| for address, telephone numbers and similar information
  
• |contacts| to configure the contact people at the client
  
• |profiles| for setting up the client's analysis profiles, templates used for repeated one click completion of analysis requests consisting of the same collection of commonly ordered analyses
  
• |specs| to configure the client's own specifications of valid ranges for analysis results for different sample types. These may differ from the specifications applied by the lab itself
  

Note the |actions| tab at far right, that'll toggle the client's action tabs menu

Set-up tabs showing with the |actions| tab highlighted

The |actions| items consist of several pages for dynamic client data, reached with the tabs:

• |samples| for viewing and editing samples
  
• |analysis requests| used to order, list and edit ARs
  
• |imports| to bulk import analysis requests per comma delimited spreadsheet
  
• |orders| to order, list and edit non analytical services or products offered by the lab
  

Action tabs shown with the |setup| tab highlighted

The |contacts| subtab on client page shows the current client contact persons, and allows the addition of new contacts with the [add new contact] button

Client contact person

The client contact person is defined, and using the [next] button, their addresses and publication preferences

The contact's Email address is important as that is the address that will be used for the contact's emailed analysis results as well as lost password requests

Publication preferences

Publication preferences specify the media in which the results of an analysis request requested for that client contact should be returned. This may be by fax, email, print or file - in the latter case, results are returned as comma delimited spreadsheet attachment to emails

Client contact publication preference

Highlight the Contacts preferred publication methods. Selected preferences are shown in orange. To select more than one preference, hold the [Ctrl] key on your keyboard down while clicking on the preference you want to select

E-mailed results for the contact can be cc'd to any of the clients' other contacts by selecting them in Contacts to cc field, typically accounts departments or QC management colleagues. These selected contacts will then be added to the analysis request forms for this contact by default

User account and login

Once the client contact has been defined, it is necessary to define a userid for that person to access the system. This is done using the |login details| subtab

Client contacts are able to create new client contacts
for their company, but they are not permitted to create login details
for the new contact. This must be requested from the lab personnel

Client contact login details

Once the client contact has a login defined, a confirmation message is presented

Confirmation of client login definition

The client may now login to the system to submit analysis requests, orders and edit set-up data like analysis profiles and specifications, and to view results

The lab maintains a set of profiles but clients may also do so for themselves and these are available on a |profiles| tab in their owns set-up area. When completing the analysis request form, the profiles are offered for selection on a drop down menu, the lab's profiles are prefixed 'lab:'. When a profile is selected on the form, the analyses included on the profile gets automatically selected

All client analysis profiles are listed on their |profiles| tab and editable by them

client profiles view

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

Click on [add new lab analysis profile] to add a new profile

The client analysis profile Title is a compulsory field and must be completed

Select which analyses to include by tick the box next to it

Once you're done, click [Save] to save your changes

Clients can set up their own specifications for analysis results that may differ from the specifications applied by the lab itself

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

client analysis sepcification

Clients can also copy the laboratory specifications to their own and then edit them  to reduce the work of setting up the specifications which could be significant. Click on [set to lab defaults]

Adding a New Lab Analysis Specification

Adding client analysis specifications

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 (min), maximum (max) and percentage error (% error) for that sample type

Note: You'll notice that some sample types, have 'specified' texts 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'

Viewing and Editing an existing Lab Analysis Specification

Click on an existing specification's sample type on the list of specifications

view of client analysis spec

If you now want to edit the analysis specification, click on the [edit] tab. The specification's screen opens and it can now be edited:

edit client analysis specification

Modify the values in the min, max and % error fields as required

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

Clients access their ARs from |analysis requests| on their actions tab menu

Analysis requests (ARs) are at the core of Bika LIMS and samples are discussed in considerable detail in the next Chapter,  Analysis Requests and Samples

Client |analysis requests| tab

Clients access their Samples from |samples| on their actions tab menu. Clients see only their own samples

Client samples view

Like most tables in Bika, list content can be sorted by column - click on the column header to sort on it. Clicking the header a second time, the sort order will be reversed. The current sort order, and which column is being used, is indicated by a small triangle next to the corresponding column header, pointing either up or down pending the sort order. See sample id in the above screen shot

Radio buttons along the top of the screen indicates list of samples that can be selected, corresponding to the status of the samples:

• All lists all the samples for the client in reverse chronological order, regardless of its status and an extra status column is included at far right to differentiate between sample statuses
• Due lists all samples for which analyses have been requested but the samples have not been 'received' at the lab and in the system yet
• Received - lists samples that arrived at the lab and have been checked into the system already
• Expired - samples that have expired and cannot be used for analysis anymore.  Only lab staff may expire samples. In future editions of Bika, sample retention periods will be set per sample type and sample expiry and disposal be automated
• Disposed - samples already disposed of by lab personnel
  

Please note the intelligent sample and request numbering: request IDs will always contain the sample ID, followed by a sequence number indicating whether it is the 1st, 2nd or other analysis request for the sample

In most cases the request will be the 1st and only AR for the sample. If there was more than one, all will be listed opposite the sample ID in the requests column

Click on the request ID to drill down to its details

Client users can view their own samples, and change the attributes of the samples as shown in the screen shot below. Only samples not received yet may be edited by clients

Click on one of the sample id, and a detailed view of the sample will be displayed:

Sample view

Click on the |edit| tab to edit the samples attributes. Clients may only edit samples in 'due' status. If the sample needs editing later, please contact the laboratory

Sample edit form

NB Screen shots here are due to change because of slightly misleading column
headers being used. On individual import views, we'll attempt to improve the
layout by displaying the header properties in 2 columns. Our apologies, the 
Bika team

The default view upon clicking the |import| tab, opens a lists of all previous imports - both status Imported and Submitted imports are listed with a status column at far right indicating the import's status

A validity column indicates whether the import made it through validation successfully or not

Click on [import analysis requests] to import a new batch of analysis requests, or on the batch ID of a previously imported batch to inspect it

If you decided to import a new batch, [browse] for the comma separated file (.csv) and click [import] on the next screen

The .csv file to be imported must adhere to a specific template and use the
titles and data for sample types, client contacts and IDs, analyses keywords,
etc. that are known in the system, or the import will not be validated

At the writing of this, 22 January 2008, the template layout has not been
finalised yet. Please contact Bika Lab Systems at info @ bikalabs.com to
obtain the latest should you require it urgently

If illegal characters are found in the file, a system error indicating the problem will be displayed. If not you'll be returned to the import listing and Valid or Invalid displayed in the validity column

You won't be allowed to submit invalid imports, drill down on the import by clicking on its batch ID to inspect it

The Remarks filed summarises the import remarks, while a Remarks column carries remarks specific to each sample

Click on the Show link for a pop-up of the analyses that was requested in the import for the corresponding sample

Valid import views will indicate Valid in its status field and  Valid batch in the import Remarks field

You may now submit this import to the database by clicking submit on its state drop down at top right

After being submitted, the batch can be looked up on the imports lists and viewed. It'll now show links to the Analysis Requests and Sample records created for it

The laboratory offers a number of items for sale to its clients. The list of items are defined by the lab manager under Products in the bika setup. These products appear in the list of items that can be ordered when placing an order

A newly placed order is in pending status and can still be altered. Once the order has been fulfilled, the status changes to dispatched and it cannot be edited anymore

The client user clicks on the |orders| tab to view existing orders and add a new order. All the orders for that company, pending and dispatched, are shown

Client orders

Click on any order to view the order detail, [add new order] to open a new order

Client order - detailed view

Click on the |edit| tab to edit the details of the order. A similar view opens when starting a new order. The Quantity fields are editable and the user may specify how many of a specific item to order - the order total and VAT are automatically totalled at the bottom of the screen as new items are added. Click [save] to save your edits

Client order edit view

Click on the |print order| tab to print the order out

Client order print view

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

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