Bika Interlab functional specification

Version 1.1, lemoene, 22 April 2006

NB Please also view the html wireframe model for Bika Interlab available from the links at left

Contents

1. Document Convention

2. The Bika Interlab LIMS functions

3. Roles and Work flow

4. Use case 1. New Samples

5. Use case 2. Member lab captures results

6. Use case 3. Member lab views statistical distribution of results

7. Use case 4. Member lab views performance data

8. Reports

9. Queries

10. Set-up

 

1. Document Convention

One analysis, many analyses
AR - Analysis Request, an 'order' for the analyses to be carried out on a sample

2. Bika Interlab LIMS functions

Use Case: A Wine Interlab organisation administers the distribution of ‘control’ wine samples for member labs to analyse and report on – for comparison and quality control purposes at the labs. The samples are not real control samples as they are taken from wine in production and the chemistry there-of unknown

Labs fetch the samples from a central distribution point and then have a week to analyse them and return the results for any number of all possible analyses listed

Cumulative results and statistical variables for each analysis are then returned to member labs in anonymous format

The Bika Interlab web based LIMS will allow members to securely submit and view results and distribution graphs on-line

Few results do not make for sound statistical analysis an set statistical minimum requirement needed for statistical summary and graphs, is maintained in the system's set-up

On the Interlab site, as much information possible is made available to members and anonymous visitors, ie about analytical methods and procedures – this implicates that Plone's content management be kept available

Content is managed by an Interlab manager - this role player does not feature any further

In later phases more detailed statistical analysis of data is foreseen

3. Roles and Work flow

3.1 Content manager - manages static web pages, some of which visible to anonymous visitors

3.2 System manager - manages the systems set-up, has access to all data - she may drill down on all member labs' analyses and for her reports totals all data. She is not allowed to alter results submitted. nobody is

3.3 Sample supplier - this role player enters new samples only, see 'New Samples' use case below

3.4 Member lab contact - Interlab member contact, sees and manages her own data only

Work flow can be described in the following Use cases

4. Use case 1. New Samples

Role player: Sample supplier

NB the sample supplier is only allowed to add new samples and view the sample list. She does not have system management or administration authorities per se

The ‘Sample supplier’ prepares samples for member labs and makes it available at the designated depot. Normally 2 samples per month per lab. Could increase. Approximately 50 member labs

4.1 when the 2 samples are ready, she logs onto the LIMS, navigates to the samples page and creates 2 new sample records. she may create any number of new 'samples'

4.2 the system generates a sample number – typically S06-060 for the 60th sample of 2006

4.3 On the ‘new sample’ page, she supplies the following info re the Sample:

Sample type ie Natural Sweet (from a drop down menu)

Sample ready date the system date when the record is created

Closing date the cut-off date after which no more results maybe submitted for the sample

she clicks [save]

4.4 the LIMS creates an Analysis Request record per sample for each lab with status 'sample_due'. The labs identify the AR by its Sample ID, the AR number is never shown

4.5 the AR contains all the analyses set-up in the system, 1 per line - the labs won't necessarily submit results for all of them

4.6 the LIMS sends all member labs email notification of the samples being ready, stating the expiry date, sample type and physical address where the samples must be fetched

4.7 the member labs fetch the samples and 'receives' them in the LIMS – the status of the lab's AR changes to 'in_the_lab'

4.8 Option: a set number of days before the sample's cut-off date, all labs who have not 'received' their samples yet, get an e-mail reminder to fetch their samples

5. Use case 2. Member lab captures results

Role player: Member lab representative

After the labs have received the samples they analyse them and submit the results on-line They are not allowed to submit results after the sample’s closing date

All the analyses in the system are automatically included on the forms for results submittal and member labs may not add or remove analyses. They may submit results for any number of analyses and not necessarily all of them

5.1 when any result is ready, the role player logs onto the LIMS and navigates to the Samples page

5.2 Samples are listed reverse chronologically with columns for

Sample number
Sample type
Sample status
Release date
Date received
Closing date

5.3 she clicks on the 'in_the_lab' sample she wants to capture results for

5.4 an ‘Analyses’ page opens with all analyses listed, columns for

Analysis
Method
Result
Unit
Z-value
Performance
Total number of results submitted (by all members)

5.5 previously submitted results values are shown but are uneditable

5.6 she enters results values where still allowed to do so

5.7 she selects the method used from a drop down menu for each value

5.8 when completed she presses [submit] – when the page refreshes the results submitted are uneditable

5.9 she remains on the same page as she might want to drill down now to see how her lab compares to other results. see paragraph Use case 3. Member lab views statistical distribution of results

5.10 she may come back later to add more results but those submitted earlier cannot be retracted or edited

5.11 Optionally, a set number of days before the closing date for the sample, all member labs who have not submitted results for all analyses for the sample, receive emails prompting them to do so for outstanding analyses

The email lists both analyses not submitted and those already submitted. Values are included for those submitted

5.12 after the the closing date all input fields become uneditable

5.13 a final version of the above mail is 'published' to all labs shortly after the sample's closing date but including the lab's actual results and statistical parameters with links to the corresponding analyses pages on the web

Averaged Stats are included under the same statistical minimum set for web views only, ie a minimum number of results values available. See below

6. Use case 3. Member lab views statistical distribution of results

Member labs get access to statistical data that include data by other labs, such as distribution graphs, under very strict rules:

A.only for those analyses the lab has submitted results for herself - to prevent biased data input!

B.all data, except the member's own, are shown anonymously

C. summary statistics and graphs are shown only (system wide) where a set statistical minimum of results were submitted - fewer data points do not make for sound statistical analysis. in this case only the few values that were submitted are tabled

Role player: Member lab representative

6.1 the role player navigates to the Samples page and clicks on the sample she wants to review results for

6.2 a ‘Analyses’ page opens with all analyses listed, whether she has submitted values or not

6.3 on the analyses page analyses and available results are listed under:

Analysis
Method
Result
Unit
Final Mean
Z-value
Performance
Total (number of submissions by all labs)

6.4 The analyses page header includes data for:

Sample number
Sample type
Status
Release date
Date received
Expiry date

6.5 the role player may drill down to statistical results pages for all analyses under the conditions listed earlier – she clicks on the analysis to open the page to view the results, graph and statistical variables

6.6 if the statistically set minimum number required results have been submitted, the page displays the graphs and statistical summaries described below

if not, then just the table of data submitted described in the next point, and the text Distribution graphs and summary statistics are only available where ## or more results were submitted

In this case, members' performance indicator and z-value are also omitted from the page's header information

With 'enough' data, the following is displayed:

a results distribution graph

this graph plots the distribution of all the results submitted for the analysis, indicating all data values on the graph as dots. The labs own value is indicated as a blue dot and the final mean of all data as a green dot

the distribution graph also displays the text: Statistical parameters may fluctuate before the closing date while results are being submitted by members. Only when the sample status indicates 'closed', are parameters final

Distribution graph example for Alcohol analysis - the member lab's own value is indicated in blue, the mean value in green

below the distribution graph summary data are tabled in a column each for the 'standard deviation' and 'mean', and rows for 'unadjusted', 'adjusted' and 'final'

Optionally, below that a graph showing results per method (if more than one method was used) and showing the average per method. the member's own value clearly indicated

Results per method graph example for Alcohol analysis - the member lab's own value is indicated in blue, the mean value in green

with this option also a table with the summarised data per method and including numbers for 'All' methods

if only one method was used throughout by all labs, this section is excluded

6.7 regardless how many results were submitted, the page shows a data table showing all the results submitted by the labs for that sample and analysis

Data can be sorted on each of these by clicking on the column header
1 row per result submitted

columns for

Result
z-value empty if not enough data, formula to be supplied
Performance empty if not enough data. A, B or C – Interpretation formula to be supplied
Method

6.8 for the member lab logged on:

her results are highlighted in the tables
and marked in different colour on the graph

7. Use case 4. Member lab views performance data

Member labs also track there historical performance to improve their methods. These stats and graphs are available from a main menu item and also a 'Historical Z-values...' button on the distribution stats (per analysis per sample) page

Role player: Member lab representative

7.1 the role player navigates to the lab's statistics page

7.2 all analyses are lists here, each linked to the member lab's historical Z-value data for the specific analysis

7.3 on the z-value page, the last year's z-values are plotted and listed

A member lab's historical z-performance graphed for an analysis

7.4 from the list, clients can drill down to the distribution stats and page (described above) for a specific date

7.5 a button, 'previous year...', links to the previous year's data

7.6 on previous years' pages, an additional button 'next year...' links to the next

8. Reports

Only the current bika report 'Analysis Totals' is available from the main menu. It list totals for the date range specified by the user. Only analyses with results submitted. A grand total at the bottom

Role player: Member lab representative
only totals for the member lab herself are reported

Role player: System manager
she gets an additional specification field to look up totals for a specific member

if she leaves this field empty, she sees the report results totaled system wide - all labs'

9. Queries

Role player: Member lab representative:
only query results for the member lab herself are reported

Role player: System manager:
she gets an additional specification field to look query for a specific member

if she leaves this field empty, she sees the query results system wide - all labs'

Analyses can be found and listed by specifying search criteria for:

Sample Type
Release date
Sample number
Analysis
Method
Status
Performance

Query results are listed under:

Analysis
Release
Method
Result
Unit
Number of values (submitted by all)
Z-Value
Performance
Status

The role player may drill down onto a specific Analysis's data or her historic z-value performance for the analysis

NB. Where the set statistically required minimum number of submitted results are not available, Z-values and performance indicators are not shown

10. Set-up

Roughly the standard bika set-up, adapted and including:

10.1 Members & Contacts

10.2 Sample Types

10.3 Analyses

A few analyses are fixed to specific methods, ie FSO2 (Ripper) and FSO2 (Aspiration). In the set-up thus it should be able to 'fix/attach' a single method to an analysis via a drop-down of all Methods. At AR creation time, these methods are automatically entered for these analyses and now modification allowed

10.4 Methods

10.5 System set-up (additional to current bika)

minimum for number of values for graphs

number of days before closing date to prompt for sample fetching

number of days before closing to prompt for result submittal

depot address for fetching samples from (the current physical address for lab)