Open Source Laboratory Information system

1. OpenLIMS
comprehensive solution for the
laboratory complement
our mission is OpenLIMS is the new generation of the Laboratory Information Management System, equipped
to provide with open architecture. This LIMS supports several local laboratories, as well as domestic labora-
a professional tory chains.
and complete OpenLIMS‘ new generation development began in 2003. The new generation development is based
lims for the on the great experiences reached during the long period of providing the first generation of LIS
laboratory (more than 250 installations in the Czech Republic and 100 installations in the Slovak Republic).
complement The works on the first generation of LIS started in 1985, and the first PC-version was installed in
1991.
Two laboratories in the Czech Republic started to work with OpenLIMS in 2005 as pilot projects.
From 2006 the system is being released for commercial use in any types of laboratories, and it is
capable of managing a wide range of laboratory chains‘ requirements. OpenLIMS supports the
following laboratory qualifications: biochemistry, hematology, virology, parasitology, immunology,
cytology, bacteriology, microbiology, genetics and pathology.
openlims OpenLIMS is a modern and flexible system, which uses the newest available technologies.
characteristics OpenLIMS has completely secure access to the data.
OpenLIMS is suitable not only for small laboratories with a single workstation, but also for wide
laboratory chains with thousands of workstations. (The biggest installation: 200 workstations
with 60 on-line connected analysers).
OpenLIMS enables management of the laboratory chain with joint data sources.
OpenLIMS enables communication with all types of analyzers and can easily define the
communication interface with external systems (HIS).
OpenLIMS includes many functions for lab assistants, chemists and laboratory managers.
OpenLIMS has important operational modules, which are accessible via WWW interface.
WWW interface enables on-line laboratory examination ordering and result-viewing.

2. OpenLIMS supports language modification and enables easy module customization according
to any specific legislation.
OpenLIMS has the user friendly interface responding to Microsoft Windows standards. The
important work forms are fully configurable and adjustable.
OpenLIMS is directly connected to Stapro HelpDesk application. An experienced team of spe-
cialists is ready to help with the laboratory processes optimalization.
OpenLIMS can be constantly monitored from the remote centre in Stapro, Czech Republic. It
enables accessibility to the critical parts of the system – database, applications and communica-
tion server.
OpenLIMS capabilities
analytical Reference range mechanism - It allows the method evaluation in nine intervals differentiated by
capabilities various parameters such as sex, age, diagnosis, collection time and other common conditions (i.e. the
dependence on the other method result). The reference range has it‘s own history, and it is possible
to change it through time. Except for the reference range (physiological range, pathological range), it
is possible to define the intervals of the feasible ranges for the numerical values entrance.
Delta Check - Once Delta Check mechanism is configured and activated, every value over the
given limits (growth/drop) of test results are checked. The evaluation may be defined by age,
sex, diagnosis or other common conditions.
Calculated tests - Common
calculated mechanism ena-
bles the immediate calcula-
tion of the results according
to the given results‘ methods
and related information.
Inconsistency and automa-
tic evaluation - According
to pre-defined rules, it is
possible to evaluate the
methods and their results
between them, together
with other patient data.
Definition of calculated test
Result history - All previous
patient results may be viewed on-line, including all evaluation and text descriptions. The result
history may be used when the results have been automatically or manually validated, when the
cumulative report has been printed and when Delta Check has been proceeded.
Redundant methods - The redundant examinations are indicated, which can produce reduction
in lab costs.
Automatic result approval - According to the reference range evaluation, Delta Check, QC
results and other conditions are the automatic result approval provided.
Manual result approval - Manual result approval may be provided in several levels – lab assistant,
chemist, doctor, etc.
QC – Internal quality control - The QC archives all samples results manually inserted, or on-
line information received from the analyzers. It enables its graphic presentation (Levey-Jen-
nings graph, Younden graph) and the comparison of the atest and aberrations. QC includes
on-line evaluation of the Westgards rules. The part of QC is also the monitoring of the result
averages, where extremes are excluded.
TAT (Total Around Time) - TAT is used for the monitoring and evaluation of the period
necessary for the manipulation with all different types of samples.

3. Security Result database - The user
access policy can be defined
separately for some users,
and integrated for others.
Access rules - The users‘
definition and allocation to
the access rights groups ena-
bles to set different access to
the modules. It also manages
the access to the operational
parts or to the methods for
each user.
Logging system - Keeps
history of all changes in
the system and its authors,
including the list of cancel-
led results/records.
Submission of requests, identifications and results
Print records Standard reports - All different kinds of working protocols, main books, name lists, extreme
result books, result list, etc.
Report generator - Flexible parametric reports and scripts, colour printing.
Automatic report creation on the background
Communication OpenLIMS has a separate communication component. It communicates with analyzers, devices
and external subjects (such as HIS, IS for general practitioners, etc.)
The communication component does not depend on the core. It enables communication with
analyzers even during possible temporary failure of the connection with OpenLIMS central
database.
The communication has been tested on more then 300 analyzers and devices.
It supports one-way and two-way communication within the batch mode and also through on-
line mode.
It supports POCT analyzers.
It provides on-line control transfer to the QC system.
It enables transfer of the failure codes from analyzers. Also, there is the possibility upon require-
ment for the automation of repeated or additional examinations according to the measurement
results.
It communicates with analyzers through USB, RS 232 or TCP/IP protocol.
It communicates with external systems in data standard (Ministry of Health of the Czech
Republic), HL7 interface. The XML format is supported.
Results Result lists - The format of result lists can be defined by users according to the type of the appli-
distribution cants.
Print reports archive - All print reports are archived, if needed with the electronic signature and
time stamp.
Electronic distribution - The selected applicants may received the results in electronic format,
such as TXT, XML and data standard (Ministry of Health of the Czech Republic). The guaran-
teed and secure transfer is provided by product called MISE.
Remote access WWW interface for examination requirement input.
WWW interface for displaying results.

4. Work Barcodes - The barcodes are
automation used for the patient identifi-
cation, sample identification
and for communication with
analyzers.
OMR (Optical Mark
Reading) - The one-way and
two-way automation optical
mark reader can be con-
nected.
Central entry - All require-
ments enter the system in
one place and are automati-
cally distributed to the ope-
rational parts of laboratories. View of result history
Sample tracking mechanism - for each sample, a track is kept in the analytical process and in the
storage room.
Sequence - Often repeated activities can be predefined and manually or automatically run, when
defined conditions are fulfilled. Sequences may be activated on the background as server processes.
Work management - Specifically defined rules help to automatically modify work when defined
conditions occur.
Statistics Statistics module - Statis-
and finance tics reports are generated
according to the applicants,
type of method and working
parts or its groups.
Financial module - It is the
separate component, which
represents the legislative
needs of specific country.
Invoicing - The user is able
to make the invoice for the
examination (preliminary Result report
or final) and also aggregate invoice for the applicant/department.
Additional Daily operation - It enables the creation of reports about all samples in specific parts of the system.
functions Daily statistics - Continuous report about the numbers of samples, daily averages and aberrations.
Daily operation control - Continuous control of the daily work, such as duplicity and
misspells.
Technology
System OpenLIMS uses the newest available development technologies. The system is developed with fol-
architecture lowing basic parameters:
component solution in Microsoft.Net and C# technology
n-tier architecture
database independents
national independents (language and application)
www interface for the system administration and for the specific components operation

5. The verified N-tier architecture represents the strict database separation, application logic and clients presenta-
databases are tion tier. The database tier fully respects the rules of SQL databases. It enables to choose the specific
Microsoft database according to the customer need and possibilities.
SQL v2000 The operation system on which is the database installed can be UNIX, LINUX or Microsoft servers.
and Oracle v9 For the OpenLIMS client part, Microsoft Windows is used. OpenLIMS works on one PC or on
larger networks. The work on large networks has a definite advantage; the database and application
server may be separated, and the output is divided according to the operation needs.
The possible OpenLIMS methods of installation:
on one workstation with OS Windows-run database, application tier and client tier
on server-run database and application tier; workstations run client tier
the individual server is used for database and application tier, on workstation-run client tier
According to the needs, the application tier may be installed on more servers/workstations. This
enables division of the load among more workstations while several workstations are in use.
For higher accessibility, it is possible to use the cluster solution for the database/application tier.
For the communication with analysers and devices, it is possible to use the individual server. It‘s
work is independent to the other parts of the system. This enables communication with analysers,
including during possible temporary failure of the main OpenLIMS database.
system OpenLIMS is developed as a
characteristic component system. The basic
services are run by the core of
the system. Other components
are added according to the labo-
ratory needs.
The core provides:
the access rights and the sys-
tem security
the documentation of all
changes made within the sys-
tem
the access to the identificati-
on register and to the results
System setup
database
the processes over the register and results database: calculation, validation, print reports, etc.
the codes administration and users‘ configuration administration
the system versions list and possible upgrade administration
The main components working over the core are:
the access to the identification, examination requirements and results input
the communication with analyzers and devices
the results presentation
the print component
the statistics including QC and financial components (invoicing, billing)
In OpenLIMS more laboratories can be defined, using the same list of patients applying for the
examination. Each laboratory can use its own code lists (methods, texts, etc.) and it‘s work can be
divided into independent parts. They may have their own parameters for work with numerical lines
of samples and for examination requirements, for results validation, for results distribution, etc.

6. The design of the entrance window for each operational laboratory part may be adjusted according
to laboratory needs.
Workstation Pentium 4 (or equivalent) PC
requirements Standard 512 MB RAM, optimal 1 GB RAM
1024x768 VGA
17“ color monitor
20 GB Hard Disk
RS232 or USB for connectivity with lab analyzers
Server Depending on the size of the laboratory, it is recommended that a single processor or dual proces-
requirements sor server with min. 2GB RAM, equipped with disk array for data storage. For data back-up, tape
or DVD RW is used.
The server accessibility will increase, when the two servers in the cluster connected to the disk array
would be installed.
Software and Server - UNIX or Linux or Microsoft SQL 2000/2005 Server
operation Database - possibilities: Oracle v9, Microsoft SQL v2000/2005
systems Application server - Microsoft SQL server 2000/2005 or Windows 2000/XP
requirements Workstation - Microsoft Windows 2000/XP and Microsoft .Net Framework
Remote administration - RDP (Remote Desktop Protokol) and active Internet
STAPRO s. r. o.
Pernstynske nam. 51
530 02 Pardubice
Czech Republic
Phone: +420 467 003 111
Fax: +420 467 003 119
E-mail: stapro@stapro.cz
www.stapro.cz
Holder of quality management certificate under ISO 9001:2000
and environmental management certificate under ISO 14001:2004

7. Block schema
of n-tier
architecture
OpenLIMS – Small
Laboratory

8. OpenLIMS
Standard
Configuration
OpenLIMS
The Laboratory
Chain

9. The List of Connected Analyzers and Devices Hoffmann-La Roche Cobas Mira+
Producer Type Hoffmann-La Roche Cobas Integra 400
Biochemical analyzers Hoffmann-La Roche Cobas Integra 700
Liasys Hoffmann-La Roche Cobas Integra 800
Abbott Alcyon Instrument Laboratory ILAB 600
Abbott Spectrum CCx Instrument Laboratory ILAB 900
Abbott Spectrum EPx Johnson&Johnson Vitros (Ektachem) 250
Abbott Aeroset Johnson&Johnson Vitros (Ektachem) 500,
AL Instruments Alixia 950
AL Instruments Mascott + Johnson&Johnson Vitros Eci
Baker ENCORE Johnson&Johnson Vitros (Ektachem) 700,
Bayer ADVIA 1650 700XR, 800
Bayer ADVIA 1200 Orto clinical diagnostic Vitros Fusion
Beckmann Synchron CX 4, CX 5 Kone Konelab 30i
Beckmann Synchron CX 7 Kone Konelab 60i
Beckmann LX 20 Kone Konelab 20i
Boehringer Mannheim Hitachi 704 Olympus AU 400, AU640
Boehringer Mannheim Hitachi 705 Olympus AU 560
Boehringer Mannheim Hitachi 717 Olympus AU 600
Boehringer Mannheim Hitachi 737 Olympus AU 800
Boehringer Mannheim Hitachi 902 Olympus AU 2700
Boehringer Mannheim Hitachi 911 Technicon Axon
Boehringer Mannheim Hitachi 912 Technicon RA 1000
Boehringer Mannheim Hitachi 917 Technicon RA XT
Boehringer Mannheim Modular Tosoh G5, Tosoh G7
Ciba Corning Alliance CL -7000 Minerals, ASTRUP, ELFO, ...
Ciba Corning Express +, 550, 560,… Variant II
Ciba Corning Merck Mega BioRAD D10
Ciba Corning Merck Selectra, Selectra ECA 180
2,VIVA Super G, Super GL
Ciba Corning Flexor F AVL AVL 945, 995
Dade (Du Pont) Dimension AR AVL AVL Compact 1
Dade (Du Pont) Dimension SMS, ES AVL AVL Compact 2
Dade (Du Pont) Dimension XL, XPAND AVL AVL Compact 3
DPC Primus CLC 385 AVL AVL OMNI
Primus PDQ AVL AVL 9181
Eppendorf ELAN AVL AVL OMNI C
Eppendorf ELAN DUO Biorad Variant
Eppendorf EPOS Ciba Corning Chiron 248
Hoffmann-La Roche Cobas Mira Ciba Corning Chiron 348
Hoffmann-La Roche Cobas Mira S Ciba Corning Chiron 644

10. Ciba Corning Chiron 850 Urilux S
Ciba Corning Chiron 865 Boehringer Mannheim Miditron Junior
Eppendorf EBIO Boehringer Mannheim Supertron
Eppendorf EFIX DOT LabUReader
Eppendorf EFOX 5053, EFIX 5055 Lachema Uriphan
fotometr - reader BTS 230 Nova Nucleus
Instrumentation Lab. EasyLite Roche Urisys 2400
Instrumentation Lab. IL 1306 Roche Urisys 1800
Instrumentation Lab. ILAB 900 Roche Urisys 1100
Labsystém FP 901 Toa Medical E.CO. Sysmex UF-50, 100
Nova Nova STP 8 Quidel UrineQuick
Nova Nova STAT PROFILE M IQ 200 IRIS
Nova Nova CCX Biomedical Immunological analyzers
Olympus HiTe320 program LIANA
Radiometer ABL 50 Vidas
Radiometer ABL 300 Abbott Architect
Radiometer ABL 330 Abbott AxSYM
Radiometer ABL 500, 510 Abbott Commander PPC
Radiometer ABL 520 Abbott IMx
Radiometer ABL 625, ABL 620 Abbott ADx
Radiometer ABL 7xx - 725,730,740 Abbott LCx
Instrumentation Lab. GEM Premier 3000 Bayer Centaur
Sebia DVS - denzitometr Beckmann Access
Sebia Hyris - denzitometr Beckmann Unicel DXI 800(=Ac-
Sebia Preference - denzi- cess)
tometr Beckmann Array System
Sebia Foresys. Capillaris Beckmann Immage
Beckman Coulter Paragon cze 2000 Beckmann LS 6500
Instrumentation Lab. Easy Blood Gas Behring Nephelometr BN 100
Arkray Osmometr OM6050 Behring Nephelometr BN2
Bayer Rapidlab 855 Behring Nephelometr BNA
BD Sedi-15 Instrument Behring Opus
Urine analyzers Behring BN Prospec
Arkray AUTION JET 4270 Boehringer Mannheim ES 300 (TWIN 300)
Arkray AUTION JET 4280 Boehringer Mannheim Elecsys 1010
Arkray Poket Chem Boehringer Mannheim Elecsys 2010
Bayer Clintec 50 Ciba Corning ACS 180
Lachema Laura Diagnostic Products DCP Imullite
Uriscan Pro+ Corp.
Bayer Clintec 500 Diagnostic Products DCP Imullite 2000,
Boehringer Mannheim Miditron M Corp. 2500

11. Diagnostic Products MAXM Abbott Abbott CellDyn 1800
Corp. Abbott Abbott CellDyn 3000
Diagnostic Products RAS Abbott Abbott CellDyn 3200
Corp. Abbott Abbott CellDyn 3500
Dynex Dynatech MRX + SW Abbott Abbott CellDyn 3700
Dynex technologie Dynex DSX Abbott Abbott CellDyn 4000
Hoffmann-La Roche Cobas Core Abbott Abbott Sapphire
Hoffmann-La Roche Cobas Core 2 Bayer Advia 60
Johnson&Johnson Ammerlite Bayer Advia 120
KIM soft program KIM-E, T, Q, ... Bayer ADVIA 70
KIM soft program KIM-W Bayer Centrallink Workcell
Relevation Technologies PHAMAS Capsystem Ciba Corning Chiron 850
Stratec Electronic Stratec Coulter Counter M-530 (4)
DiaForin Etimax 3000 Coulter MAX´M (3-5 p Diff)
Adaltis Coulter HMX
Kryptor Coulter GENS (5p diff)
Laison Coulter MD 18, MD II -18
AIA 600 Coulter MD 8
AIA 360 Coulter Onyx (3-5 p Diff)
Biorad Evolis Coulter S560 (5)
RADIM(SEAC) BRIO Coulter STK-S (5 p Diff)
RADIM(SEAC) DELTA Coulter STKR (5p? diff)
RADIM(SEAC) ALISEI Coulter T540 (5)
ABI PRISM 700 Coulter T660 (6)
RIA analyzers Coulter T840 (8)
Berthold LBIS, LB 2104 (fluores- Coulter T890 (8)
cence)
Coulter ACT, ACT 8, ACT 2
Berthold LB 958
Coulter ACT 5 diff
Hewlett-Packard Cobra II
Coulter LH750
PharmaTech Wizard 1480
Dannam Excell 16
RIA LABECO JNG-402,403 with
Diatron Abbacus
program RIA LABECO
Hoffmann-La Roche Cobas Micros
Stratec Electronic Stratec RIA with
program TSRINV Hoffmann-La Roche Cobas Minos, STX,
STEL
Data submission (differential, ...)
Hoffmann-La Roche Cobas Vega (5 p Diff)
Elstasit UPD
MS Labboratories MS 8 II (diff)
Eola
MS Labboratories MS 4
Blood picture analyzers
Nihon Kohden Celltac alfa(MEK6318)
HY CELL + (14-16)
Nihon Kohden Celltac F, Celltac E
Abbott Abbott CellDyn 1200
Nihon Kohden Celltac F - double
Abbott Abbott CellDyn 1600
MUREX Minilyser 2001
Abbott Abbott CellDyn 1700

12. Serono Serono Baker System Toa Medical E.CO. Sysmex CA-5000
9000 Toa Medical E.CO. Sysmex CA-6000
Serono Serono Baker 9018 Toa Medical E.CO. SYSMEX CA 7000
Tecan Miniswift AMAX
Toa Medical E.CO. Sysmex F-500 (5) Rack Rotor
Toa Medical E.CO. Sysmex F-800 (8) Organon technika Coag a Mate
Toa Medical E.CO. Sysmex K-1000 Organon technika Thrombolyser Compact
Toa Medical E.CO. Sysmex KX-21 (3 p X
Diff) Interpretive programs, LIS connection
Toa Medical E.CO. Sysmex K-4500 ALPHA
Toa Medical E.CO. Sysmex K-800 (8) Hem-Himas interpretation Bianta
Toa Medical E.CO. Sysmex NE-1500 Hem-Himas interperetation Cractes
Toa Medical E.CO. Sysmex SE-9000 Immunotech Winliana
Toa Medical E.CO. Sysmex SF-3000 Roche PSM without result
Toa Medical E.CO. Sysmex XT 1800i transfer
Toa Medical E.CO. Sysmex XT 2000i Roche PSM with result transfer
Toa Medical E.CO. Sysmex XE 2100 Roche PSM direct regime
Melet Schloesing lab. MS 95 Beckman Remisol
AU Micros 60
Diamond Diagnostics Pentra 80
DiameD AG Diamed, SW Maestro
Mythic 18
Biosen C-line
Coagulometers
Behnk Electronik CL 4
Behnk Electronik CM 2
Behnk Electronik CL 2
Behnk Electronik Trombostat
Behring Fibrintimer A
Behring Fibrintimer BF10
Behring BCF
Instrumentation Lab. ACL 100-300
Instrumentation Lab. ACL Futura
Instrumentation Lab. ACL Advance
Instrumentation Lab. ACL 9000
Instrumentation Lab. ACL 7000
Stago ST4
Stago Compact
Toa Medical E.CO. Sysmex CA-500,CA-
540, CA-560
Toa Medical E.CO. Sysmex CA-1000
Toa Medical E.CO. Sysmex CA-1500