OpenLIMS                   comprehensive solution for the                   laboratory complement  our mission is   OpenLI...
OpenLIMS supports language modification and enables easy module customization according                 to any specific le...
Security    	 Result database - The user                   access policy can be defined                   separately for s...
Work       	 Barcodes - The barcodes are automation        used for the patient identifi-                   cation, sample...
The verified   N-tier architecture represents the strict database separation, application logic and clients presenta- data...
The design of the entrance window for each operational laboratory part may be adjusted according               to laborato...
Block schema      of n-tier  architectureOpenLIMS – Small    Laboratory
OpenLIMS     Standard Configuration       OpenLIMSThe Laboratory          Chain
The List of Connected Analyzers and Devices        Hoffmann-La Roche        Cobas Mira+Producer                Type       ...
Ciba Corning           Chiron 850                                        Urilux SCiba Corning           Chiron 865        ...
Diagnostic Products       MAXM                       Abbott              Abbott CellDyn 1800Corp.                         ...
Serono                  Serono Baker System   Toa Medical E.CO.         Sysmex CA-5000                        9000        ...
Upcoming SlideShare
Loading in …5



Published on

Open Source Laboratory Information system

Published in: Health & Medicine
  • Be the first to comment

  • Be the first to like this

No Downloads
Total views
On SlideShare
From Embeds
Number of Embeds
Embeds 0
No embeds

No notes for slide


  1. 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. 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 bycapabilities 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. 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 resultsPrint 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 backgroundCommunication 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. 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. 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 acharacteristic 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. 6. The design of the entrance window for each operational laboratory part may be adjusted according to laboratory needs. Workstation Pentium 4 (or equivalent) PCrequirements 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/XPrequirements 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: Holder of quality management certificate under ISO 9001:2000 and environmental management certificate under ISO 14001:2004
  7. 7. Block schema of n-tier architectureOpenLIMS – Small Laboratory
  8. 8. OpenLIMS Standard Configuration OpenLIMSThe Laboratory Chain
  9. 9. The List of Connected Analyzers and Devices Hoffmann-La Roche Cobas Mira+Producer Type Hoffmann-La Roche Cobas Integra 400Biochemical analyzers Hoffmann-La Roche Cobas Integra 700 Liasys Hoffmann-La Roche Cobas Integra 800Abbott Alcyon Instrument Laboratory ILAB 600Abbott Spectrum CCx Instrument Laboratory ILAB 900Abbott Spectrum EPx Johnson&Johnson Vitros (Ektachem) 250Abbott Aeroset Johnson&Johnson Vitros (Ektachem) 500,AL Instruments Alixia 950AL Instruments Mascott + Johnson&Johnson Vitros EciBaker ENCORE Johnson&Johnson Vitros (Ektachem) 700,Bayer ADVIA 1650 700XR, 800Bayer ADVIA 1200 Orto clinical diagnostic Vitros FusionBeckmann Synchron CX 4, CX 5 Kone Konelab 30iBeckmann Synchron CX 7 Kone Konelab 60iBeckmann LX 20 Kone Konelab 20iBoehringer Mannheim Hitachi 704 Olympus AU 400, AU640Boehringer Mannheim Hitachi 705 Olympus AU 560Boehringer Mannheim Hitachi 717 Olympus AU 600Boehringer Mannheim Hitachi 737 Olympus AU 800Boehringer Mannheim Hitachi 902 Olympus AU 2700Boehringer Mannheim Hitachi 911 Technicon AxonBoehringer Mannheim Hitachi 912 Technicon RA 1000Boehringer Mannheim Hitachi 917 Technicon RA XTBoehringer Mannheim Modular Tosoh G5, Tosoh G7Ciba Corning Alliance CL -7000 Minerals, ASTRUP, ELFO, ...Ciba Corning Express +, 550, 560,… Variant IICiba Corning Merck Mega BioRAD D10Ciba Corning Merck Selectra, Selectra ECA 180 2,VIVA Super G, Super GLCiba Corning Flexor F AVL AVL 945, 995Dade (Du Pont) Dimension AR AVL AVL Compact 1Dade (Du Pont) Dimension SMS, ES AVL AVL Compact 2Dade (Du Pont) Dimension XL, XPAND AVL AVL Compact 3DPC Primus CLC 385 AVL AVL OMNI Primus PDQ AVL AVL 9181Eppendorf ELAN AVL AVL OMNI CEppendorf ELAN DUO Biorad VariantEppendorf EPOS Ciba Corning Chiron 248Hoffmann-La Roche Cobas Mira Ciba Corning Chiron 348Hoffmann-La Roche Cobas Mira S Ciba Corning Chiron 644
  10. 10. Ciba Corning Chiron 850 Urilux SCiba Corning Chiron 865 Boehringer Mannheim Miditron JuniorEppendorf EBIO Boehringer Mannheim SupertronEppendorf EFIX DOT LabUReaderEppendorf EFOX 5053, EFIX 5055 Lachema Uriphanfotometr - reader BTS 230 Nova NucleusInstrumentation Lab. EasyLite Roche Urisys 2400Instrumentation Lab. IL 1306 Roche Urisys 1800Instrumentation Lab. ILAB 900 Roche Urisys 1100Labsystém FP 901 Toa Medical E.CO. Sysmex UF-50, 100Nova Nova STP 8 Quidel UrineQuickNova Nova STAT PROFILE M IQ 200 IRISNova Nova CCX Biomedical Immunological analyzersOlympus HiTe320 program LIANARadiometer ABL 50 VidasRadiometer ABL 300 Abbott ArchitectRadiometer ABL 330 Abbott AxSYMRadiometer ABL 500, 510 Abbott Commander PPCRadiometer ABL 520 Abbott IMxRadiometer ABL 625, ABL 620 Abbott ADxRadiometer ABL 7xx - 725,730,740 Abbott LCxInstrumentation Lab. GEM Premier 3000 Bayer CentaurSebia DVS - denzitometr Beckmann AccessSebia Hyris - denzitometr Beckmann Unicel DXI 800(=Ac-Sebia Preference - denzi- cess) tometr Beckmann Array SystemSebia Foresys. Capillaris Beckmann ImmageBeckman Coulter Paragon cze 2000 Beckmann LS 6500Instrumentation Lab. Easy Blood Gas Behring Nephelometr BN 100Arkray Osmometr OM6050 Behring Nephelometr BN2Bayer Rapidlab 855 Behring Nephelometr BNABD Sedi-15 Instrument Behring OpusUrine analyzers Behring BN ProspecArkray AUTION JET 4270 Boehringer Mannheim ES 300 (TWIN 300)Arkray AUTION JET 4280 Boehringer Mannheim Elecsys 1010Arkray Poket Chem Boehringer Mannheim Elecsys 2010Bayer Clintec 50 Ciba Corning ACS 180Lachema Laura Diagnostic Products DCP Imullite Uriscan Pro+ Corp.Bayer Clintec 500 Diagnostic Products DCP Imullite 2000,Boehringer Mannheim Miditron M Corp. 2500
  11. 11. Diagnostic Products MAXM Abbott Abbott CellDyn 1800Corp. Abbott Abbott CellDyn 3000Diagnostic Products RAS Abbott Abbott CellDyn 3200Corp. Abbott Abbott CellDyn 3500Dynex Dynatech MRX + SW Abbott Abbott CellDyn 3700Dynex technologie Dynex DSX Abbott Abbott CellDyn 4000Hoffmann-La Roche Cobas Core Abbott Abbott SapphireHoffmann-La Roche Cobas Core 2 Bayer Advia 60Johnson&Johnson Ammerlite Bayer Advia 120KIM soft program KIM-E, T, Q, ... Bayer ADVIA 70KIM soft program KIM-W Bayer Centrallink WorkcellRelevation Technologies PHAMAS Capsystem Ciba Corning Chiron 850Stratec 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 2Berthold LB 958 Coulter ACT 5 diffHewlett-Packard Cobra II Coulter LH750PharmaTech Wizard 1480 Dannam Excell 16RIA LABECO JNG-402,403 with Diatron Abbacus program RIA LABECO Hoffmann-La Roche Cobas MicrosStratec Electronic Stratec RIA with program TSRINV Hoffmann-La Roche Cobas Minos, STX, STELData submission (differential, ...) Hoffmann-La Roche Cobas Vega (5 p Diff)Elstasit UPD MS Labboratories MS 8 II (diff) Eola MS Labboratories MS 4Blood picture analyzers Nihon Kohden Celltac alfa(MEK6318) HY CELL + (14-16) Nihon Kohden Celltac F, Celltac EAbbott Abbott CellDyn 1200 Nihon Kohden Celltac F - doubleAbbott Abbott CellDyn 1600 MUREX Minilyser 2001Abbott Abbott CellDyn 1700
  12. 12. Serono Serono Baker System Toa Medical E.CO. Sysmex CA-5000 9000 Toa Medical E.CO. Sysmex CA-6000Serono Serono Baker 9018 Toa Medical E.CO. SYSMEX CA 7000Tecan Miniswift AMAXToa Medical E.CO. Sysmex F-500 (5) Rack RotorToa Medical E.CO. Sysmex F-800 (8) Organon technika Coag a MateToa Medical E.CO. Sysmex K-1000 Organon technika Thrombolyser CompactToa Medical E.CO. Sysmex KX-21 (3 p X Diff) Interpretive programs, LIS connectionToa Medical E.CO. Sysmex K-4500 ALPHAToa Medical E.CO. Sysmex K-800 (8) Hem-Himas interpretation BiantaToa Medical E.CO. Sysmex NE-1500 Hem-Himas interperetation CractesToa Medical E.CO. Sysmex SE-9000 Immunotech WinlianaToa Medical E.CO. Sysmex SF-3000 Roche PSM without resultToa Medical E.CO. Sysmex XT 1800i transferToa Medical E.CO. Sysmex XT 2000i Roche PSM with result transferToa Medical E.CO. Sysmex XE 2100 Roche PSM direct regimeMelet Schloesing lab. MS 95 Beckman Remisol AU Micros 60Diamond Diagnostics Pentra 80DiameD AG Diamed, SW MaestroMythic 18 Biosen C-lineCoagulometersBehnk Electronik CL 4Behnk Electronik CM 2Behnk Electronik CL 2Behnk Electronik TrombostatBehring Fibrintimer ABehring Fibrintimer BF10Behring BCFInstrumentation Lab. ACL 100-300Instrumentation Lab. ACL FuturaInstrumentation Lab. ACL AdvanceInstrumentation Lab. ACL 9000Instrumentation Lab. ACL 7000Stago ST4Stago CompactToa Medical E.CO. Sysmex CA-500,CA- 540, CA-560Toa Medical E.CO. Sysmex CA-1000Toa Medical E.CO. Sysmex CA-1500