OpenSpecimen

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OpenSpecimen
Developer(s) Krishagni Solutions Pvt. Ltd.
Initial release September 25, 2014 (2014-09-25)[1]
Stable release

7.0.b3  (May 6, 2020; 2 months ago (2020-05-06))

[±]
Preview release 6.3RC4  (January 28, 2020; 5 months ago (2020-01-28)) [±]
Written in Java
Operating system Cross-platform
Type Laboratory informatics software
License(s) BSD 3-Clause License[2][3]
Website OpenSpecimen.org

OpenSpecimen is a free and open source biobanking informatics platform that is used in 20+ biobanks in eight countries across the globe.[4] OpenSpecimen streamlines the process of collecting high quality standards-based (SNOMED, LOINC, ICD, etc) data. OpenSpecimen allows users to collect disease-specific annotations, clinical and pathology data, study-specific parameters, patient questionnaires, QA/QC data, specimen lifecycle events, and any other site-specific custom data. OpenSpecimen also contains a reporting module extract data from all types of datasets. OpenSpecimen exposes REST APIs to enable integration with other clinical databases and instruments. Those APIs can also be used to develop custom user interfaces and workflows.

The software comes in a free Community edition and a priced Enterprise edition, with the various Pro versions including support and additional plug-ins.[5] Krishagni Solutions Pvt. Ltd. leads development and maintenance of the software for the OpenSpecimen user community. The company also sells a number of professional support services, including developer support, remote server maintenance, customization, and data migration support.[5]

Product history

OpenSpecimen was originally developed by Krishagni as caTissue Plus, a free open-source biobanking LIMS/LIS heavily modeled after the National Cancer Institute's caTissue product.[6] Krishagni also offered fee-based support services for the free software.

In July 2014, Krishangi revealed caTissue Plus was being rewritten as OpenSpecimen, with the rewrite tentatively set to be complete by March 2015. The company stated on their website: "caTissue is a 10 year old code base. The design and architecture is old technology-based, difficult to maintain and add new featured [sic] on top of it."[7] On July 22, release candidate one of the software was released to GitHub.[8] Several other release candidates were made available, culminating in the first version 1.0 stable release of the software on September 25.[1]

Features

Features of OpenSpecimen include[9]:

  • Role-based user authentication & authorization
  • Storage and inventory management
  • Planned and unplanned biospecimen collections
  • Participants and informed consents
  • Track specimen lifecycle events
  • Custom fields and forms
  • Complete audit trial
  • Disease or study based annotations
  • Bulk upload data in CSV files
  • Upload files: consent forms, pathology reports, images etc.
  • Specimen request and distribution
  • Shipping and tracking
  • Reports: data query, pivot table, export
  • Scheduled reports
  • Generation and printing of labels and barcodes

Upcoming features include[10]:

  • Configurable user interface
  • Invoicing module
  • Mobile application

As of 2014, development of the platform is ongoing; for information on the most current release and all associated features, visit the project's website.


Product: OpenSpecimen
Experiment, patient, and data management
Sample login and management?Y[6]
Sample tracking?Y[6]
Sample and/or result batching?Y[11]
Task and event scheduling?Y[12]
Option for manual result entry?Y[11]
Multiple data viewing methods?Y[13]
Configurable templates and forms?Y[6]
Data and trend analysis?Y[14]
Data and equipment sharing?Y[15]
Data mining?
Customizable fields and/or interface?Y[6]
Query capability?Y[6]
Import data?Y[16]
Internal file or data linking?Y[17]
External file or data linking?Y[18]
ELN support or integration?
Export data to MS Excel?Y[12]
Raw data management?
Data warehouse?Y[19]
Project and/or task management?
Test, experiment, and/or trial management?Y[20]
Inventory management?Y[21]
Document and/or image management?Y[6]
Patient and case management?Y[22]
Workflow management?
Specification management?
Customer and physician management?Y[6]
Billing and revenue management?Y[6]
Quality, security, and compliance
Regulatory compliance?Y[12]
QA / QC functions?Y[23]
Performance evaluation?
Audit trail?Y[24]
Chain of custody?Y[25]
Configurable roles and security?Y[22]
Data normalization?
Data validation?Y[26]
Data encryption?
Version control?
Automatic data backup?
Environmental monitoring?
Reporting, barcoding, and printing
Custom reporting?Y[12]
Synoptic reporting?
Report printing?Y[12]
Label support?Y[27]
Barcode and/or RFID support?Y[12]
Export to PDF?Y[12]
Export to MS Word?
Export to HTML and/or XML?
Fax integration?
Email integration?Y[12]
Base functionality
Administrator management?Y[22]
Modular?Y[6]
Instrument interfacing and management?Y[28]
Mobile device integration?
Third-party software integration?Y[29]
Alarms and/or alerts?Y[30]
Work-related time tracking?
Voice recognition system?
External monitoring?
Messaging?
Commenting?
Multilingual?
Network-capable?Y[9]
Web client or portal?Y[11]
Online or integrated help?Y[6]
Software as a service delivery model?Y[5]
Usage-based cost?Y[5]
Industries served
biotechnology, clinical, clinical research, life sciences, pathology, pharmaceutical, public health and service

Pricing

The Community edition is free and open-source, available under the BSD 3-Clause License.[2][3]

A dedicated OpenSpecimen trial version is also offered for 30 days, which is configured according to the end users' needs. OpenSpecimen experts guide the end-user through the installation, setup, and training process.

Pricing for the Silver Enterprise version is $10,000, while the Gold Enterprise is $20,000.

Packages and their features can be compared on the pricing page.

Hardware/software requirements

Software Requirements

  • Apache 2.2
  • JBoss-5.1.0.GA
  • MySQL 5.1.x or Oracle 10g or Oracle 11g
  • Windows server or any Linux server (Ubuntu, CentOS, Fedora, etc)
  • Ant 1.7.1

One can download all the OpenSpecimen prerequisites from here.

Hardware Requirements

  • 4 GB RAM
  • 100 GB HDD
  • Server class CPU

Deployment strategies

  • For QA / test environments a single-server machine can be used to deploy both the database and app server (JBoss).
  • For production environments the database and app server (JBoss) should be deployed on two different servers.

Integration Strategies

  • HL7-based integration: OpenSpecimen servers should be able to receive HL7 messages from the server (i.e. in terms of VPN/network).
  • Barcode printers: The barcode printer should be in the same network accessible to OpenSpecimen server.

For more about installation requirements and instructions, consult the documentation.

Videos, screenshots, and other media

Entities using OpenSpecimen

Examples of organizations using OpenSpecimen include[5]:

  • Washington University (U.S.)
  • Johns Hopkins University (U.S.)
  • University of Michigan (U.S.)
  • University of Nebraska (U.S.)
  • Edward Cancer Center (U.S.)
  • Notre Dame University (U.S.)
  • Thomas Jefferson University (U.S.)
  • University of Missouri (U.S.)
  • University of Texas Southwestern Medical Center (U.S.)
  • University of Leicester (U.K.)
  • BRISSKit (U.K.)
  • University of New South Wales (Australia)
  • St. Vincent's Hospital (Australia)
  • Victorian Cancer Biobank (Australia)
  • Singapore Health (Singapore)
  • Sapien Biosciences (India)
  • Aga Khan University (Pakistan)
  • Children's Cancer Hospital (Egypt)
  • National Cancer Institute (Egypt)
  • King Hussein Cancer Center (Jordan)

See also

External links

References

  1. 1.0 1.1 "Release of os-v1.0". GitHub. https://github.com/krishagni/openspecimen/releases/tag/os-v1.0. Retrieved 17 October 2014. 
  2. 2.0 2.1 "Free & Open Source". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/feature/free-open-source. Retrieved 17 October 2014. 
  3. 3.0 3.1 "openspecimen / LICENSE.md". GitHub. 24 September 2014. https://github.com/krishagni/openspecimen/blob/trunk/LICENSE.md. Retrieved 17 October 2014. 
  4. "20 biobanks across 8 countries use OpenSpecimen". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/blog/20-biobanks-across-8-countries-use-openspecimen. Retrieved 10 November 2014. 
  5. 5.0 5.1 5.2 5.3 5.4 "OpenSpecimen Professional Support Services". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/pricing. Retrieved 17 October 2014. 
  6. 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 "caTissue Plus - Feature rich, Faster, Better UI". Krishagni Solutions Pvt. Ltd. Archived from the original on 05 November 2013. https://web.archive.org/web/20131105105123/http://www.catissueplus.org/plus. Retrieved 08 May 2013. 
  7. "OpenSpecimen". OpenSpecimen Support Center. Krishagni Solutions Pvt. Ltd. 21 July 2014. https://catissueplus.atlassian.net/wiki/display/CAT/OpenSpecimen. Retrieved 16 September 2014. 
  8. "Release OS-v1.0_RC1". GitHub. https://github.com/krishagni/openspecimen/releases/tag/OS-v1.0_RC1. Retrieved 17 October 2014. 
  9. 9.0 9.1 "OpenSpecimen". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org. Retrieved 10 November 2014. 
  10. "[OpenSpecimen Upcoming release information"]. Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/blog/openspecimen-upcoming-release-information. Retrieved 10 November 2014. 
  11. 11.0 11.1 11.2 "OpenSpecimen - Rapid Data Entry". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/feature/rapid-data-entry. Retrieved 16 September 2014. 
  12. 12.0 12.1 12.2 12.3 12.4 12.5 12.6 12.7 "OpenSpecimen - Data Retrieval and Reporting". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/feature/data-retrieval-and-reporting. Retrieved 16 September 2014. 
  13. "OpenSpecimen - Specimen Catalog". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/x/c4Ah. Retrieved 9 October 2014. 
  14. "OpenSpecimen Webinar Series". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/OpenSpecimen+Webinar+Series. Retrieved 10 November 2014. 
  15. "Sharing Specimen-Lists". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/Sharing+Specimen-Lists. Retrieved 10 November 2014. 
  16. "OpenSpecimen - Bulk Upload Excel". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/feature/bulk-upload-excel. Retrieved 16 September 2014. 
  17. "OpenSpecimen - Custom Forms". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/Custom+Forms+Tutorials. Retrieved 7 November 2014. 
  18. "OpenSpecimen - Integration". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/Integration. Retrieved 7 November 2014. 
  19. "OpenSpecimen - Specimen Catalog". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/x/c4Ah. Retrieved 7 November 2014. 
  20. "OpenSpecimen - Annotations". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/feature/annotations. Retrieved 16 September 2014. 
  21. "OpenSpecimen - Storage Utilization". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/x/BwCcAQ. Retrieved 9 October 2014. 
  22. 22.0 22.1 22.2 "OpenSpecimen - Multi-Site Support". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/feature/multi-site-support. Retrieved 16 September 2014. 
  23. "OpenSpecimen - Overview". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/Overview. Retrieved 10 November 2014. 
  24. "OpenSpecimen - Audit Trail". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/x/QICxAQ. Retrieved 9 October 2014. 
  25. "OpenSpecimen - Specimen Lifecycle Events". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/Specimen+Lifecycle+Events. Retrieved 10 November 2014. 
  26. "Is OpenSpecimen CFR Part 11 complaint?". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/pages/viewpage.action?pageId=19562969. Retrieved 10 November 2014. 
  27. "OpenSpecimen - Label Generation and Printing". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/x/PIAh. Retrieved 9 October 2014. 
  28. "OpenSpecimen - Create Equipment". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/Create+Equipment. Retrieved 13 November 2014. 
  29. "OpenSpecimen - Programmatic Access (API)". Krishagni Solutions Pvt. Ltd. http://www.catissueplus.org/feature/programmatic-access-api. Retrieved 16 September 2014. 
  30. "OpenSpecimen - Storage Container Alarms". Krishagni Solutions Pvt. Ltd. https://catissueplus.atlassian.net/wiki/display/CAT/Storage+Container+Feature+Requests. Retrieved 12 November 2014.