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Biorepositories Core Resource - Researcher Resources | UC Davis CTSC

Researcher Resources

The Biospecimen Informatics Core (BIC) supports biospecimen-based research across UC Davis through coordinated informatics infrastructure, standardized workflows, and expert guidance. Our approach integrates specimen management with thoughtful data architecture to ensure collections are compliant, sustainable, and positioned for meaningful scientific impact.
Starting or Expanding Biospecimen Collection?
  • two people talking

    We provide consultation on:

    • Study design and biospecimen workflows
    • Consent strategy and regulatory considerations
    • Specimen processing and annotation standards
    • Data structure and metadata best practices
    • Long-term sustainability planning
    • Freezerworks™ LIMS implementation and configuration

    Whether launching a new disease-focused biobank or refining an existing collection, our team can help.

    Request a consultation

Virtual Biospecimen Discovery

The Virtual Biospecimen Discovery tool facilitates collaboration by increasing visibility of institutionally held collections while respecting governance boundaries.

Learn more about Virtual Discovery

Freezerworks Support

We provide implementation, configuration, training, and ongoing support for Freezerworks LIMS, hosted securely within the UC Davis Health network.

Freezerworks resources and training

Biospecimen Best Practices

Access guidance and institutional standards related to:

  • Data governance and annotation
  • Chain-of-custody documentation
  • Clinical trial specimen workflows
  • Regulatory considerations
Relevant Literature

  • Challenges and Driving Forces for Business Plans in Biobanking 
    Macheiner, T. et al. Biopreservation and Biobanking 2017 Apr 13; 15(2): 121-125.
  • The Need for Research Infrastructures: A Narrative Review of Large-Scale Research Infrastructures in Biobanking 
    Larsson, A. Biopreservation and Biobanking 2017 Feb 21; Epub.
  • Quality Management of Biorepositories 
    Grizzle, W.E., et al. Biopreservation and Biobanking 2015 Jun 1; 13(3): 183-194.
  • A novel cross-disciplinary multi-institute approach to translational cancer research: lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)
    Patel A.A., et al. Cancer Inform. 2007 Jun 8;3:255-74.
  • Case studies of existing human tissue repositories: "best practices" for a biospecimen resource for the genomic and proteomic era
    Eiseman E., et al. 2003. Santa Monica, CA: RAND Corporation.
  • Centralized biorepositories for genetic and genomic research
    Ginsburg G.S., Burke T.W. and Febbo P. JAMA. 2008 Mar 19;299(11):1359-61.
  • Electronic medical records for genetic research: results of the eMERGE Consortium
    Kho A.N., et al. Sci Transl Med. 2011 Apr 20;3(79):79re1.
  • Issues in collecting, processing and storing human tissues and associated information to support biomedical research
    Grizzle W.E., et al. Cancer Biomark. 2010;9(1-6):531-49.
  • Multi-institutional tumor banking: lessons learned from a pancreatic cancer biospecimen repository
    Demeure M.J., et al. Pancreas. 2010 Oct;39(7):949-54.
  • Review of Developing and Organizing an Institutional Biospecimen Repository, edited by Donna E. Hansel and Scott D. Jewell
    Bui M. and Pham V. Biopreserv Biobank. 2015 Aug;13(4):303.
  • The boom and bust cycle of biobanking —thinking through the life cycle of biobanks
    Tupasela A. and Stephens N. Croat Med J. 2013 Oct 28;54(5):501-3.
  • The Mayo Clinic Biobank: a building block for individualized medicine 
    Olson J.E., et al. Mayo Clin Proc. 2013 Sep;88(9):952-62.
  • What are the biggest challenges and opportunities for biorepositories in the next three to five years?
    Betsou F., et al. Biopreserv Biobank. 2010 Jun;8(2):81-8.

  • Centralized biorepositories for genetic and genomic research
    Ginsburg G.S., Burke T.W. and Febbo P. JAMA. 2008 Mar 19;299(11):1359-61.
  • Experiences with obtaining informed consent for genomic sequencing
    Bernhardt B.A., et al. Am J Med Genet A. 2015 Nov;167(11):2635-46.
  • Public attitudes to human genetic information: People's Panel quantitative study conducted for the Human Genetics Commission
    Human Genetics Commission (Great Britain). London: Human Genetics Commission, 2001 March.

  • Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking
    Bendou, H. et al. Biopreservation and Biobanking. 2017 Apr;15(2): 116-120.
  • Selecting a Laboratory Information Management System for Biorepositories in Low and Middle-Income Countries: The H3Africa Experience and Lessons Learned
    Kyobe, S. et al. Biopreservation and Biobanking. 2017 Apr;15(2): 112-115.
  • The State of Cloud-Based Biospecimen and Biobank Data Management Tools
    Paul S., Gade A., Mallipeddi S. Biopreservation and Biobanking. 2017 Mar 16;15(2).
  • A call to standardize preanalytic data elements for biospecimens, Part II
    Robb J.A., et al. Arch Pathol Lab Med. 2015 Sep;139(9):1125-8
  • A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research
    Amin W., et al. J Pathol Inform. 2010 Aug 10;1.
  • An informatics model for tissue banks —Lessons learned from the Cooperative Prostate Cancer Tissue Resource
    Patel A.A., et al. BMC Cancer. 2006 May 5;6:120.
  • Automated web-based request mechanism for workflow enhancement in an academic customer-focused biorepository
    McDonald S.A., et al. Biopreserv Biobank. 2012 Feb;10(1):48-54.
  • BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing
    Pang C., et al. J Am Med Inform Assoc. 2015 Jan;22(1):65-75.
  • Information systems as infrastructure for university research now and in the future
    Rice M.L. (Editor) 2012. University of Kansas Merrill Advanced Studies Center (1): 65–75.
  • Public trust in health information sharing: implications for biobanking and electronic health record systems
    Platt J. and Kardia S. J Pers Med. 2015 Feb 3;5(1):3-21.
  • Sharing and reuse of sensitive data and samples: supporting researchers in identifying ethical and legal requirements
    Sariyar M., et al. Biopreserv Biobank. 2015 Aug;13(4):263-70.
  • Six methodological steps to build medical data warehouses for research
    Szirbika N.B., et al. Int J Med Inform. 2006 Sep;75(9):683-91.
  • The Enterprise Data Trust at Mayo Clinic: a semantically integrated warehouse of biomedical data
    Chute C.G., et al. J Am Med Inform Assoc. 2010 Mar-Apr;17(2):131-5.
  • The informatics challenges facing biobanks: a perspective from a United Kingdom Biobanking Network
    Quinlan P.R., et al. Biopreserv Biobank. 2015 Oct;13(5):363-70.
  • Biobanking with Big Data: A Need for Developing "Big Data Metrics"
    Zisis, K. Biopreserv Biobank. 2016 Oct;14(5):450-1.

  • Standard Versus Simplified Consent Materials for Biobank Participation: Differences in Patient Knowledge and Trial Accrual
    Garrett, S.B., et al. J. Empir. Res. Hum. Res. Ethics. 2017 Oct;12(4): 1-9
  • Ethical Legal and Social Issues of Biobanking: Past, Present, and Future
    Bledsoe, M. Biopreserv Biobanking. 2017 Apr;15(2): 142-147
  • A systematic literature review of individuals' perspectives on broad consent and data sharing in the United States
    Garrison N.A., et al. Genet Med. 2015 Nov 19.
  • Active choice but not too active: Public perspectives on biobank consent models
    Simon C.M., et al. Genet Med. 2011 Sep;13(9):821-31.
  • Alternative consent approaches for biobank research
    Maschke K.J. Lancet Oncol. 2006 Mar;7(3):193-4.
  • "Broad" consent, exceptions to consent and the question of using biological samples for research purposes different from the initial collection purpose
    Petrini C. Soc Sci Med. 2010 Jan;70(2):217-20.
  • Broad consent for research with biological samples: workshop conclusions
    Grady C., et al. Am J Bioeth. 2015;15(9):34-42.
  • Developing a simplified consent form for biobanking
    NIH broad sample consent form language from the National Institutes of Health (NIH) National Institute of Neurological Disorders and Stroke (NINDS). 2014.
  • Dynamic consent: a patient interface for twenty-first century research networks
    Kaye J., et al. Eur J Hum Genet. 2015 Feb;23(2):141-6.
  • EngageUC: developing an efficient and ethical approach to biobanking research at the University of California
    Garrett S.B., et al. Clin Transl Sci. 2015 Aug;8(4):362-6.
  • Facilitating autonomy with broad consent
    Spellecy R. Am J Bioeth. 2015;15(9):43-4.
  • Linking broad consent to biobank governance: support from a deliberative public engagement in California
    Garrett S.B., et al. Am J Bioeth. 2015;15(9):56-7.
  • Models of consent to return of incidental findings in genomic research
    Appelbaum P.S., et al. Hastings Cent Rep. 2014 Jul-Aug;44(4):22-32.
  • Moral concerns and the willingness to donate to a research biobank
    Tomlinson T., et al. JAMA. 2015 Jan 27;313(4):417-9.
  • Open consent, biobanking and data protection law: can open consent be ‘informed’ under the forthcoming data protection regulation?
    Hallinan D. and Friedewald M. Life Sci Soc Policy. 2015;11:1.
  • Research guideline recommendations for broad consent forms in biobank research and how they are currently addressed in practice
    Strech D., et al. Am J Bioeth. 2015;15(9):60-3.
  • Researchers' views on informed consent for return of secondary results in genomic research
    Appelbaum P.S., et al. Genet Med. 2015 Aug;17(8):644-50. 
  • Should donors be allowed to give broad consent to future biobank research?
    Hansson M.G., et al. Lancet Oncol. 2006 Mar;7(3):266-9.
  • Template for informed consent concerning the donation, storage, and utilization of biological materials as well as collecting, processing, and usage of (related) data in biobanks
    Permanent Working Party of the German Medical Ethics Committees approved by the General Assembly. 2013 Sep.

  • Financial Sustainability of Biobanks: From Theory to Practice
    Yuille M., et al. Biopreserv Biobank. 2017 Apr;15(2): 85-92.
  • Addressing the challenge of financial sustainability in biobanking
    Campos A.H., et al. Biopreserv Biobank. 2015 Dec;13(6):387-95.
  • Biobank finances: a socio-economic analysis and review
    Gee S., et al. Biopreserv Biobank. 2015 Dec;13(6):435-51.
  • Biobankonomics: developing a sustainable business model approach for the formation of a human tissue biobank
    Vaught J., et al. J Natl Cancer Inst Monogr. 2011;2011(42):24-31.
  • Finding the path to biobank sustainability through sound business planning
    Henderson M., et al. Biopreserv Biobank. 2015 Dec;13(6):385-6.
  • Public biobanks: calculation and recovery of costs
    Clément B., et al. Sci Transl Med. 2014 Nov 5;6(261):261fs45.
  • Sustainability in biobanking
    Simeon-Dubach D. and Henderson M.K. Biopreserv Biobank. 2014 Oct;12(5):287-91.
  • Sustainability in the modern biorepository environment from the perspective of the Tissue Procurement Core at the University of Iowa
    Galbraith J.W. Biopreserv Biobank. 2015 Dec;13(6):430-2.
  • How Biobanks Are Assessing and Measuring Their Financial Sustainability
    Brown, T., et al. Biopreserv Biobank. 2016 Nov; 1-7 [Epub].
  • Methods to Improve Sustainability of a Large Academic Biorepository
    Kelly, SM., et al. Biopreserv Biobank. 2016 Nov; 1-6 [Epub].
  • Achieving and Maintaining Sustainability in Biobanking Through Business Planning, Marketing, and Access
    Henderson, MK., et al. Biopreserv Biobank. 2016 Nov; 1-2 [Epub].

  • ISBER Goes Global
    Schacter B. Biopreserv Biobank. 2017 Apr;15(2): 173.
  • Banking brain tumor specimens using a university core facility
    Bregy A., et al. Biopreserv Biobank. 2015 Aug;13(4):280-6.
  • Biobanking for research: a survey of patient population attitudes and understanding
    Rahm A.K., et al. J Community Genet. 2013 Oct;4(4):445-50.
  • Personal medicine—the new banking crisis
    Scott C.T., et al. Nat Biotechnol. 2012 Feb 8;30(2):141-7.
  • Providing contemporary access to historical biospecimen collections: development of the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC)
    Giffen C.A., et al. Biopreserv Biobank. 2015 Aug;13(4):271-9.
  • Top considerations for using social media in research—it all starts with a plan
    Quorum Review IRB. 2015 Sep;1-6.
  • Consent and Biospecimen Collection in Human Research
    Brown, T. and Sapsford, K. (2019, January). Consent and Biospecimen Collection in Human Research. Retrieved from https://www.bioivt.com