Hostname: page-component-586b7cd67f-tf8b9 Total loading time: 0 Render date: 2024-11-27T21:22:50.188Z Has data issue: false hasContentIssue false
  • English
  • Français

NexusLIMS: A Laboratory Information Management System for Shared-Use Electron Microscopy Facilities

Published online by Cambridge University Press:  28 April 2021

Joshua A. Taillon Open the ORCID record for Joshua A. Taillon [Opens in a new window] ,
Thomas F. Bina ,
Raymond L. Plante ,
Marcus W. Newrock ,
Gretchen R. Greene  and
June W. Lau
Joshua A. Taillon*
Affiliation:
Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Boulder, CO80305, USA
Thomas F. Bina
Affiliation:
Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD20899, USA Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD20899, USA
Raymond L. Plante
Affiliation:
Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD20899, USA
Marcus W. Newrock
Affiliation:
Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD20899, USA
Gretchen R. Greene
Affiliation:
Office of Data and Informatics, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD20899, USA
June W. Lau
Affiliation:
Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD20899, USA
*
*Author for correspondence: Joshua A. Taillon, E-mail: [email protected]
Get access

Abstract

This work introduces NexusLIMS, an electron microscopy laboratory information management system designed and implemented by the Office of Data and Informatics and the Materials Science and Engineering Division at NIST for a multi-user electron microscopy co-op facility. NexusLIMS comprises network infrastructure, shared information technology resources, a custom software package to harvest and extract experimental information and construct experimental metadata records, and an intuitive web-based user-facing interface for searching, browsing, and examining research data. These metadata records conform to the Nexus Experiment schema, which is introduced in this work. The NexusLIMS suite of tools requires minimal input and adjustments to user behavior, instead relying on existing organizational procedures and the collection of information from a multitude of sources to construct a complete picture and record of a research experiment. The underlying infrastructure and design considerations for a multi-user data management system are discussed. The core codebase for NexusLIMS is made publicly available alongside this work, and its modular design encourages the adaptation of the presented methods at other research organizations.

Keywords

data managementlaboratory information managementmetadata extractionopen source softwareuser facilityelectron microscopy
Type
Software and Instrumentation
Information
Microscopy and Microanalysis , Volume 27 , Issue 3 , June 2021 , pp. 511 - 527
Check for updates
Copyright
Copyright © National Institute of Standards and Technology 2021 outside of the United States of America. As a work owned by the United States Government, this Contribution is not subject to copyright within the United States. Outside of the United States, Cambridge University Press is the nonexclusively licensed publisher of the Contribution. Published by Cambridge University Press on behalf of the Microscopy Society of America

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

†

Current address: Department of Biomedical Engineering, Columbia University, New York, NY, USA.

References

Abbott Laboratories (2020). Laboratory information management system (LIMS)—STARLIMS. Available at https://web.archive.org/web/20200803100114/https://www.informatics.abbott/us/en/offerings/lims (retrieved August 3, 2020).Google Scholar
Allcock, W, Bresnahan, J, Kettimuthu, R, Link, M, Dumitrescu, C, Raicu, I & Foster, I (2005). The globus striped GridFTP framework and server. In ACM/IEEE SC 2005 Conference (SC’05), vol. 2005, pp. 1–11. Seattle, WA: IEEE. Available at http://ieeexplore.ieee.org/document/1560006/.Google Scholar
Arkilic, A, Allan, DB, Caswell, TA, Li, L, Lauer, K & Abeykoon, S (2017). Towards integrated facility-wide data acquisition and analysis at NSLS-II. Synchrotron Radiat News 30, 44–45.CrossRefGoogle Scholar
Bika Lab Systems (2020). Bika open source LIMS. Available at https://web.archive.org/web/20200811104846/https://www.bikalims.org/ (retrieved August 11, 2020).Google Scholar
Blaiszik, B, Chard, K, Pruyne, J, Ananthakrishnan, R, Tuecke, S & Foster, I (2016). The materials data facility: Data services to advance materials science research. JOM 68, 2045–2052.CrossRefGoogle Scholar
Borgman, CL (2010). Scholarship in the Digital Age: Information, Infrastructure, and the Internet. Cambridge, MA: MIT Press.Google Scholar
Carey, NS, Budavári, T, Daphalapurkar, N & Ramesh, KT (2016). Data integration for materials research. Integr Mater Manuf Innov 5, 143–153.CrossRefGoogle Scholar
CARPi, N, Minges, A & Piel, M (2017). eLabFTW: An open source laboratory notebook for research labs. J Open Source Softw 2, 146.CrossRefGoogle Scholar
Center for Hierarchical Materials Design (2020). Data and database efforts. Available at https://web.archive.org/web/20200710235929/https://chimad.northwestern.edu/news-events/CHiMaD_Data_Database_Efforts.html (retrieved September 27, 2020).Google Scholar
Cheung, K, Hunter, J & Drennan, J (2009). MatSeek: An ontology-based federated search interface for materials scientists. IEEE Intell Syst 24, 47–56.CrossRefGoogle Scholar
Coordinated Science Laboratory, UIUC (2020). 4CeeD+Jupyter. Available at https://web.archive.org/web/20201230005737/https://t2c2.csl.illinois.edu/4ceedjupyter/ (retrieved December 20, 2020).Google Scholar
Corporation for National Research Initiatives (2020). Handle.Net Registry. Available at https://web.archive.org/web/20200901232239/https://handle.net/index.html (retrieved September 30, 2020).Google Scholar
Dataworks Development, Inc (2020). Freezerworks—Laboratory software for freezer and biorepository tracking. Available at https://web.archive.org/web/20200919013601/https://freezerworks.com/ (retrieved September 19, 2020).Google Scholar
de la Pena, F, Ostasevicius, T, Tonaas Fauske, V, Burdet, P, Jokubauskas, P, Nord, M, Sarahan, M, Prestat, E, Johnstone, DN, Taillon, J, Caron, J, Furnival, T,, MacArthur, KE, Eljarrat, A, Mazzucco, S, Migunov, V, Aarholt, T, Walls, M, Winkler, F, Donval, G, Martineau, B, Garmannslund, A, Zagonel, LF & Iyengar, I (2017). Electron microscopy (big and small) data analysis with the open source software package HyperSpy. Microsc Microanal 23, 214–215.CrossRefGoogle Scholar
de la Peña, F, Prestat, E, Fauske, VT, Burdet, P, Jokubauskas, P, Nord, M, Furnival, T, Ostasevicius, T, MacArthur, KE, Johnstone, DN, Sarahan, M, Lähnemann, J, Taillon, JA, Migunov, V, Eljarrat, A, Aarholt, T, Caron, J, Mazzucco, S, Martineau, B, Somnath, S, Poon, T, Walls, M, Slater, T, Winkler, F, Tappy, N, Donval, G, Myers, JC, McLeod, R & Hoglund, ER (2020). HyperSpy 1.6.0. Available at https://github.com/hyperspy/hyperspy.Google Scholar
Dima, A, Bhaskarla, S, Becker, C, Brady, M, Campbell, C, Dessauw, P, Hanisch, R, Kattner, U, Kroenlein, K, Newrock, M, Peskin, A, Plante, R, Li, SY, Rigodiat, PF, Amaral, GS, Trautt, Z, Schmitt, X, Warren, J & Youssef, S (2016). Informatics infrastructure for the materials genome initiative. JOM 68, 2053–2064.CrossRefGoogle Scholar
Ecma International (2020). Introducing JavaScript object notation. Available at https://web.archive.org/web/20200927011530/https://www.json.org/json-en.html (retrieved September 28, 2020).Google Scholar
Gibbon, GA (1996). A brief history of LIMS. Lab Autom Inf Manag 32, 1–5.CrossRefGoogle Scholar
Helu, M & Hedberg, T Jr. (2015). Enabling smart manufacturing research and development using a product lifecycle test bed. Procedia Manuf 1, 86–97.CrossRefGoogle ScholarPubMed
Hipp, RD (2020). SQLite. Available at https://web.archive.org/web/20200927012340/https://www.sqlite.org/index.html.Google Scholar
Jacobsen, MD, Fourman, JR, Porter, KM, Wirrig, EA, Benedict, MD, Foster, BJ & Ward, CH (2016). Creating an integrated collaborative environment for materials research. Integr Mater Manuf Innov 5, 232–244.CrossRefGoogle Scholar
Kluyver, T, Ragan-Kelley, B, Pérez, F, Granger, B, Bussonnier, M, Frederic, J, Kelley, K, Hamrick, J, Grout, J, Corlay, S, Ivanov, P, Avila, D, Abdalla, S & Willing, C (2016). Jupyter notebooks—A publishing format for reproducible computational workflows. In Positioning and Power in Academic Publishing: Players, Agents and Agendas, Loizides F & Schmidt B (Eds.), pp. 87–90. Amsterdam, Netherlands: IOS Press.Google Scholar
Lau, JW, Devers, RF, Newrock, M & Greene, G (2019). Laboratory information management systems for electron microscopy: Evaluation of the 4CeeD data curation platform. J Res Natl Inst Stand Technol 124, 124034.CrossRefGoogle Scholar
Microscopy Society of America: Standards Committee (2019). MSA / MAS / AMAS Hyper-Dimensional Data File Specification- Version 1.02, https://web.archive.org/web/20200921123650/https://www.microscopy.org/resources/scientific_data/HMSA_Specification-20191120.pdf (accessed September 21, 2020).Google Scholar
Nguyen, P, Chan, M, Mchenry, K, Paquin, N, Konstanty, S, Nicholson, T, O'Brien, T, Schwartz-Duval, A, Spila, T, Nahrstedt, K, Campbell, RH & Gupta, I (2017). 4CeeD: Real-time data acquisition and analysis framework for material-related cyber-physical environments. In 2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), pp. 11–20. IEEE. Available at https://ieeexplore.ieee.org/document/7973684/.Google Scholar
Plante, RL, Taillon, JA, Lau, JW, Greene, GR & Newrock, MW (2020). Nexus-Experiment: An XML schema for describing data collected from electron microscopes. NIST Public Data Repository. Available at https://data.nist.gov/od/id/mds2-2245.Google Scholar
Rose, S, Borchert, O, Mitchell, S & Connelly, S (2020). Zero trust architecture. Tech. rep., National Institute of Standards and Technology, Gaithersburg, MD. Available at https://nvlpubs.nist.gov/nistpubs/SpecialPublications/NIST.SP.800-207.pdf.CrossRefGoogle Scholar
Scott, JHJ (2015). Strategies for managing information technology (IT) in microscopy facilities. Microsc Microanal 21, 373–374.CrossRefGoogle Scholar
Taillon, JA, Devers, RF, Plante, RL, Newrock, MW, Lau, JW & Greene, G (2019). Harvesting microscopy experimental context with a configurable laboratory information management system. Microsc Microanal 25, 140–141.CrossRefGoogle ScholarPubMed
Taillon, JA, Plante, RL, Newrock, MW, Greene, GR & Lau, JW (2020). NexusLIMS: A python package for EM experiment metadata management. NIST Public Data Repository. https://doi.org/10.18434/mds2-2355CrossRefGoogle Scholar
The PyInstaller Development Team (2020). PyInstaller. Available at https://web.archive.org/web/20200926012000/http://www.pyinstaller.org/.Google Scholar
The World Wide Web Consortium (W3C) (2020). Cascading style sheets. Available at https://web.archive.org/web/20201006201653/https://www.w3.org/Style/CSS/Overview.en.html (retrieved October 6, 2020).Google Scholar
Thomas, D & Hunt, A (2019). DRY—The evils of duplication. In The Pragmatic Programmer, The Pragmatic Bookshelf , 2nd ed. Boston, MA: Addison-Wesley. Available at https://pragprog.com/titles/tpp20/the-pragmatic-programmer-20th-anniversary-edition/.Google Scholar
Tidwell, D (2008). XSLT. Sebastopol, CA: O'Reilly.Google Scholar
Vixie, P, Mašláňová, M, Dean, C & Mráz, T (2013). cron. Available at https://web.archive.org/web/20200707115220/https://man7.org/linux/man-pages/man8/cron.8.html (retrieved September 29, 2020).Google Scholar
Vlist, E (2002). XML Schema. Sebastopol, CA: O'Reilly.Google Scholar
Warren, JA & Ward, CH (2018). Evolution of a materials data infrastructure. JOM 70, 1652–1658.CrossRefGoogle Scholar
White, RR & Munch, K (2014). Handling large and complex data in a photovoltaic research institution using a custom laboratory information management system. MRS Proceedings, vol. 1654, mrsf13–1654–nn11–04. Available at https://www.cambridge.org/core/product/identifier/S1946427414000311/type/journal_article.Google Scholar
Wikimedia Foundation, Inc (2020). Wikipedia: The free encyclopedia. Available at https://web.archive.org/web/20200930035725/https://www.wikipedia.org/ (retrieved September 30, 2020).Google Scholar
Wilkinson, MD, Dumontier, M, Aalbersberg, IJ, Appleton, G, Axton, M, Baak, A, Blomberg, N, Boiten, JW, da Silva Santos, LB, Bourne, PE, Bouwman, J, Brookes, AJ, Clark, T, Crosas, M, Dillo, I, Dumon, O, Edmunds, S, Evelo, CT, Finkers, R, Gonzalez-Beltran, A, Gray, AJ, Groth, P, Goble, C, Grethe, JS, Heringa, J, ’t Hoen, PA, Hooft, R, Kuhn, T, Kok, R, Kok, J, Lusher, SJ, Martone, ME, Mons, A, Packer, AL, Persson, B, Rocca-Serra, P, Roos, M, van Schaik, R, Sansone, SA, Schultes, E, Sengstag, T, Slater, T, Strawn, G, Swertz, MA, Thompson, M, van der Lei, J, van Mulligen, E, Velterop, J, Waagmeester, A, Wittenburg, P, Wolstencroft, K, Zhao, J & Mons, B (2016). The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018.CrossRefGoogle ScholarPubMed
Wittenburg, P, Hellström, M, Zwölf, CM, Abroshan, H, Asmi, A, Di Bernardo, G, Couvreur, D, Gaizer, T, Holub, P, Hooft, R, Häggström, I, Koureas, D, Kuchinke, W, Milanesi, L, Rosato, A, Padfield, J, Staiger, C, van Uytvanck, D & Tobias, W (2017). Persistent identifiers: Consolidated assertions. Tech. rep. GEDE: Group of European Data Experts. Available at https://www.rd-alliance.org/system/files/PID-report_v6.1_2017-12-13_final.pdf.Google Scholar
Zakutayev, A, Wunder, N, Schwarting, M, Perkins, JD, White, R, Munch, K, Tumas, W & Phillips, C (2018). An open experimental database for exploring inorganic materials. Sci Data 5, 180053.CrossRefGoogle ScholarPubMed