The End-to-End Provenance Project

Data provenance is a machine-readable summary of the collection and computational history of a dataset. Data provenance confers or adds value to a dataset, helps reproduce computational analyses, or validates scientific conclusions. The people of the End-to-End Provenance Project are a community of professionals who have developed software tools to collect and use data provenance. Data provenance is a machine-readable summary of the collection and computational history of a dataset. Data provenance confers or adds value to a dataset, helps reproduce computational analyses, or validates scientific conclusions. The people of the End-to-End Provenance Project are a community of professionals who have developed software tools to collect and use data provenance. Provenance is the chronological history of creation, ownership, chain of custody, and location of an object. In its original and still most frequently used sense, provenance is used to authenticate and trace the legitimate ownership of a work of art; it confers, creates, or adds value to the work itself. But provenance can be constructed, identified, or traced for any object, including data.1Becker R.A. Chambers J.M. Auditing of Data Analyses.SIAM J. Sci. Statist. Comput. 1986; 9: 78-80Google Scholar Data provenance is analogous to provenance of a work of art in that it includes the chronological history of a datum or entire dataset from the point at which it was collected (by a person or sensor), created (by a computational process), or derived (from other data). Similarly, data provenance confers or adds value—as trustworthiness—to data, but data provenance also can be used to reproduce computational analyses and validate scientific conclusions. In short, whereas the existence of provenance establishes value of artwork, the use of provenance establishes value of data. For more than a decade, our group (Box 1; Figure 1) has guided the development of a set of tools (Figure 2) that uses data provenance to enhance trustworthiness and reproducibility of data,[2Boose E.R. Lerner B.A. Replication of data analyses: provenance in R.in: Shavit A. Ellison A.M. Stepping in the Same River Twice: Replication in Biological Research. Yale University Press, 2017: 195-212Crossref Google Scholar] the associated analytical processes (software) that created them,[3Lerner B. Boose E. Perez L. Using introspection to collect provenance in R.Informatics. 2018; 5: 12Crossref Scopus (4) Google Scholar] and the publications and conclusions derived from them.[4Pasquier T. Lau M.K. Trisovic A. Boose E.R. Couturier B. Crosas M. Ellison A.M. Gibson V. Jones C.R. Seltzer M. If these data could talk.Sci. Data. 2017; 4: 170114Crossref PubMed Scopus (20) Google Scholar]Box 1The Current Main Characters of the End-to-End Provenance ProjectThe Visionary: Margo Seltzer is Canada 150 Research Chair in computer systems and the Cheriton Family chair in computer science at the University of British Columbia. She studies systems sensu lato—systems for capturing and using data provenance, file systems, databases, transaction processing systems, storage and analysis of graph-structured data, new architectures for parallelizing execution, and systems for discrete optimization.The Developers and Maintainers: Emery Boose and Barbara Lerner have been our system designers and developers from the get-go. Emery is information manager and a senior scientist at the Harvard Forest. His research interests include data provenance, ecoinformatics, hurricane modeling, meteorology, and hydrology. Barbara is a professor of computer science at Mount Holyoke College. She develops software that data analysts can use to help understand their scripts and is passionate about increasing participation of women in computing. Elizabeth Fong is a software developer and researcher at Mount Holyoke College and a former data engineering fellow at Insight Data Science. She is interested in data provenance, data engineering, and computational biology.The Translator: Aaron Ellison is the senior research fellow in ecology at Harvard University and a senior ecologist and the deputy director of the Harvard Forest. His overlapping interests in ecological processes, publishing and open science, and cultural and technical challenges for collecting provenance and archiving data have positioned him as the person who brings reality into software engineering and translates software engineering concepts back to domain scientists.Undergraduates who have worked on the project are listed in Table 1.Figure 2Our End-to-End Provenance ToolsShow full captionTools include packages for the R software system that take advantage of a lightweight provenance collection tool (rdtLite) that collects provenance during a console session or as an R script executes. Taking advantage of the prov.json-encoded provenance and internal parsing and graphing functions (provParseR, provGraphR), provSummarizeR provides a high-level summary of the computing environment, loaded libraries, sourced scripts, and I/O; provExplainR helps users identify differences in results derived from multiple executions of a script; and provDebugR supports “time-traveling debugging” of a script without the need to set breakpoints or insert print statements and rerun the script. containR is a provenance-based virtual machine for reproduction and re-execution of R scripts. ProvBuild provides provenance-based debugging tools and builds off the noWorkflow project. CamFlow (Cambridge information flow architecture) is a Linux security module designed to capture data provenance for the purpose of system auditing. It is being leveraged by Unicorn, an anomaly based detector of advanced persistent threats (APTs) that are otherwise difficult to detect because of their “low-and-slow” attack patterns and frequent use of zero-day exploits.8Han X. Pasquier T. Bates A. Mickens J. Seltzer M. UNICORN: Runtime Provenance-Based Detector for Advanced Persistent Threats.arXiv. 2020; (2001.01525)https://arxiv.org/abs/2001.01525Google ScholarView Large Image Figure ViewerDownload (PPT) The Visionary: Margo Seltzer is Canada 150 Research Chair in computer systems and the Cheriton Family chair in computer science at the University of British Columbia. She studies systems sensu lato—systems for capturing and using data provenance, file systems, databases, transaction processing systems, storage and analysis of graph-structured data, new architectures for parallelizing execution, and systems for discrete optimization.The Developers and Maintainers: Emery Boose and Barbara Lerner have been our system designers and developers from the get-go. Emery is information manager and a senior scientist at the Harvard Forest. His research interests include data provenance, ecoinformatics, hurricane modeling, meteorology, and hydrology. Barbara is a professor of computer science at Mount Holyoke College. She develops software that data analysts can use to help understand their scripts and is passionate about increasing participation of women in computing. Elizabeth Fong is a software developer and researcher at Mount Holyoke College and a former data engineering fellow at Insight Data Science. She is interested in data provenance, data engineering, and computational biology.The Translator: Aaron Ellison is the senior research fellow in ecology at Harvard University and a senior ecologist and the deputy director of the Harvard Forest. His overlapping interests in ecological processes, publishing and open science, and cultural and technical challenges for collecting provenance and archiving data have positioned him as the person who brings reality into software engineering and translates software engineering concepts back to domain scientists. Undergraduates who have worked on the project are listed in Table 1. Tools include packages for the R software system that take advantage of a lightweight provenance collection tool (rdtLite) that collects provenance during a console session or as an R script executes. Taking advantage of the prov.json-encoded provenance and internal parsing and graphing functions (provParseR, provGraphR), provSummarizeR provides a high-level summary of the computing environment, loaded libraries, sourced scripts, and I/O; provExplainR helps users identify differences in results derived from multiple executions of a script; and provDebugR supports “time-traveling debugging” of a script without the need to set breakpoints or insert print statements and rerun the script. containR is a provenance-based virtual machine for reproduction and re-execution of R scripts. ProvBuild provides provenance-based debugging tools and builds off the noWorkflow project. CamFlow (Cambridge information flow architecture) is a Linux security module designed to capture data provenance for the purpose of system auditing. It is being leveraged by Unicorn, an anomaly based detector of advanced persistent threats (APTs) that are otherwise difficult to detect because of their “low-and-slow” attack patterns and frequent use of zero-day exploits.8Han X. Pasquier T. Bates A. Mickens J. Seltzer M. UNICORN: Runtime Provenance-Based Detector for Advanced Persistent Threats.arXiv. 2020; (2001.01525)https://arxiv.org/abs/2001.01525Google Scholar But the provenance of our End-to-End Provenance project spans a much longer period of time. The roots of our End-to-End project extend back more than two decades in time to the LASER (laboratory for advanced software engineering research) group at the University of Massachusetts at Amherst, led by Professors Leon Osterweil and Lori Clarke. Two members of our current team, Emery Boose and Aaron Ellison, worked with LASER on a project aimed at establishing a process-definition formalism that could be used to describe scientific workflows. In those early days, we were interested in collecting provenance to be able to evaluate the correctness of the workflows that were carried out; the LASER group, including Barbara Lerner (then a research assistant professor at the University of Massachusetts), developed Little-JIL,5Cass A.G. Lerner B.S. McCall E.K. Osterweil L.J. Sutton S.M.J. Wise A. Little-JIL/Juliette: a process definition language and interpreter.in: Proceedings of the 2000 International Conference on Software Engineering. IEEE, 2000: 754-757Crossref Google Scholar a graphical language with rigorously defined operational semantics in which one could program coordination among processes, document their execution sequence, and re-execute them. Over time we shifted our focus from Little-JIL to R, a language widely used by scientists for data analysis and statistics.6R Development Core TeamR: A language and environment for statistical computing. R Foundation for Statistical Computing, 2020Google Scholar In a fortuitous coincidence, Barbara Lerner and Margo Seltzer served together on an grant-review panel for the National Science Foundation’s Computer and Information Science and Engineering directorate. In discussing research over a break, they learned of their shared interest in provenance, and particularly in developing provenance support for languages that scientists actively used. They shared a vision to bring provenance tools to domain scientists instead of trying to convince them to change how they worked. Bringing in Margo (then a professor of computer science at Harvard) and her group broadened our overall focus beyond evaluating workflows to include system-level processes, provenance storage, and end-to-end solutions. The tools that we have developed, informed by this broadened perspective, transparently capture and use data provenance from workflows and analytical pipelines in multiple languages (R, Python) and more generically (Camflow) (Figure 2). These tools, and provenance-based tools developed by other groups (see summary in Lerner et al.3Lerner B. Boose E. Perez L. Using introspection to collect provenance in R.Informatics. 2018; 5: 12Crossref Scopus (4) Google Scholar), improve transparency, trustworthiness, and reproducibility of data analysis and associated results and facilitate debugging and improve understanding of why different runs of a seemingly identical script can yield different outcomes. More recent applications of provenance include its use in system security, including visualization and explanation of software faults, intrusion detection, and compliance with regulations involving protection of personal data.7Pasquier T. Eyers D. Seltzer M. From Here to Provtopia,.in: Gadepally V. Heterogeneous Data Management, Polystores, and Analytics for Healthcare. 2019: 54-67Crossref Scopus (3) Google Scholar A thorough review of these topics will be part of a future paper in Patterns, and all packages discussed are available from https://end-to-end-provenance.github.io/. The End-to-End group is, of course, much larger than the PIs and senior scientists. In fact, much of the behind-the-scenes work has been done by teams of undergraduates participating in the Harvard Forest Summer Undergraduate Research Program and a handful of graduate students (Xueyuan Han, Jingmei Hu, Jackson Okuhn, Narun Raman) and postdocs (Matthew Lau [now with the Chinese Academy of Sciences] and Thomas Pasquier [now at the University of Bristol]). Although most of the undergraduates have gone on to careers in data science and software engineering in the private sector, Morgan Vigil is now an assistant professor in computer science at Northern Arizona University, and Joe Wonsil is now a PhD student with Margo Seltzer at the University of British Columbia (Table 1). As all the participants of the End-to-End Provenance project grow their careers, spread throughout the world, and continue to develop more useful tools, awareness of their provenance will ensure that the people behind the tools are valued, too.Table 1Undergraduate Students Who Have Worked on the End-to-End Provenance Project in the Last Decade and Their Post-graduate TrajectoriesREU yearStudentInstitutionGraduatedPresent position2009Cory Teshera-SterneMt. Holyokea4-year liberal arts college2010Data Coordinator, NeighborWorks Home Partners2010Morgan VigilWestmonta4-year liberal arts college2011Asst. Prof. of CS, Northern Arizona U.Sofiya TaskovaMt. Holyokea4-year liberal arts college2012Sr. Software Engineer, Reddit2011Andy KaldunskiRipona4-year liberal arts collegeDeceasedGarrett RosenblattRochester2013Software Development Engineer, Amazon2012Miruna OprescuHarvard2015Sr Data & Applied Scientist, Microsoft ResearchYujia ZhouDickinsona4-year liberal arts college2013PhD Analyst, L.E.K. Consulting2013Shay AdamsMt. Holyokea4-year liberal arts college2014Application Developer, U WisconsinVasco CarinhasPuerto Rico––2014Luis PerezHarvard2016Research Engineer, DeepMindNikki HofflerMt. Holyokea4-year liberal arts college2016IT Auditor, Eli Lilly & Co.2015Marios DardasHoly Crossa4-year liberal arts college2016Data Analyst, McKinsey & Co.Lia PoulosMt. Holyokea4-year liberal arts college––2016Alex LiuAmhersta4-year liberal arts college2019Flow Volatility Trading Analyst, Barclays Investment BankMoe Pwint PhyuMt. Holyokea4-year liberal arts college2018Software Development Engineer, Workday2017Connor Gregorich-TrevorGrinnella4-year liberal arts college––Jen JohnsonMiddleburya4-year liberal arts college––2018Orenna BrandColumbiaEnrolled–Joe WonsilCarthagea4-year liberal arts college2019PhD student, U. British Columbia2019Khanh NgoMt. Holyokea4-year liberal arts collegeEnrolled–Erick OduniyiKansasEnrolled–a 4-year liberal arts college Open table in a new tab Our work on end-to-end provenance has been supported by grants from the US National Science Foundation ( DEB-1237491 , DBI-1459519 , and SSI-1450277 ), a Charles Bullard Fellowship to B.S.L. at Harvard University , and a faculty fellowship to B.S.L. from Mount Holyoke College . This paper is a contribution from the Harvard Forest Long-Term Ecological Research (LTER) program, supported since 1990 by the US National Science Foundation.

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