Bertram Ludäscher

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Research Output

2019

Computing environments for reproducibility: Capturing the “Whole Tale”

Brinckman, A., Chard, K., Gaffney, N., Hategan, M., Jones, M. B., Kowalik, K., Kulasekaran, S., Ludäscher, B., Mecum, B. D., Nabrzyski, J., Stodden, V., Taylor, I. J., Turk, M. J. & Turner, K., May 2019, In : Future Generation Computer Systems. 94, p. 854-867 14 p.

Research output: Contribution to journalArticle

Implementing computational reproducibility in the Whole Tale environment

Chard, K., Gaffney, N., Jones, M. B., Kowalik, K., Ludaescher, B., Nabrzyski, J., Stodden, V., Taylor, I., Turk, M. J. & Willis, C., Jun 17 2019, P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019. Association for Computing Machinery, Inc, p. 17-22 6 p. (P-RECS 2019 - Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems, co-located with HPDC 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Possible worlds explorer: Datalog and answer set programming for the rest of us

Gupta, S., Cheng, Y. Y. & Ludäscher, B., Jan 1 2019, In : CEUR Workshop Proceedings. 2368, p. 44-55 12 p.

Research output: Contribution to journalConference article

PUG: a framework and practical implementation for why and why-not provenance

Lee, S., Ludäscher, B. & Glavic, B., Feb 1 2019, In : VLDB Journal. 28, 1, p. 47-71 25 p.

Research output: Contribution to journalArticle

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

Franz, N. M., Musher, L. J., Brown, J. W., Yu, S. & Ludäscher, B., Feb 2019, In : PLoS computational biology. 15, 2, e1006493.

Research output: Contribution to journalArticle

Open Access
2018

Full of beans: A study on the alignment of two flowering plants classification systems

Cheng, Y. Y. & Ludäscher, B., Jan 1 2018, In : CEUR Workshop Proceedings. 2200, p. 53-63 11 p.

Research output: Contribution to journalConference article

Provenance summaries for answers and nonanswers

Lee, S., Ludäscher, B. & Glavic, B., Jan 1 2018, In : Proceedings of the VLDB Endowment. 11, 12, p. 1954-1957 4 p.

Research output: Contribution to journalConference article

Semantic mediation to improve reproducibility for biomolecular NMR analysis

Gryk, M. R. & Ludäscher, B., Jan 1 2018, Transforming Digital Worlds - 13th International Conference, iConference 2018, Proceedings. Chowdhury, G., McLeod, J., Gillet, V. & Willett, P. (eds.). Springer-Verlag Berlin Heidelberg, p. 620-625 6 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10766 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Validation and inference of schema-level workflow data-dependency annotations

Bowers, S., McPhillips, T. & Ludäscher, B., Jan 1 2018, Provenance and Annotation of Data and Processes - 7th International Provenance and Annotation Workshop, IPAW 2018, Proceedings. Belhajjame, K., Gehani, A. & Alper, P. (eds.). Springer-Verlag Berlin Heidelberg, p. 128-141 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11017 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2017

Agreeing to disagree: Reconciling conflicting taxonomic views using a logic-based approach

Cheng, Y. Y., Franz, N., Schneider, J., Yu, S., Rodenhausen, T. & Ludäscher, B., Jan 1 2017, In : Proceedings of the Association for Information Science and Technology. 54, 1, p. 46-56 11 p.

Research output: Contribution to journalArticle

A SQL-Middleware unifying why and why-not provenance for first-order queries

Lee, S., Köhler, S., Ludäscher, B. & Glavic, B., May 16 2017, Proceedings - 2017 IEEE 33rd International Conference on Data Engineering, ICDE 2017. IEEE Computer Society, p. 485-496 12 p. 7930001. (Proceedings - International Conference on Data Engineering).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Insider Attack Identification and Prevention in Collection-Oriented Dataflow-Based Processes

Sarkar, A., Köhler, S., Ludäscher, B. & Bishop, M., Jun 2017, In : IEEE Systems Journal. 11, 2, p. 522-533 12 p.

Research output: Contribution to journalArticle

Logic-based schema alignment for natural history museum databases

Thomer, A., Cheng, Y. Y., Schneider, J., Twidale, M. & Ludascher, B., Jan 1 2017, In : Knowledge Organization. 44, 7, p. 545-558 14 p.

Research output: Contribution to journalArticle

Workflows and provenance: Toward information science solutions for the natural sciences

Gryk, M. R. & Ludäscher, B., Mar 1 2017, In : Library Trends. 65, 4, p. 555-562 8 p.

Research output: Contribution to journalArticle

2016

DataONE: A data federation with provenance support

Cao, Y., Jones, C., Cuevas-Vicenttín, V., Jones, M. B., Ludäscher, B., McPhillips, T., Missier, P., Schwalm, C., Slaughter, P., Vieglais, D., Walker, L. & Wei, Y., Jan 1 2016, Provenance and Annotation of Data and Processes - 6th International Provenance and Annotation Workshop, IPAW 2016, Proceedings. Glavic, B. & Mattoso, M. (eds.). Springer-Verlag Berlin Heidelberg, p. 230-234 5 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9672).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Decision-making system and operational risk framework for hierarchical production planning

Vargas, A., Day, S., Boza, A., Ortiz, A., Ludäscher, B., Sacala, I. S. & Moisescu, M. A., Jan 1 2016, In : Control Engineering and Applied Informatics. 18, 3, p. 72-81 10 p.

Research output: Contribution to journalArticle

Implementing unified why- and why-not provenance through games

Lee, S., Köhler, S., Ludäscher, B. & Glavic, B., Jan 1 2016, Provenance and Annotation of Data and Processes - 6th International Provenance and Annotation Workshop, IPAW 2016, Proceedings. Glavic, B. & Mattoso, M. (eds.). Springer-Verlag, p. 209-213 5 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9672).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building

Cui, H., Xu, D., Chong, S. S., Ramirez, M., Rodenhausen, T., Macklin, J. A., Ludäscher, B., Morris, R. A., Soto, E. M. & Koch, N. M., Nov 17 2016, In : BMC bioinformatics. 17, 1, 471.

Research output: Contribution to journalArticle

Names are not good enough: Reasoning over taxonomic change in the Andropogon complex

Franz, N. M., Chen, M., Kianmajd, P., Yu, S., Bowers, S., Weakley, A. S. & Ludäscher, B., Jan 1 2016, In : Semantic Web. 7, 6, p. 645-667 23 p.

Research output: Contribution to journalArticle

Two influential primate classifications logically aligned

Franz, N. M., Pier, N. M., Reeder, D. M., Chen, M., Yu, S., Kianmajd, P., Bowers, S. & Ludäscher, B., Jan 1 2016, In : Systematic biology. 65, 4, p. 561-582 22 p.

Research output: Contribution to journalArticle

Using a Computational Study of Hydrodynamics in the Wax Lake Delta to Examine Data Sharing Principles

Zhang, Q., Imker, H., Li, C., Ludäscher, B. & Senseney, M., 2016, In : International Journal of Digital Curation. 11, 2, p. 138-155

Research output: Contribution to journalArticle

Yin & Yang: Demonstrating complementary provenance from noWorkflow & yesWorkflow

Pimentel, J. F., Dey, S., McPhillips, T., Belhajjame, K., Koop, D., Murta, L., Braganholo, V. & Ludaescher, B., Jan 1 2016, Provenance and Annotation of Data and Processes - 6th International Provenance and Annotation Workshop, IPAW 2016, Proceedings. Glavic, B. & Mattoso, M. (eds.). Springer-Verlag, p. 161-165 5 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9672).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2015

Computing location-based lineage from workflow specifications to optimize provenance queries

Dey, S., Köhler, S., Bowers, S. & Ludaescher, B., Jan 1 2015, Provenance and Annotation of Data and Processes - 5th International Provenance and Annotation Workshop, IPAW 2014, Revised Selected Papers. Plale, B., Ludäscher, B. & Ludäscher, B. (eds.). Springer-Verlag, p. 180-193 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8628).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Improving workflow design using abstract provenance graphs

Song, T., Dey, S., Bowers, S. & Ludäscher, B., Jan 1 2015, Provenance and Annotation of Data and Processes - 5th International Provenance and Annotation Workshop, IPAW 2014, Revised Selected Papers. Plale, B., Ludäscher, B. & Ludäscher, B. (eds.). Springer-Verlag, p. 226-228 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8628).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Provenance-based searching and ranking for scientific workflows

Cuevas-Vicenttín, V., Ludäscher, B. & Missier, P., Jan 1 2015, Provenance and Annotation of Data and Processes - 5th International Provenance and Annotation Workshop, IPAW 2014, Revised Selected Papers. Plale, B., Ludäscher, B. & Ludäscher, B. (eds.). Springer-Verlag, p. 209-214 6 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8628).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Provenance for explaining taxonomy alignments

Chen, M., Yu, S., Kianmajd, P., Franz, N., Bowers, S. & Ludäscher, B., Jan 1 2015, Provenance and Annotation of Data and Processes - 5th International Provenance and Annotation Workshop, IPAW 2014, Revised Selected Papers. Plale, B., Ludäscher, B. & Ludäscher, B. (eds.). Springer-Verlag, p. 258-260 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8628).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

ProvenanceMatrix: A visualization tool for multi-taxonomy alignments

Dang, T., Franz, N., Ludaescher, B. & Forbes, A. G., Jan 1 2015, In : CEUR Workshop Proceedings. 1456, p. 13-24 12 p.

Research output: Contribution to journalConference article

Provenance storage, querying, and visualization in PBase

Cuevas-Vicenttín, V., Kianmajd, P., Ludäscher, B., Missier, P., Chirigati, F., Wei, Y., Koop, D. & Dey, S., Jan 1 2015, Provenance and Annotation of Data and Processes - 5th International Provenance and Annotation Workshop, IPAW 2014, Revised Selected Papers. Plale, B., Ludäscher, B. & Ludäscher, B. (eds.). Springer-Verlag Berlin Heidelberg, p. 239-241 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8628).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Reasoning over taxonomic change: Exploring alignments for the Perelleschus Use Case

Franz, N. M., Chen, M., Yu, S., Kianmajd, P., Bowers, S. & Ludäscher, B., Feb 20 2015, In : PloS one. 10, 2, e0118247.

Research output: Contribution to journalArticle

2014

A hybrid diagnosis approach combining black-box and white-box reasoning

Chen, M., Yu, S., Franz, N., Bowers, S. & Ludäscher, B., Jan 1 2014, Rules on the Web: From Theory to Applications - 8th International Symposium, RuleML 2014, Co-located with the 21st European Conference on Artificial Intelligence, ECAI 2014, Proceedings. Springer-Verlag, p. 127-141 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8620 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Insider attack identification and prevention using a declarative approach

Sarkar, A., Köhler, S., Riddle, S., Ludäescher, B. & Bishop, M., Nov 13 2014, Proceedings - 2014 IEEE Security and Privacy Workshops, SPW 2014. Institute of Electrical and Electronics Engineers Inc., p. 265-276 12 p. 6957311. (Proceedings - IEEE Symposium on Security and Privacy; vol. 2014-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2013

A declarative approach to customize workflow provenance

Dey, S. & Ludascher, B., May 2 2013, Joint EDBT/ICDT 2013 Workshops - Proceedings. p. 9-16 8 p. (ACM International Conference Proceeding Series).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

AutoDrug: Fully automated macromolecular crystallography workflows for fragment-based drug discovery

Tsai, Y., McPhillips, S. E., González, A., McPhillips, T. M., Zinn, D., Cohen, A. E., Feese, M. D., Bushnell, D., Tiefenbrunn, T., Stout, C. D., Ludaescher, B., Hedman, B., Hodgson, K. O. & Soltis, S. M., May 1 2013, In : Acta Crystallographica Section D: Biological Crystallography. 69, 5, p. 796-803 8 p.

Research output: Contribution to journalArticle

Euler/X: A toolkit for logic-based taxonomy integration

Chen, M., Yu, S., Franz, N., Bowers, S. & Ludäscher, B., Jan 1 2013, In : Technische Berichte des Instituts fur Informatik der Christian-Albrechts-Universitat zu Kiel. 1306 REPORT NO., p. 219-224 6 p.

Research output: Contribution to journalConference article

First-order provenance games

Köhler, S., Ludaescher, B. & Zinn, D., Dec 1 2013, In Search of Elegance in the Theory and Practice of Computation: Essays Dedicated to Peter Buneman. Tannen, V., Wong, L., Libkin, L., Fan, W., Fourman, M. & Tan, W-C. (eds.). p. 382-399 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8000).

Research output: Chapter in Book/Report/Conference proceedingChapter

On implementing provenance-aware regular path queries with relational query engines

Dey, S., Cuevas-Vicenttín, V., Köhler, S., Gribkoff, E., Wang, M. & Ludäscher, B., May 2 2013, Joint EDBT/ICDT 2013 Workshops - Proceedings. p. 214-223 10 p. (ACM International Conference Proceeding Series).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Semantic annotation of mutable data

Morris, R. A., Dou, L., Hanken, J., Kelly, M., Lowery, D. B., Ludäscher, B., Macklin, J. A. & Morris, P. J., Nov 4 2013, In : PloS one. 8, 11, e76093.

Research output: Contribution to journalArticle

2012

Database support for exploring scientific workflow provenance graphs

Anand, M. K., Bowers, S. & Ludäscher, B., Jul 9 2012, Scientific and Statistical Database Management - 24th International Conference, SSDBM 2012, Proceedings. p. 343-360 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7338 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Declarative datalog debugging for mere mortals

Köhler, S., Ludäscher, B. & Smaragdakis, Y., Oct 10 2012, Datalog in Academia and Industry - Second International Workshop, Datalog 2.0, Proceedings. p. 111-122 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7494 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Declarative rules for inferring fine-grained data provenance from scientific workflow execution traces

Bowers, S., McPhillips, T. & Ludäscher, B., Nov 7 2012, Provenance and Annotation of Data and Processes - 4th International Provenance and Annotation Workshop, IPAW 2012, Revised Selected Papers. p. 82-96 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7525 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kurator: A Kepler package for data curation workflows

Dou, L., Cao, G., Morris, P. J., Morris, R. A., Ludäscher, B., Macklin, J. A. & Hanken, J., Jan 1 2012, In : Procedia Computer Science. 9, p. 1614-1619 6 p.

Research output: Contribution to journalConference article

Modeling and querying scientific workflow provenance in the D-OPM

Cuevas-Vicenttin, V., Dey, S., Wang, M. L. Y., Song, T. & Ludascher, B., Dec 1 2012, Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012. p. 119-128 10 p. 6495809. (Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Reconciling provenance policy conflicts by inventing anonymous nodes

Dey, S., Zinn, D. & Ludäscher, B., Feb 21 2012, The Semantic Web: ESWC 2011 Workshops, Revised Selected Papers. p. 172-185 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7117 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Sliding window calculations on streaming data using the Kepler scientific workflow system

Köhler, S., Gulati, S., Cao, G., Hart, Q. & Ludäscher, B., Jan 1 2012, In : Procedia Computer Science. 9, p. 1639-1646 8 p.

Research output: Contribution to journalConference article

Win-Move is Coordination-Free (Sometimes)

Zinn, D., Green, T. J. & Ludäscher, B., Jul 23 2012, Database Theory - ICDT 2012: 15th International Conference on Database Technology, Proceedings. p. 99-113 15 p. (ACM International Conference Proceeding Series).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Workflows for microarray data processing in the Kepler environment

Stropp, T., McPhillips, T., Ludäscher, B. & Bieda, M., May 17 2012, In : BMC bioinformatics. 13, 1, 102.

Research output: Contribution to journalArticle

2011

A data model for analyzing user collaborations in workflow-driven e-science

Altintas, I., Anand, M. K., Vuong, T. N., Bowers, S., Ludaescher, B. & Sloot, P. M. A., Sep 1 2011, In : International Journal of Computers and their Applications. 18, 3, p. 160-179 20 p.

Research output: Contribution to journalArticle

Improving workflow fault tolerance through provenance-based recovery

Köhler, S., Riddle, S., Zinn, D., McPhillips, T. & Ludäscher, B., Aug 11 2011, Scientific and Statistical Database Management - 23rd International Conference, SSDBM 2011, Proceedings. p. 207-224 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6809 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

ProPub: Towards a declarative approach for publishing customized, policy-aware provenance

Dey, S. C., Zinn, D. & Ludäscher, B., Aug 11 2011, Scientific and Statistical Database Management - 23rd International Conference, SSDBM 2011, Proceedings. p. 225-243 19 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6809 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution