Karthik Ram

Publications

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Support Scientific Software Infrastructure By Requiring SBOMs For Federally Funded Research

James Howison and Karthik Ram

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Building an Open Science Monitoring Framework with open technologies

Dacos, M., Crawford, S., Jeangirard, E., Montgomery, L., Neylon, C., Becerril, A., Priem, J., Lopez, P., Stegeman, I., Rafols, I., Persic, A., Fressengeas, N., Waltman, L., Kramer, B., Hrynaszkiewicz, I., Larivière, V., Naim, K., Erdmann, C., Mejias, G., Ram, K., de Bruin, J., Romary, L., Bracco, L.

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The R Developer Community Does Have a Strong Software Engineering Culture

Maëlle Salmon and Karthik Ram , The R Journal (2021) 13:2, pages 673-696

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Common Sense Approaches to Sharing Tabular Data Alongside Publication

Nicholas J Tierney and Karthik Ram. Patterns Volume 2, Issue 12, 10 December 2021, 100368

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Mining Software Entities in Scientific Literature: Document-level NER for an Extremely Imbalance and Large-scale Task

Patrice Lopez, Caifan Du, Johanna Cohoon, Karthik Ram and James Howison

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The role of metadata in reproducible computational research

Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Stian Soiland-Reyes, Karthik Ram, Jane Greenberg. Patterns

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The Rockerverse: Packages and Applications for Containerization with R.

Daniel Nst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daroczi, Mark Edmondson, Colin Fay, Ellis Hughes, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Nitesh Turaga, Craig Willis, Nan Xiao, & Charlotte Van Petegem. arXiv The R Journal (2020), 12:1, pages 437-461

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Giving software its due through community-driven review and publication

Barba, Lorena A and Bazán, Juanjo and Brown, Jed and Guimera, Roman V and Gymrek, Melissa and Hanna, Alex and Heagy, Lindsey J and Huff, Kathryn D and Katz, Daniel S and Madan, Christopher R and et al. OSF

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Community Of Practice Around Peer-review For Long-term Research Software Sustainability.

Ram, K, Boettiger, C, Chamberlain, S, Ross, N, Salmon, M, Butland. Computing in Science & Engineering. 10.1109/MCSE.2018.2882753

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Enforcing public data archiving policies in academic publishing: A study of ecology journals.

Sholler, D, Ram, K., Boettiger, C., Katz, Daniel S. 2019. Big Data and Society.

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Hack Weeks as a model for Data Science Education and Collaboration.

Daniela Huppenkothen and Anthony Arendt and David W. Hogg and Karthik Ram and Jake VanderPlas and Ariel Rokem. Proceedings of the National Academy of Sciences.

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Conceptualization of a US Research Software Sustainability Institute (URSSI)

JC Carver, S Gesing, DS Katz, K Ram, N Weber. Computing in Science & Engineering 20 (3), 4-9

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Journal of Open Source Software (JOSS): design and first-year review

Arfon M Smith, Kyle E Niemeyer, Daniel S Katz, Lorena A Barba, George Githinji, Melissa Gymrek, Kathryn D Huff, Christopher R Madan, Abigail Cabunoc Mayes, Kevin M Moerman, Pjotr Prins, Karthik Ram, Ariel Rokem, Tracy K Teal, Roman Valls Guimera

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Sustainable computational science: the ReScience initiative.

Rougier NP, Hinsen K, Alexandre F, Arildsen T, Barba LA, Benureau FCY, Brown CT, de Buyl P, Caglayan O, Davison AP, Delsuc M, Detorakis G, Diem AK, Drix D, Enel P, Girard B, Guest O, Hall MG, Henriques RN, Hinaut X, Jaron KS, Khamassi M, Klein A, Manninen T, Marchesi P, McGlinn D, Metzner C, Petchey O, Plesser HE, Poisot T, Ram K, Ram Y, Roesch E, Rossant C, Rostami V, Shifman A, Stachelek J, Stimberg M, Stollmeier F, Vaggi F, Viejo G, Vitay J, Vostinar AE, Yurchak R, Zito T. PeerJ Computer Science 3:e142

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Building Towards a Future Where Reproducible, Open Science is the Norm

Ram, K and Marwick B. 2017. In Kitzes, J., Turek, D., & Deniz, F. (Eds.). The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences. Oakland, CA: University of California Press.

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Reproducible Workflows For Understanding Large Scale Ecological Effects Of Climate Change.

Ram, K. 2017. In Kitzes, J., Turek, D., & Deniz, F. (Eds.). The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences. Oakland, CA: University of California Press.

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Point of view: How open science helps researchers succeed

Erin C McKiernan, Philip E Bourne, C Titus Brown, Stuart Buck, Amye Kenall, Jennifer Lin, Damon McDougall, Brian A Nosek, Karthik Ram, Courtney K Soderberg, Jeffrey R Spies, Kaitlin Thaney, Andrew Updegrove, Kara H Woo, Tal Yarkoni. eLife 5. e16800

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Building Software, Building Community: Lessons from the rOpenSci Project.

Boettiger, C., Chamberlain, S., Hart, E., and Ram, K.. Journal of Open Research Software,3(1), e8.

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Data Carpentry: Workshops to Increase Data Literacy for Researchers

Tracy K. Teal, Karen A. Cranston, Hilmar Lapp, Ethan White, Greg Wilson, Karthik Ram, Aleksandra Pawlik. International Journal of Digital Curation. Vol 10 No 1 (2015)

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The importance of individual variation in development in stage-structured population modeling.

de Valpine P., Knape J., Scranton K, Ram K., Mills N.J. 2014 Ecology Lettesr

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The utility of repeated presence data as a surrogate for counts: a case study using butterflies.

Casner, K. L., Forister, M. L., Ram, K., and Shapiro, A. M. Journal of Insect Conservation, 1–15. doi:10.1007/s10841-013-9610-8

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The Case for Open Preprints in Biology

Desjardins-Proulx P, White EP, Adamson JJ, Ram K, Poisot T, et al. PLoS Biology 11(5):e1001563. doi:10.1371/journal.pbio.1001563

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Git can facilitate greater reproducibility and increased transparency in science.

Ram, K. Source Code in Medicine and Biology 8:7 doi:10.1186/1751-0473-8-7

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Climate and Vegetation Phenology – Predicting the Effects of Warming Temperatures.

Christopher C. Wilmers, Karthik Ram, Fred G. R. Watson, P. J. White, Douglas W. Smith, and Taal Levi. In Yellowstone’s Wildlife In Transition. Harvard University Press.

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Trends in use of scientific workflows: Insights from a public repository and guidelines for best practices.

Littauer, R, Ram, K, Ludäscher, B, Michener, WM, Koskela, R. International Journal of Data Curation, Vol. 7:2.

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Metapopulation dynamics explains paradox of long-term persistence of a subterranean trophic cascade.

Ram, K, Preisser, E.L, Gruner, D.S. and Strong, D.R. {Ecology}. 30(5):505–523. 2011.

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Heterogeneity mediates long-term persistence of a microparasite mediated trophic cascade.

Dugaw, C.J. and K. Ram. Oecologia. 30(5):505–523.

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Long-term dynamics of a subterranean trophic cascade in space and time.

Ram, K., Gruner, D.S., Preisser, E.L., McLaughlin, J.P. and Strong D.R. Journal of Nematology. 40(2): 85–92.

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Soil mediates the interaction of coexisting entomopathogenic nematodes with an insect host.

Gruner, D.S., K. Ram and D.R. Strong. Journal of Invertebrate Pathology 94(1): 12-19

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