Hello! I’m Dr. Noam Ross, and welcome to my personal website. I’m a disease ecologist and I study the emergence, dynamics, and spread of wildlife diseases and how those diseases spill over between species, including into humans. I’m interested in how to predict these spillovers in time and space, and in using models that mix mechanistic and non-parametric components to do so. These days I get to do this work as Principal Scientist for Computational Research at EcoHealth Alliance.

I am a practitioner and advocate of reproducible research, open science, and justice and inclusion in my fields. I am a founding editor for software peer-review at rOpenSci, and have a variety of projects related to reproducibility using R statistical computer language.

Musings, Explorations, and Announcements

It’s generally impossible to only use services, private or government, that perfectly align with one’s values, so one must opt to choose one’s battles. The controversy over GitHub’s contract with U.S. Immigration and Customs Enforcement is the latest such battle in the open-source software world. GitHub employees and users are trying to pressure GitHub to drop the contract, as a way to place greater pressure on ICE and the U.S. government to curtail crimes and human rights abuses.

A letter to GitHub signed by many open-source maintainers has raised the profile of this campaign. It stops short of calling for users to abandon GitHub, but many users concerned about this issue are searching for alternatives and considering how much they are locked in to GitHub’s ecosystem. I realize that I’m fairly locked in myself, in both personal and professional projects. While I’m not prepared to leave GitHub entirely, I wanted to see how hard it would be to set up a system where I have greater control. So here is documentation of setting up a git hosting service with using Gitea and nearlyfreespeech.net.

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I’m recruiting a Research Software Engineer to join my team at EcoHealth Alliance in New York. Details and how to apply can be found at https://www.ecohealthalliance.org/career/research-software-engineer.

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Drake, Docker, and Gitlab-CI

24 September 2019

For a number of reasons I’ve been trying out GitLab as a replacement for for both GitHub and various continuous integration systems, and have been exploring configurations useful for model-fitting pipelines. I turned one of these into an example repository that shows how to use GitLab together with the Rocker Docker images and the drake build system to reproducibly run a project pipeline, using the cacheing functionality across all three tools to make things reasonably speedy and enable both local and remote builds.

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A New Website

9 August 2019

For me, the task of building a personal website is fraught with so many of my technical, aesthetic, and personal hangups that I hadn’t updated mine since mid-graduate school. Thanks to consistent pestering by Maëlle, though, I finally got around to re-building this one using a modern toolkit. Hopefully I can keep it up to date.

Here are some of the pieces that I used to build it:

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See my original post for background and updates. I was glad to see the announcement from the DataCamp Board that, after a long period of silence and inaction, the company is taking seriously an incident of sexual misconduct and re-examining its approach to the issue and its relationship with concerned instructors. The CEO’s leave of absence and the engagement of Ms. Bhargava indicate a turn in the right direction.

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Recent Works

  • Colin Carlson, Maxwell Farrell, Zoe Grange, Barbara Han, Nardus Mollentze, Alexandra Phelan, Angela Rasmussen, Gregory Albery, Bernard Bett, David Brett-Major, Lily Cohen, Tad Dallas, Evan Eskew, Anna Fagre, Kristian Forbes, Rory Gibb, Sam Halabi, Charlotte Hammer, Rebecca Katz, Jason Kindrachuk, Renata Muylaert, Felicia Nutter, Joseph Ogola, Kevin Olival, Michelle Rourke, Sadie Ryan, Noam Ross, Stephanie Seifert, Tarja Sironen, Claire Standley, Kishana Taylor, Marietje Venter and Paul Webala (2021, preprint) Zoonotic Risk Technology Enters the Viral Emergence Toolkit. doi:10.20944/preprints202104.0200.v1
  • Emma Mendelsohn, Noam Ross, Allison M. White, Karissa Whiting, Cale Basaraba, Brooke Watson Madubuonwu, Erica Johnson, Mushtaq Dualeh, Zach Matson, Sonia Dattaray, Nchedochukwu Ezeokoli, Melanie Kirshenbaum Lieberman, Jacob Kotcher, Samantha Maher, Carlos Zambrana-Torrelio and Peter Daszak (2020) Extracting novel antimicrobial emergence events from scientific literature and medical reports. doi:10.12688/f1000research.26870.1
  • Melinda K. Rostal, Sarah Cleaveland, Claudia Cordel, Lara van Staden, Louise Matthews, Assaf Anyamba, William B. Karesh, Janusz T. Paweska, Daniel T. Haydon and Noam Ross (2020) Farm-Level Risk Factors of Increased Abortion and Mortality in Domestic Ruminants during the 2010 Rift Valley Fever Outbreak in Central South Africa. doi:10.3390/pathogens9110914
  • Jonathan H. Epstein, Simon J. Anthony, Ariful Islam, A. Marm Kilpatrick, Shahneaz Ali Khan, Maria D. Balkey, Noam Ross, Ina Smith, Carlos Zambrana-Torrelio, Yun Tao, Ausraful Islam, Phenix Lan Quan, Kevin J. Olival, M. Salah Uddin Khan, Emily S. Gurley, M. Jahangir Hossein, Hume E. Field, Mark D. Fielder, Thomas Briese, Mahmudur Rahman, Christopher C. Broder, Gary Crameri, Lin-Fa Wang, Stephen P. Luby, W. Ian Lipkin and Peter Daszak (2020) Nipah virus dynamics in bats and implications for spillover to humans. doi:10.1073/pnas.2000429117
  • Gregory F. Albery, Evan A. Eskew, Noam Ross and Kevin J. Olival (2020) Predicting the global mammalian viral sharing network using phylogeography. doi:10.1038/s41467-020-16153-4
  • R, Coronavirus, and Pandemic Prevention, New York Open Statistical Programming Meetup, Apr 20, 2020        
  • Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daroczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Péter Sólymos, Tyson Lee Swetnam, Nitesh Turaga, Charlotte Van Petegem, Jason Williams, Craig Willis and Nan Xiao (2020, preprint) The Rockerverse: Packages and Applications for Containerization with R. doi:
  • Colin J. Carlson, Gregory F. Albery, Cory Merow, Christopher H. Trisos, Casey M. Zipfel, Evan A. Eskew, Kevin J. Olival, Noam Ross and Shweta Bansal (2020, preprint) Climate change will drive novel cross-species viral transmission. doi:10.1101/2020.01.24.918755
  • Evan A. Eskew, Allison M. White, Noam Ross, Kristine M. Smith, Katherine F. Smith, Jon Paul Rodríguez, Carlos Zambrana-Torrelio, William B. Karesh and Peter Daszak (2020) United States wildlife and wildlife product imports from 2000–2014. doi:10.1038/s41597-020-0354-5