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Lofgren Lab Resources

About This Document

This document is meant as a living repository of the resources available to members of the Lofgren Lab.

Computational Resources

Servers:

  • Hera: Dr. Lofgren's office houses "Hera", an 8-core Linux server with 64 MB of RAM and an nVidia K40 Tesla GPU. This server is suitable for both large, single-threaded taks and small scale parallel tasks.

    • Access: Several options exist for access to Hera, all of which require some initial account setup: Direct access in Dr. Lofgren's office, SSH access, or web-based access to R or Python via RStudio Server and JupyterHub (JupyterHub is a work in progress).

    • Installed software: R, Anaconda Python, StochPy

Cluster Computing:

  • Kamiak: Kamiak is the HPC cluster at WSU. The cluster works via a "condo" model, meaning that there is a common pool of resources, and labs may buy additional nodes, which they get priority access to (as well as priority access to the cluster as a whole). The Lofgren Lab owns several nodes on Kamiak, and when signing up for an account you should identify Dr. Lofgren as your PI to access these resources.

    • If Dr. Lofgren is not your PI, speak to him about arranging for access - there are several ways to do this.

Cloud Computing:

The Lofgren Lab occasionally makes use of cloud computing based resources for applications that are not suitable for hosting on a WSU server. At present, these are primarily used for quick setup/teardown servers for demos at workshops, etc.

  • AWS: The Lofgren Lab has an account with Amazon Web Services, which provides a large number of cloud based services, including servers, storage, load balancers, etc. Speak to Dr. Lofgren about access to this account, or if you need resources set up.

    • Currently hosted applications: Zeke

  • DigitalOcean: The Lofgren Lab has an account with Digital Ocean. While the offerings at Digital Ocean are less expansive compared to AWS, they are often somewhat easier to setup, and are especially well suited to small-scale, temporary setups. Speak to Dr. Lofgren about access to this account, or if you need resources set up.

    • Currently hosted applications: None

Code Repositories

GitHub: All members of the Lofgren Lab are expected to have a GitHub account, and to primarily used GitHub for version control and code sharing, following the best practices for scientific computing. Academic accounts are available that dramatically increase the number of private repositories you can have, etc.

In addition to your personal repository, the Lofgren Lab maintains a group account for widely shared repositories (including the one where these documents are stored). Ask Dr. Lofgren to set you up with access to this group.

Collaboration Tools

Desks, Workspaces, etc.

Desks are a somewhat fluid resource within the Allen Center. While the Lofgren Lab does not have dedicated lab space (not being a wet-lab), we have access to desks on the 3rd floor near 311 (Dr. Lofgren's office). Finding a desk that is open may require some planning and effort.

Conference rooms can also be booked for small group meetings, brainstorming sessions, group coding, etc. Email Kristina Elkins to reserve a room.

  • Current Reservations: None

Lab Library

Dr. Lofgren's office contains a large number of books, journal back issues, etc. that may be useful. Members of the Lofgren Lab are free to borrow these books, but please let Dr. Lofgren know if you have done so.

Journals

  • Infection Control and Hospital Epidemiology
  • American Journal of Epidemiology
  • Epidemiology
  • Bulletin of Mathematical Biology
  • SIAM Review
  • ACM Communications
  • Science

Statistics

Infectious Diseases

Programming

Version:

0.3